Antiviral Therapy Utilization and 10-Year Outcomes in Resected Hepatitis B Virus- and Hepatitis C Virus-Related Hepatocellular Carcinoma

PURPOSE

There are limited data on antiviral treatment utilization and its impact on long-term outcomes of hepatitis B virus (HBV)- and hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC) after hepatic resection. We aimed to determine the utilization and impact of antivirals in HBV- and HCV-related HCC.

METHODS

This cohort study included 1,906 participants (1,054 HBV-related HCC and 852 HCV-related HCC) from 12 international sites. All participants had HBV- or HCV-related HCC and underwent curative surgical resection. The primary outcome was the utilization of antiviral therapy, and the secondary outcome was long-term overall survival (OS).

RESULTS

The mean (±standard deviation [SD]) age was 62.1 (±11.3) years, 74% were male, and 84% were Asian. A total of 47% of the total cohort received antiviral therapy during a mean (±SD) follow-up of 5.0 (±4.3) years. The overall antiviral utilization for participants with HBV-related HCC was 57% and declined over time, from 65% before 2010, to 60% from 2010 to 2015, to 47% beyond 2015, P < .0001. The overall utilization of antivirals for HCV-related HCC was 35% and increased over time, from 24% before 2015 to 74% from 2015 and beyond, P < .0001. The 10-year OS was lower in untreated participants for both HBV (58% v 61%) and HCV participants (38% v 82%; both P < .0001). On multivariable Cox regression analysis adjusted for relevant confounders, antiviral therapy initiated before or within 6 months of HCC diagnosis was independently associated with lower mortality in both HBV- (adjusted hazard ratio [aHR], 0.60 [95% CI, 0.43 to 0.83]; P = .002) and HCV-related HCC (aHR, 0.18 [95% CI, 0.11 to 0.31]; P < .0001).

CONCLUSION

Antiviral therapy is associated with long-term survival in people with HBV- or HCV-related HCC who undergo curative resection but is severely underutilized.

A simple agglutination system for rapid antigen detection from large sample volumes with enhanced sensitivity

Lateral flow assays (LFAs) provide a simple and quick option for diagnosis and are widely adopted for point-of-care or at-home tests. However, their sensitivity is often limited. Most LFAs only allow 50 μL samples while various sample types such as saliva could be collected in much larger volumes. Adapting LFAs to accommodate larger sample volumes can improve assay sensitivity by increasing the number of target analytes available for detection. Here, a simple agglutination system comprising biotinylated antibody (Ab) and streptavidin (SA) is presented. The Ab and SA agglutinate into large aggregates due to multiple biotins per Ab and multiple biotin binding sites per SA. Dynamic light scattering (DLS) measurements showed that the agglutinated aggregate could reach a diameter of over 0.5 μm and over 1.5 μm using poly-SA. Through both experiments and Monte Carlo modeling, we found that high valency and equivalent concentrations of the two aggregating components were critical for successful agglutination. The simple agglutination system enables antigen capture from large sample volumes with biotinylated Ab and a swift transition into aggregates that can be collected via filtration. Combining the agglutination system with conventional immunoassays, an agglutination assay is proposed that enables antigen detection from large sample volumes using an in-house 3D-printed device. As a proof-of-concept, we developed an agglutination assay targeting SARS-CoV-2 nucleocapsid antigen for COVID-19 diagnosis from saliva. The assay showed a 10-fold sensitivity enhancement when increasing sample volume from 50 μL to 2 mL, with a final limit of detection (LoD) of 10 pg mL-1 (∼250 fM). The assay was further validated in negative saliva spiked with gamma-irradiated SARS-CoV-2 and showed an LoD of 250 genome copies per μL. The proposed agglutination assay can be easily developed from existing LFAs to facilitate the processing of large sample volumes for improved sensitivity.

Racial and Ethnic Disparities in Characteristics and Care Patterns of Chronic Hepatitis B Patients in the United States

BACKGROUND & AIMS

Chronic hepatitis B (CHB) disproportionately impacts foreign-born patients and those of Asian or Black race. Given the paucity of data, we aimed to study the impact of race and ethnicity on CHB patient characteristics and management.

METHODS

A retrospective analysis of adult CHB patients using data recorded in the deidentified Optum Clinformatics Data Mart Database (January 2003‒March 2021) was performed. We characterized and examined the rates of receiving adequate treatment evaluation (measuring hepatitis B virus DNA and alanine transaminase) and hepatitis B virus treatment among the racial and ethnic groups.

RESULTS

The study cohort included 42,140 patients: age, 51.9 ± 15.1 years; 56.1% male; 47% Asian; 26% White; 11% Black; and 7% Hispanic. Thirty-three percent of White and 48% of Asian patients had an annual household income greater than $100,000 US compared with 16% for Black and 25% for Hispanic patients (P < .001), with similar disparities in educational levels. Approximately one third of White (29.3%), Black (35.1%), and Hispanic (35.4%), and half of Asian (49.9%) patients received adequate evaluation (P < .001). Among patients who met American Association for the Study of Liver Diseases treatment criteria, treatment rates were similar among White (60.8%; P = .09) and Black (62.8%; P = .48), but lower among Hispanic (54.7%; P = .03), as compared with Asian patients (65.4%). On multivariable logistic regression adjusted for age, sex, provider type, viral co-infection, and fatty liver disease, Hispanic patients were less likely to receive treatment (adjusted hazard ratio, 0.69; 95% CI, 0.53‒0.91; P = .01) compared with Asian patients.

CONCLUSIONS

Compared with Asian CHB patients, non-Asian patients were less likely to undergo adequate evaluation and Hispanic patients were less likely to receive treatment for CHB. Additional efforts are needed to improve CHB management, especially for non-Asian patients.

Renal Outcomes With Tenofovir Alafenamide in Liver Transplant Recipients

Tenofovir disoproxil fumarate (TDF) is associated with a higher risk of nephrotoxicity compared with entecavir (ETV) or tenofovir alafenamide (TAF).1,2 One-fifth of transplant recipients develop chronic kidney disease (CKD) within 5 years after transplantation, contributed by the use of nephrotoxic immunosuppressive medications.3 Prior studies conducted in the nontransplant setting reported superior renal safety in TAF compared with TDF but data in liver transplant (LT) recipients have so far been limited to small case series.1,4-6 Therefore, the goals of this study were to examine changes in renal function in a large multicenter cohort of LT recipients with chronic hepatitis B who were treated with TAF, TDF, or ETV for the prevention of hepatitis B virus (HBV) reinfection or reactivation from receipt of a positive HBV core antibody graft.

Circularly distributed multipliers with deterministic moduli assessing the stability of quasiperiodic response

The stability and bifurcation of a periodic solution of a dynamical system can be handled well by using the Floquet multipliers of the perturbed system with periodic coefficients. However, for a quasiperiodic (QP) response as a natural extension of a periodic one, it is much more difficult to do it quantitatively. Therefore, proposed here is an approach for defining and obtaining effective multipliers for QP stability. The proposed approach is based on a series of auxiliary variables via which the perturbed system with QP coefficients is transformed approximately into a constant one, whereupon the multipliers are obtained efficiently by performing eigenvalue analysis on the constant coefficient matrix. The major finding involves circularly distributed multipliers with deterministic moduli, with the QP response being stable if all the moduli are less than or equal to unity; otherwise it is unstable. When the QP response degenerates to periodic due to the reducibility of fundamental frequencies, the proposed approach exactly provides the Floquet multipliers for the periodic solution. From this respect, the obtained multipliers can be considered to some extent as being a generalization for QP response of the Floquet multipliers for a periodic solution.

Exosome Processing and Characterization Approaches for Research and Technology Development

Exosomes are extracellular vesicles that share components of their parent cells and are attractive in biotechnology and biomedical research as potential disease biomarkers as well as therapeutic agents. Crucial to realizing this potential is the ability to manufacture high-quality exosomes; however, unlike biologics such as proteins, exosomes lack standardized Good Manufacturing Practices for their processing and characterization. Furthermore, there is a lack of well-characterized reference exosome materials to aid in selection of methods for exosome isolation, purification, and analysis. This review informs exosome research and technology development by comparing exosome processing and characterization methods and recommending exosome workflows. This review also provides a detailed introduction to exosomes, including their physical and chemical properties, roles in normal biological processes and in disease progression, and summarizes some of the on-going clinical trials.

Model-based assessment of mammalian cell metabolic functionalities using omics data

Omics experiments are ubiquitous in biological studies, leading to a deluge of data. However, it is still challenging to connect changes in these data to changes in cell functions because of complex interdependencies between genes, proteins, and metabolites. Here, we present a framework allowing researchers to infer how metabolic functions change on the basis of omics data. To enable this, we curated and standardized lists of metabolic tasks that mammalian cells can accomplish. Genome-scale metabolic networks were used to define gene sets associated with each metabolic task. We further developed a framework to overlay omics data on these sets and predict pathway usage for each metabolic task. We demonstrated how this approach can be used to quantify metabolic functions of diverse biological samples from the single cell to whole tissues and organs by using multiple transcriptomic datasets. To facilitate its adoption, we integrated the approach into GenePattern (www.genepattern.org-CellFie).

[Construction and evaluation of a novel diagnosis pathway for 2019-Corona Virus Disease]

Objective: To construct and evaluate a diagnosis pathway (Xiangya pathway) for Corona Virus Disease 2019 (COVID-19). Methods: Consecutive subjects aged ≥12 years old who were screened for COVID-19 were included in Xiangya Hospital of Central South University from January 23 to February 3, 2020, and the subjects were further divided into the inception cohort and the validation cohort. The gender, age, onset time of disease of the subjects were recorded. The information of epidemiological history, fever, and the declined blood lymphocytes were collected as clinical indicators, CT scan was used to evaluate the possibility of COVID-19 and range of lung involvement. According to the current Chinese national standards, throat swabs of suspected cases were collected and the nucleic acid of COVID-19 was detected by reverse transcription-polymerase chain reaction (RT-PCR). The Xiangya pathway was constructed with multi-indexes, compared with clinical indicators, CT results and Chinese national standards, their effectiveness of detecting confirmed cases were verified in the inception and validation cohort. Results: A total of 382 consecutive adults who was screened for COVID-19 were included, and 261 cases were in the inception cohort and 121 cases were in the validation cohort. Among the 382 cases, 192 were males (50.3%) and 190 were females (49.7%), with a median age of 35 years (range: 15-92 years). There were 183 cases (47.9%) with epidemiological history, 275 cases (72.0%) with fever, 212 cases (55.5%) with decreased peripheral blood lymphocytes, 114 cases (29.8%) with positive CT findings, 43 cases (11.3%) with positive CT-COVID-19, and 30 cases (7.9%) with positive virus nucleic acid by throat swab. Compared with clinical indicators, the sensitivity and specificity of CT were 0.950 and 0.704, respectively. The accuracy of CT to make a definite diagnosis was higher than that of epidemiological history, fever, and declined blood lymphocyte count (0.809 vs 0.660, 0.532, 0.596, P=0.001, 0.002, 0.003, respectively). The sensitivity of this pathway and the pathway recommended by the Health Commission of China were both high (all were 1.000), while the specificity and accuracy of the Xiangya pathway were higher than the one recommended by the Health Commission (0.872 vs 0.765, 0.778 vs 0.592, both P<0.001). The CT-COVID-19 reduced the missed diagnosis rate caused by false negative of nucleic acid test (31 vs 64), with difference rate of 51.6%, and the positive rate of nucleic acid test was 64.5% (20/31). In validation cohort, the specificity and accuracy of the Xiangya pathway was 0.967, the positive rate of nucleic acid test was 76.9%(10/13). Conclusions: The Xiangya pathway can predict the nucleic acid test results of COVID-19, and can be applied as a reliable strategy to screen patients with suspected COVID-19 among people aged ≥12 years in areas other than Hubei during the epidemic period of COVID-19. The cohort size needs to be increased for further validation.

Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen

The unique capability of acetogens to ferment a broad range of substrates renders them ideal candidates for the biotechnological production of commodity chemicals. In particular the ability to grow with H₂:CO₂ or syngas (a mixture of H₂/CO/CO₂) makes these microorganisms ideal chassis for sustainable bioproduction. However, advanced design strategies for acetogens are currently hampered by incomplete knowledge about their physiology and our inability to accurately predict phenotypes. Here we describe the reconstruction of a novel genome-scale model of metabolism and macromolecular synthesis (ME-model) to gain new insights into the biology of the model acetogen Clostridium ljungdahlii. The model represents the first ME-model of a Gram-positive bacterium and captures all major central metabolic, amino acid, nucleotide, lipid, major cofactors, and vitamin synthesis pathways as well as pathways to synthesis RNA and protein molecules necessary to catalyze these reactions, thus significantly broadens the scope and predictability. Use of the model revealed how protein allocation and media composition influence metabolic pathways and energy conservation in acetogens and accurately predicted secretion of multiple fermentation products. Predicting overflow metabolism is of particular interest since it enables new design strategies, e.g. the formation of glycerol, a novel product for C. ljungdahlii, thus broadening the metabolic capability for this model microbe. Furthermore, prediction and experimental validation of changing secretion rates based on different metal availability opens the window into fermentation optimization and provides new knowledge about the proteome utilization and carbon flux in acetogens.

Acetogens are renowned for their potential biotechnological applications. The model acetogen Clostridium ljungdahlii has been studied intensively for its ability to produce biofuels from sustainable resources, like syngas. We describe a novel genome-scale model of metabolism and gene expression (ME-model) to gain insights into this model acetogen. This first ME-model for a Gram-positive bacterium contains all major metabolic and biosynthetic pathways and calculates accurate proteome allocations under diverse growth conditions, thereby significantly broadening the scope of predictability of metabolic models. Furthermore, the ME-model enables rational medium design for improved production. Our experimental validation implies wide applicability to others strains for rapid improvement of yield and titer in biotechnology-relevant applications.

Transoral vertical ramus osteotomy fixed with Kirschner pins

Transoral vertical ramus osteotomy (VRO) has been condemned because the condyle has the potential to sag, and because it needs lengthy maxillomandibular fixation. We have therefore introduced a simple method of fixation, and examined its effectiveness and complications. After the osteotomy, the proximal and distal segments are trimmed to adapt to each other. Four Kirschner (K) pins 0.9mm in diameter are inserted percutaneously from the proximal to the distal segment while the condyle is positioned in the glenoid fossa. This is followed by a brief period of maxillomandibular fixation. We have reviewed the records of 95 patients who had unilateral or bilateral vertical ramus osteotomy fixed with K pins, after which the mean (SD) period of fixation was 19 (11) days. Fixation failed in two patients because excursion of the jaw was either too heavy or too early. The fixations were redone. All other fixations remained stable, including the 20 dual-jaw procedures in which VRO preceded maxillary osteotomy. The mean (SD) maximal mouth opening at final follow-up was 44 (7) mm, and in only one patient was it less than 30mm. Numbness of the lip or chin developed in seven patients, five of whom had other anterior mandibular procedures. Four patients had discomfort on palpation of the site of the pins, and one required removal. The new method was effective, and resulted in few complications within its limitations.

COBRAme: A computational framework for genome-scale models of metabolism and gene expression

Genome-scale models of metabolism and macromolecular expression (ME-models) explicitly compute the optimal proteome composition of a growing cell. ME-models expand upon the well-established genome-scale models of metabolism (M-models), and they enable a new fundamental understanding of cellular growth. ME-models have increased predictive capabilities and accuracy due to their inclusion of the biosynthetic costs for the machinery of life, but they come with a significant increase in model size and complexity. This challenge results in models which are both difficult to compute and challenging to understand conceptually. As a result, ME-models exist for only two organisms (Escherichia coli and Thermotoga maritima) and are still used by relatively few researchers. To address these challenges, we have developed a new software framework called COBRAme for building and simulating ME-models. It is coded in Python and built on COBRApy, a popular platform for using M-models. COBRAme streamlines computation and analysis of ME-models. It provides tools to simplify constructing and editing ME-models to enable ME-model reconstructions for new organisms. We used COBRAme to reconstruct a condensed E. coli ME-model called iJL1678b-ME. This reformulated model gives functionally identical solutions to previous E. coli ME-models while using 1/6 the number of free variables and solving in less than 10 minutes, a marked improvement over the 6 hour solve time of previous ME-model formulations. Errors in previous ME-models were also corrected leading to 52 additional genes that must be expressed in iJL1678b-ME to grow aerobically in glucose minimal in silico media. This manuscript outlines the architecture of COBRAme and demonstrates how ME-models can be created, modified, and shared most efficiently using the new software framework.

[Surveillance of contamination level and antimicrobial resistance analysis of Salmonella on broiler carcasses after chilling in 4 poultry slaughterhouses of Henan Province]

Objective: Tests were carried out for obtaining contamination level and antimicrobial resistance of Salmonella on broiler carcasses after chilling in four poultry slaughterhouses in Henan. Methods: Totally, two hundred sixty nine broiler carcasses after chilling were collected in four slaughterhouses with the daily slaughter amount around 15 000 to 50 000. For qualitative analysis of Salmonella EFSA method was used and for quantitative analysis of Salmonella modified Rappaport-Vassiliadis most probable number (MSRV-MPN) method was used. All of the isolates were subjected to antimicrobial susceptibility testing of 8 antibiotics by minimum inhibitory concentration (MIC). Results: Overall, 48.7% (131/269) of the broiler carcasses after chilling were contaminated by Salmonella, and the average of contamination level is 1.32 most probable number MPN/g. Eight serotypes were detected. The dominant serotype is Salmonella enteritidis (93, 71.0%) followed by Salmonella Indiana (21, 16.0%). Only 2 (1.5%) Salmonella enteritidis strains were sensitive to all the tested antibiotics and the remaining 129 isolates were resistant to at least one kind of eight class antibiotics. Among them, resistant to NAL was the common (104, 79.4%) and 51 (38.9%) Salmonella isolates were multidrug-resistant. Conclusion: The contamination rate and multiple antimicrobial resistant of Salmonella on broiler carcasses after chilling from slaughterhouses was very serious, while the isolates contained various serotypes.

Aerobic Biodegradation of OCDD by P. Mendocina NSYSU: Effectiveness and Gene Inducement Studies

  The goals of this study were to assess the effectiveness of (1) enhancing octachlorinated dibenzo-p-dioxin (OCDD) biodegradation under aerobic conditions by Pseudomonas mendocina NSYSU (P. Mendocina NSYSU) with the addition of lecithin, and (2) inducing OCDD ring-cleavage genes by pentachlorophenol (PCP) and OCDD addition. P. Mendocina NSYSU could biodegrade OCDD via aerobic cometabolism and lecithin was used as a primary substrate. Approximately 74 and 67% of OCDD biodegradation was observed after 60 days of incubation with lecithin and glucose supplement, respectively. Lecithin was also used as the solubilization additive resulting in OCDD solubilization and enhanced bioavailability of OCDD to P. Mendocina NSYSU. Two intradiol and extradiol ring-cleavage dioxygenase genes (Pmen_0474 and Pmen_2526) were identified from gene analyses. Gene concentration was significantly enhanced after the inducement by PCP and OCDD. Higher gene inducement efficiency was obtained using PCP as the inducer, and Pmen_2526 played a more important role in OCDD biodegradation.

[Expression of PAK1 in bladder cancer and its influence on invasion of bladder cancer cells]

Objective: To investigate the expression of p21-activated kinase 1 (PAK1) in bladder cancer and its biological influence on invasion ability of bladder cancer cells. Methods: A total of 54 paraffin-embedded bladder cancer tissue samples and 12 normal bladder tissue specimens were retrieved in Jinshan Hospital Affiliated to Fudan University between January 2009 and December 2012. The expression of PAK1 in these tissues was detected by immunohistochemical staining. The PAK1 mRNA and protein levels were measured in bladder cancer cell lines and human normal bladder epithelial cell line using real-time, fluorescence-based quantitative polymerase chain reaction (RT-PCR) and Western blot, respectively. A stable PAK1 gene silencing bladder cancer cell strain 5637 were successfully constructed. After treatment with PAK1 RNA interference(RNAi), the ability of migration and invasion of the 5637 cell was evaluated using a Transwell system. Results: The expression of PAK1 proteins was significantly higher in bladder cancer tissues than in normal bladder tissues (28/54 vs 1/12, P<0.05). The overexpression of PAK1 was positively correlated with high histological grade, lymph node metastasis, and tumor size (all P<0.05). The mRNA level and protein level of PAK1 was much higher in bladder cancer cell lines T24, 5637 than human normal urothelial cell line SV-HUC-1.PCR and Western blot showed satisfactory inhibitory effect of PAK1 short hairpin RNA (shRNA) on PAK1 expression in 5637 bladder cancer cells. The number of PAK1 RNAi-treated 5637 cells traversed the membrane was decreased compared with the control group in migration and invasion assays. Conclusions: Overexpression of PAK1 in bladder cancer tissues may be an important feature of bladder cancer and related with the metastasis and invasion of bladder cancer. The molecular mechanisms involved in regulation of PAK1 expression needs further research.

Recon 2.2: from reconstruction to model of human metabolism

INTRODUCTION

The human genome-scale metabolic reconstruction details all known metabolic reactions occurring in humans, and thereby holds substantial promise for studying complex diseases and phenotypes. Capturing the whole human metabolic reconstruction is an on-going task and since the last community effort generated a consensus reconstruction, several updates have been developed.

OBJECTIVES

We report a new consensus version, Recon 2.2, which integrates various alternative versions with significant additional updates. In addition to re-establishing a consensus reconstruction, further key objectives included providing more comprehensive annotation of metabolites and genes, ensuring full mass and charge balance in all reactions, and developing a model that correctly predicts ATP production on a range of carbon sources.

METHODS

Recon 2.2 has been developed through a combination of manual curation and automated error checking. Specific and significant manual updates include a respecification of fatty acid metabolism, oxidative phosphorylation and a coupling of the electron transport chain to ATP synthase activity. All metabolites have definitive chemical formulae and charges specified, and these are used to ensure full mass and charge reaction balancing through an automated linear programming approach. Additionally, improved integration with transcriptomics and proteomics data has been facilitated with the updated curation of relationships between genes, proteins and reactions.

RESULTS

Recon 2.2 now represents the most predictive model of human metabolism to date as demonstrated here. Extensive manual curation has increased the reconstruction size to 5324 metabolites, 7785 reactions and 1675 associated genes, which now are mapped to a single standard. The focus upon mass and charge balancing of all reactions, along with better representation of energy generation, has produced a flux model that correctly predicts ATP yield on different carbon sources.

CONCLUSION

Through these updates we have achieved the most complete and best annotated consensus human metabolic reconstruction available, thereby increasing the ability of this resource to provide novel insights into normal and disease states in human. The model is freely available from the Biomodels database (http://identifiers.org/biomodels.db/MODEL1603150001).

Identification of natural recombinants derived from PCV2a and PCV2b

Porcine circovirus type 2 (PCV2) is considered to be the main pathogen in PC-associated diseases, and significantly affects the global pig-producing industry. PCV2 continuously evolves by point mutations and genome recombinations. In the present study, we aimed to further identify recombinant PCV2 strains. We used polymerase chain reaction to detect PCV2 in the carcasses of pigs with suspected infections from different regions of Guangdong Province in China. DNA was extracted from samples with confirmed infection and full- genome amplification, sequencing, phylogenetic tree construction, gene recombination detection, and sequence alignment were performed in gene recombination analysis. Our results show that recombination occurred between the strains SHC (DQ104421) and ZhuJi2003 (AY579893). The recombination resulted in three recombinants: GD003 (KM503044), GD005 (KM487708), and GD008 (KM487709). Further analyses revealed that these novel recombinants appeared to result from recombination between the PCV2a and PCV2b strains, with crossover regions located in ORF2. This study was a comprehensive analysis that used several different methods, which demonstrated that a cluster of PCV2 strains resulted from the same type of inter-genotypic recombination pattern, with a breakpoint in the structural protein coding region. The results of our study provide both information on the recombination mechanism and disease pathogenesis and useful data for the prevention of PCV2 in the swine industry.

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

Background

Membranes play a crucial role in cellular functions. Membranes provide a physical barrier, control the trafficking of substances entering and leaving the cell, and are a major determinant of cellular ultra-structure. In addition, components embedded within the membrane participate in cell signaling, energy transduction, and other critical cellular functions. All these processes must share the limited space in the membrane; thus it represents a notable constraint on cellular functions. Membrane- and location-based processes have not yet been reconstructed and explicitly integrated into genome-scale models.

Results

The recent genome-scale model of metabolism and protein expression in Escherichia coli (called a ME-model) computes the complete composition of the proteome required to perform whole cell functions. Here we expand the ME-model to include (1) a reconstruction of protein translocation pathways, (2) assignment of all cellular proteins to one of four compartments (cytoplasm, inner membrane, periplasm, and outer membrane) and a translocation pathway, (3) experimentally determined translocase catalytic and porin diffusion rates, and (4) a novel membrane constraint that reflects cell morphology. Comparison of computations performed with this expanded ME-model, named iJL1678-ME, against available experimental data reveals that the model accurately describes translocation pathway expression and the functional proteome by compartmentalized mass.

Conclusion

iJL1678-ME enables the computation of cellular phenotypes through an integrated computation of proteome composition, abundance, and activity in four cellular compartments (cytoplasm, periplasm, inner and outer membrane). Reconstruction and validation of the model has demonstrated that the iJL1678-ME is capable of capturing the functional content of membranes, cellular compartment-specific composition, and that it can be utilized to examine the effect of perturbing an expanded set of network components. iJL1678-ME takes a notable step towards the inclusion of cellular ultra-structure in genome-scale models.

Electronic supplementary material

The online version of this article (doi:10.1186/s12918-014-0110-6) contains supplementary material, which is available to authorized users.

Enhanced anaerobic biodegradation of OCDD-contaminated soils by Pseudomonas mendocina NSYSU: microcosm, pilot-scale, and gene studies

In this study, microcosm and pilot-scale experiments were performed to investigate the capability and effectiveness of Pseudomonas mendocina NSYSU (P. mendocina NSYSU) on the bioremediation of octachlorodibenzo-p-dioxin (OCDD)-contaminated soils. The objectives were to evaluate the (1) characteristics of P. mendocina NSYSU, (2) feasibility of enhancing OCDD biodegradation with the addition of P. mendocina NSYSU and lecithin, and (3) variation in microbial diversity and genes responsible for the dechlorination of OCDD. P. mendocina NSYSU was inhibited when salinity was higher than 7%, and it could biodegrade OCDD under reductive dechlorinating conditions. Lecithin could serve as the solubilization agent causing the enhanced solubilization and dechlorination of OCDD. Up to 71 and 62% of OCDD could be degraded after 65 days of incubation under anaerobic conditions with and without the addition of lecithin, respectively. Decreased OCDD concentrations caused significant increase in microbial diversity. Results from the pilot-scale study show that up to 75% of OCDD could be degraded after a 2.5-month operational period with lecithin addition. Results from the gene analyses show that two genes encoding the extradiol/intradiol ring-cleavage dioxygenase and five genes encoding the hydrolase in P. mendocina NSYSU were identified and played important roles in OCDD degradation.

Phage display discovery of novel molecular targets in glioblastoma-initiating cells

Glioblastoma is the most common primary intrinsic brain tumor and remains incurable despite maximal therapy. Glioblastomas display cellular hierarchies with self-renewing glioma-initiating cells (GICs) at the apex. To discover new GIC targets, we used in vivo delivery of phage display technology to screen for molecules selectively binding GICs that may be amenable for targeting. Phage display leverages large, diverse peptide libraries to identify interactions with molecules in their native conformation. We delivered a bacteriophage peptide library intravenously to a glioblastoma xenograft in vivo then derived GICs. Phage peptides bound to GICs were analyzed for their corresponding proteins and ranked based on prognostic value, identifying VAV3, a Rho guanine exchange factor involved tumor invasion, and CD97 (cluster of differentiation marker 97), an adhesion G-protein-coupled-receptor upstream of Rho, as potentially enriched in GICs. We confirmed that both VAV3 and CD97 were preferentially expressed by tumor cells expressing GIC markers. VAV3 expression correlated with increased activity of its downstream mediator, Rac1 (ras-related C3 botulinum toxin substrate 1), in GICs. Furthermore, targeting VAV3 by ribonucleic acid interference decreased GIC growth, migration, invasion and in vivo tumorigenesis. As CD97 is a cell surface protein, CD97 selection enriched for sphere formation, a surrogate of self-renewal. In silico analysis demonstrated VAV3 and CD97 are highly expressed in tumors and inform poor survival and tumor grade, and more common with epidermal growth factor receptor mutations. Finally, a VAV3 peptide sequence identified on phage display specifically internalized into GICs. These results show a novel screening method for identifying oncogenic pathways preferentially activated within the tumor hierarchy, offering a new strategy for developing glioblastoma therapies.

Application of polycolloid-releasing substrate to remediate trichloroethylene-contaminated groundwater: a pilot-scale study

The objectives of this pilot-scale study were to (1) evaluate the effectiveness of bioremediation of trichloroethylene (TCE)-contaminated groundwater with the supplement of slow polycolloid-releasing substrate (SPRS) (contained vegetable oil, cane molasses, surfactants) under reductive dechlorinating conditions, (2) apply gene analyses to confirm the existence of TCE-dechlorinating genes, and (3) apply the real-time polymerase chain reaction (PCR) to evaluate the variations in TCE-dechlorinating bacteria (Dehalococcoides spp.). Approximately 350L of SPRS solution was supplied into an injection well (IW) and groundwater samples were collected and analyzed from IW and monitor wells periodically. Results show that the SPRS caused a rapid increase of the total organic carbon concentration (up to 5794mg/L), and reductive dechlorination of TCE was significantly enhanced. TCE dechlorination byproducts were observed and up to 99% of TCE removal (initial TCE concentration=1872μg/L) was observed after 50 days of operation. The population of Dehalococcoides spp. increased from 4.6×10(1) to 3.41×10(7)cells/L after 20 days of operation. DNA sequencing results show that there were 31 bacterial species verified, which might be related to TCE biodegradation. Results demonstrate that the microbial analysis and real-time PCR are useful tools to evaluate the effectiveness of TCE reductive dechlorination.

Effect of the IkBα mutant gene delivery to mesenchymal stem cells on rat chronic pancreatitis

This study aimed to investigate the effect of inhibitors of the NF-kΒ alpha mutant gene (IkBaM) delivery to mensenchymal stem cells (MSCs) on rat chronic pancreatitis (CP). A total of 120 Sprague-Dawley rats were randomly divided into 6 groups of 20: Group A was injected with sterile saline solution, Group B was injected with allogenic MSCs, Group C1 was injected with allogenic IkBαM-MSCs cultured in vitro 4 h before CP modeling, Group C2 was injected with allogenic IkBαM-MSCs cultured in vitro during CP modeling, Group C3 was cultured with allogenic IkBαM-MSCs cultured in vitro 4 h after CP modeling, and Group D was injected with rAAV2-MSCs. Cytokine levels of ICAM-1, CTGF, IL-1, IL-6, IL-8, TNF-α, TIMP-1, TIMP-2, IL-10, FN, MMP-1, MMP-2, MMP-3, and MMP-9 were examined. The results indicated that allogenic IκBαM-MSCs could reduce pro-inflammatory cytokine levels and increase anti-inflammatory cytokine levels in CP. The allogenic IkBαM-MSCs reduced the activation and promoted the apoptosis of pancreatic stellate cells in the rat model of CP. IkBαM-MSCs influenced the proliferation and apoptosis of pancreatic stellate cells by regulating the activation of the PPAR, MAPK, mTOR, TGF-β, NOD-like receptor, Notch, WNT, TGF-β1-SMAD-2/3, and P53 signal transduction pathways.

Biodegradation of Polychlorinated Dibenzo--Dioxins by Strain NSYSU

The dioxin-degrading bacterium strain NSYSU (NSYSU strain) has been isolated from dioxin-contaminated soil by selective enrichment techniques. In the present study, the NSYSU strain was investigated for its capability to biodegrade polychlorinated dibenzo--dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) under aerobic and anaerobic conditions. High-resolution gas chromatography-mass spectrometry and a chemically activated luciferase gene expression bioassay were performed to determine the presence of dioxin compounds. The results indicate that the NSYSU strain could degrade PCDDs and PCDFs under anaerobic conditions in liquid cultures. The main intermediates of the dechlorination process were identified. The results of the bioreactor test indicate that the NSYSU strain could also degrade PCDDs and PCDFs effectively in soil slurries under aerobic conditions. Results from the bioreactor experiment show that approximately 98 and 97% of octachlorodibenzofuran and OCDD were degraded, respectively. The dioxin concentrations in soil slurry decreased from 5823 to 1198 pg toxic equivalency g, resulting in total dioxin removal of 79%. These first findings suggest that the NSYSU strain has the potential to be an effective tool for the bioremediation of soils contaminated with highly recalcitrant organic compounds.

Turbulence under the microscope

Our objective was to observe a new form of turbulence caused bybiological effects - biological micro-turbulence and explore itsprocess and controlling factors. The methods used were proteusmirabilis CGCs micro-cultured to render the occurrence of the specific movement on micro-organic suspension and its controllingfactors were determined by comparison with the control trials.The results showed that turbulence under the microscope was generally in a mass but partially regular. It was also confirmedthat the turbulence under the microscope exhibited hollow effect,temperature-dependent switching on of occurrence and self-controlof suspension quantity. It is clarified that this new form ofturbulence is a spontaneous and self-control process, which providesan experimental model with controllable conditions for studies ofturbulence and a new way for researches on the mechanism andphysiological functions of the flow of body liquid.

Use of specific gene analysis to assess the effectiveness of surfactant-enhanced trichloroethylene cometabolism

The objective of this study was to evaluate the effectiveness of in situ bioremediation of trichloroethylene (TCE)-contaminated groundwater using specific gene analyses under the following conditions: (1) pretreatment with biodegradable surfactants [Simple Green™ (SG) and soya lecithin (SL)] to enhance TCE desorption and dissolution, and (2) supplementation with SG, SL, and cane molasses as primary substrates to enhance the aerobic cometabolism of TCE. Polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), and nucleotide sequence analysis were applied to monitor the variations in specific activity-dependent enzymes and dominant microorganisms. Results show that TCE-degrading enzymes, including toluene monooxygenase, toluene dioxygenase, and phenol monooxygenase, were identified from sediment samples collected from a TCE-spill site. Results from the microcosm study show that addition of SG, SL, or cane molasses can enhance the aerobic cometabolism of TCE. The TCE degradation rates were highest in microcosms with added SL, the second highest in microcosms containing SG, and lowest in microcosms containing cane molasses. This indicates that SG and SL can serve as TCE dissolution agents and act as primary substrates for indigenous microorganisms. Four dominant microorganisms (Rhodobacter sp., Methyloversatilis sp., Beta proteobacterium sp., and Hydrogenophaga pseudoflava) observed in microcosms might be able to produce TCE-degrading enzymes for TCE cometabolic processes.

Constructed wetland for water quality improvement: a case study from Taiwan

In Taiwan, more than 20% of the major rivers are mildly to heavily polluted by domestic, industrial, and agricultural wastewaters due to the low percentage of sewers connected to wastewater treatment plants. Thus, constructed or engineered wetlands have been adopted as the major alternatives to clean up polluted rivers. Constructed wetlands are also applied as the tertiary wastewater treatment systems for the wastewater polishment to meet water reuse standards with lower operational costs. The studied Kaoping River Rail Bridge Constructed Wetland (KRRBCW) is the largest constructed wetland in Taiwan. It is a multi-function wetland and is used for polluted creek water purification and secondary wastewater polishment before it is discharged into the Kaoping River. Although constructed wetlands are feasible for contaminated water treatment, wetland sediments are usually the sinks for organics and metals. In this study, water and sediment samples were collected from the major wetland basins in KRRBCW. The investigation results show that more than 97% of total coliforms (TC), 55% of biochemical oxygen demand (BOD), and 30% of nutrients [e.g. total nitrogen (TN), total phosphorus (TP)] were removed via the constructed wetland system. However, results from the sediment analyses show that wetland sediments contained high concentrations of metals (e.g. Cu, Fe, Zn, Cr, and Mn), organic contents (sediment oxygen demand = 1.7 to 7.6 g O(2)/m(2) d), and nutrients (up to 18.7 g/kg of TN and 1.22 g/kg of TN). Thus, sediments should be excavated periodically to prevent the release the pollutants into the wetland system and causing the deterioration of wetland water quality. Results of polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), and nucleotide sequence analysis reveal that a variation in microbial diversity in the wetland systems was observed. Results from the DGGE analysis indicate that all sediment samples contained significant amounts of microbial ribospecies, which might contribute to the carbon degradation and nitrogen removal. Gradual disappearance of E. coli was also observed along the flow courses through natural attenuation mechanisms.

Severity of Clostridium difficile-associated diarrhea in solid organ transplant patients

Clostridium difficile-associated diarrhea (CDAD) has a wide spectrum of disease severity. Studies have implicated immunosuppressants as a risk factor for severe disease. We hypothesized that solid organ transplant (SOT) patients with CDAD would be at greater risk for severe disease because of their profound immunosuppression. Adult SOT patients with CDAD seen at Duke University Medical Center between 1999 and 2003 were compared with a reference group of non-transplant patients with CDAD. The primary outcome was the development of complicated colitis defined as death, intensive care unit admission, or urgent colectomy within 30 days of diagnosis. A secondary outcome was relapse within 60 days. Eighty transplant and 86 non-transplant cases were reviewed. There was no significant difference in the development of complicated colitis (13.8% vs. 7.0%) or relapse rates (6.2% vs. 7.0%) between the 2 groups. In the entire sample, 18.5% of patients receiving corticosteroids unrelated to transplantation relapsed as compared with 4.5% not receiving corticosteroids (risk ratio 4.3, P=0.02). In conclusion, no significant difference was found in severity of CDAD between SOT patients and non-transplant patients. Exposure to corticosteroids was significantly associated with an increased risk of relapse and may warrant a longer treatment course.

Secondary metabolites from higher fungi in China and their biological activity

As a part of our search for naturally occurring bioactive metabolites from higher fungi, we investigated the chemical constituents of basidiomycetes and ascomycetes fungi (Albatrellus confluens, Albatrellus dispansus, Boletus edulis, Boletopsis grisea, Bondarzewia berkeleyi, Cortinarius tenuipes, Cortinarius vibratilis, Daldinia concentrica, Engleromyces goetzii, Hydnum repandum, Hebeloma versipelle, Hygrophorus eburnesus, Lactarius deliciosus, Lactarius hatsudake, Lactarius hirtipes, Lactarius mitissimus, Lactarius rufus, Paxillus panuoides, Pulveroboletus ravenelii, Russula cyanoxantha, Russula foetens, Russula lepida, Russula nigricans, Sarcodon laevigatum, Sarcodon scabrosus, Shiraia bambusicola, Thelephora aurantiotincta, Thelephora ganbajun, Tricholomopsis rutilans, Tylopilus virens, Tuber indicum, Xylaria euglossa, etc.), and isolated a number of novel terpenoids, phenolics, and nitrogen-containing compounds. The isolation, structural elucidation, and biologically activity of the new compounds are discussed.

Enzymatic degradation of nitriles by Klebsiella oxytoca

Klebsiella oxytoca, isolated from cyanide-containing wastewater, was able to utilize many nitriles as sole source of nitrogen. The major objective of this study was to explore the ability of K. oxytoca to utilize some nitriles and then further evaluate the pathways of transformation of cyanide compounds by K. oxytoca. Results from this study indicate that succinonitrile and valeronitrile were the most optimal sources of nitrogen for the growth of K. oxytoca. The biodegradation of acetonitrile proceeded with the formation of acetamide followed by acetic acid. The production of ammonia was also detected in this biodegradation experiment. Similar results were observed in the propionitrile biodegradation experiments. Collectively, this study suggests that the breakdown of acetonitrile or propionitrile by this bacterium was via a two-step enzymatic hydrolysis with amides as the intermediates and organic acids plus with ammonia as the end products.

Anatomically discrete functional effects of adenoviral clostridial light chain gene-based synaptic inhibition in the midbrain

The gene for the Light Chain fragment of Tetanus Toxin (LC) induces synaptic inhibition by preventing the release of synaptic vesicles. The present experiment applied this approach within the rat midbrain in order to demonstrate that LC gene expression can achieve functionally and anatomically discrete effects within a sensitive brain structure. The deep layers of the superior colliculus/deep mesencephalic nucleus (dSC/DpMe) that are located in the rostral midbrain has been implicated in fear-induced increase of the acoustic startle reflex (fear potentiated startle) but exists in close proximity to neural structures important for a variety of critical functions. The dSC/DpMe of adult rats was injected bilaterally with adenoviral vectors for LC, green fluorescent protein, or vehicle. Synaptobrevin was depleted in brain regions of adenoviral LC expression. LC gene expression in the dSC/DpMe inhibited the increase in startle amplitude seen with the control viral infection, and blocked context-dependent potentiation of startle induced by fear conditioning. Although LC gene expression reduced the absolute amount of cue-specific fear potentiated startle, it did not decrease percent potentiated startle to a cue, nor did it reduce fear-induced contextual freezing, nonspecific locomotor activity, or general health, indicating that its effects were functionally and anatomically specific. Thus, vector-driven LC expression inhibits the function of deep brain nuclei without altering the function of surrounding structures supporting its application to therapeutic neuromodulation.

Factors affecting the biodegradation of PCP by Pseudomonas mendocina NSYSU

A pentachlorophenol (PCP) degrading bacterium was isolated from PCP-contaminated soils and identified as Pseudomonas mendocina NSYSU (P. mendocina NSYSU). The main objectives of this study were to (1) clarify the factors affecting the ability and efficiency of PCP biodegradation by P. mendocina NSYSU, and (2) optimize the use of this bacterium in bioremediation of PCP. Microcosm experiments were conducted to fulfill the objectives. In batch cultures, P. mendocina NSYSU used PCP as its sole source of carbon and energy and was capable of completely degrading this compound. This was confirmed by the stoichiometric release of chloride ion. Moreover, P. mendocina NSYSU was able to mineralize a high concentration of PCP (150 mg/L). Results from the oxygen concentration experiment reveal that the growth of P. mendocina NSYSU was inhibited under low oxygen and anaerobic conditions. Results indicate that the optimal growth conditions for P. mendocina NSYSU include the following: slightly acidic (6<pH<7), aerobic, and relatively moderate ambient temperature (20 degrees C<temperature<30 degrees C) conditions. Addition of extra carbon sources (sodium acetate and glucose) could not enhance the PCP biodegradation. No PCP byproducts were detected after eight days of incubation in this study. This suggests that P. mendocina NSYSU is able to effectively biodegrade PCP and its biodegradation byproducts without the accumulation of inhibitory toxic compounds. Results from this study could be used to assist the optimization of its use in bioremediation of PCP.

Thrombosed basilar apex aneurysm presenting as a third ventricular mass and hydrocephalus

Aneurysms presenting as third ventricular masses are uncommon; most are giant aneurysms arising from the basilar apex. We present a case of a thrombosed basilar apex aneurysm presenting as a third ventricular mass and hydrocephalus in a 55-year-old man. The case is unique in the literature as the aneurysm was completely thrombosed and angiographically occult. The lesion was explored to verify the diagnosis and a third ventriculostomy resolved the patient's symptoms. Completely thrombosed aneurysms should be considered in the differential diagnosis of symptomatic third ventricular masses, even when angiographic studies are negative. The literature on aneurysms presenting as third ventricular masses is reviewed.

Adenoviral clostridial light chain gene-based synaptic inhibition through neuronal synaptobrevin elimination

Clostridial neurotoxins have assumed increasing importance in clinical application. The toxin's light chain component (LC) inhibits synaptic transmission by digesting vesicle-docking proteins without directly altering neuronal health. To study the properties of LC gene expression in the nervous system, an adenoviral vector containing the LC of tetanus toxin (AdLC) was constructed. LC expressed in differentiated neuronal PC12 cells was shown to induce time- and concentration-dependent digestion of mouse brain synaptobrevin in vitro as compared to control transgene products. LC gene expression in the rat lumbar spinal cord disrupted hindlimb sensorimotor function in comparison to control vectors as measured by the Basso-Beattie-Bresnahan (BBB) scale (P<0.001) and rotarod assay (P<0.003). Evoked electromyography (EMG) showed increased stimulus threshold and decreased response current amplitude in LC gene-transferred rats. At the peak of functional impairment, neither neuronal TUNEL staining nor reduced motor neuron density could be detected. Spontaneous functional recovery was observed to parallel the cessation of LC gene expression. These results suggest that light chain gene delivery within the nervous system may provide a nondestructive means for focused neural inhibition to treat a variety of disorders related to excessive synaptic activity, and prove useful for the study of neural circuitry.

Two new steryl esters from the basidiomycete Tricholomopsis rutilans

Two new steryl esters with a polyhydroxylated ergostane-type nucleus, 3beta,5alpha-dihydroxy-(22E,24R)-ergosta-7,22-dien-6beta-yl oleate (1) and 3beta,5alpha-dihydroxy-(22E,24R)-ergosta-22-en-7-one-6beta-yl oleate (2), were isolated from the fruiting bodies of the basidiomycete Tricholomopsis rutilans along with three known sterols (3, 4, and 5). The structures of compounds 1 and 2 were established on the basis of spectroscopic means and chemical methods.

Endoscopic-assisted craniofacial resection of esthesioneuroblastoma: minimizing facial incisions--technical note and report of 3 cases

The surgical management of esthesioneuroblastoma with anterior skull base involvement has traditionally been craniofacial resection, which combines a bifrontal craniotomy with a transfacial approach. The latter usually involves a disfiguring facial incision, mid-facial degloving, lateral rhinotomy, and/or extensive facial osteotomies, which may be cosmetically displeasing to the patient. The advent of angled endoscopes has provided excellent magnification and illumination for surgeons to remove tumors using minimally invasive techniques. The authors describe their experience with three cases of esthesioneuroblastoma, which were surgically removed using a transnasal endoscopic approach, avoiding transfacial incisions. Preoperative radiographs were reviewed and tumors were staged according to the Kadish staging system. One patient had a recurrent esthesioneuroblastoma (Kadish stage B), which was removed entirely through a transnasal endoscopic approach. Two patients had intracranial extension (Kadish stage C), which were resected with a combined approach, endoscopically from below and a bifrontal craniotomy from above, to remove intracranial disease. All patients underwent reconstruction of the anterior skull base. Esthesioneuroblastomas confined to the nasal and paranasal cavities (Kadish stage A and B) were readily accessible through the transnasal endoscopic approach. If there was significant intracranial disease (Kadish stage C), adding a bifrontal craniotomy provided excellent exposure for complete resection of involved tumor. All patients underwent complete tumor resection with negative margins. None developed a cerebrospinal fluid (CSF) leak. The endoscopic-assisted craniofacial approach for the surgical management of esthesioneuroblastomas provides excellent exposure, adequate visualization, and the cosmetic benefit of avoiding an external facial incision.

Evaluation of natural and enhanced PCP biodegradation at a former pesticide manufacturing plant

Pentachlorophenol (PCP) has been used in the past as a pesticide, herbicide, antifungal agent, bactericide, and wood preservative. Thus, PCP is among the most ubiquitous chlorinated compounds found in groundwater contamination. A former pesticide manufacturing plant located in southern Taiwan has been identified as a PCP spill site. In this study, groundwater samples collected from the PCP site were analyzed to assess the occurrence of natural PCP biodegradation. Microcosm experiments were conducted to (1) evaluate the feasibility of biodegrading PCP by indigenous microbial consortia under aerobic and cometabolic conditions, and (2) determine the potential of enhancing PCP biodegradation using cane molasses and biological sludge cake as the substitute primary substrates under cometabolic conditions. The inocula used in this microcosm study were aquifer sediments collected from the PCP site and activated sludges collected from the municipal and industrial wastewater treatment plants. Results from this field investigation indicate that the natural biodegradation of PCP is occurring and causing the decrease in PCP concentration. Microcosm results show that the indigenous microorganisms can biodegrade PCP under both aerobic and aerobic cometabolism conditions. A PCP-degrading bacterium was isolated from the collected aquifer sediments and identified as Pseudomonas mendocina NSYSU via some biochemical tests and further conformation of DNA sequencing. In batch cultures, P. mendocina NSYSU used PCP as its sole source of carbon and energy. The isolated bacterium, P. mendocina NSYSU, was capable of completely degrading PCP as indicated by the increase in biomass formation with the decrease in PCP concentrations occurred in the carbon-free medium simultaneously. Results indicate that the in situ or on-site aerobic bioremediation using indigenous microorganisms or inoculated bacteria would be a feasible technology to clean up the studied PCP-contaminated site. Results from this study will be useful in designing a scale-up in situ or on-site PCP bioremediation system (e.g., on-site bioreactor) for field application.

Biotransformation of cyanide to methane and ammonia by Klebsiella oxytoca

Klebsiella oxytoca, isolated from cyanide-containing industrial wastewater, was shown to be able to biodegrade cyanide to non-toxic endproducts using cyanide as the sole nitrogen source. In this study, ammonia was one of the detected endproduct of cyanide biodegradation by the concentrated resting cells of K. oxytoca. Moreover, cyanide has been shown to be biotransformed to methane through the actions of concentrated resting cells. Biodegradation of cyanide by cell-free extracts was not observed, which might be due to the inactivation of nitrogenase (an oxygen-labial enzyme) caused by the oxygen exposure after cell disruption. Results show that the cyanide consumption by resting cells of K. oxytoca was induced when the pretreatment of these cells with cyanide was conducted. However, the cyanide-degrading capability of resting cells pretreated with ammonia was inhibited. The inhibition of cyanide degradation by resting cells of K. oxytoca was affected by the ammonia concentration. This might result from the suppression of nitrogenase activity of K. oxytoca by ammonia since nitrogenase was suggested to be the sole cyanide-degrading enzyme during the cyanide degradation process. Results from this study also show that the processes of cyanide biodegradation and ammonia production by resting cells occurred simultaneously. This suggests that the utilization of cyanide as nitrogen source by K. oxytoca might proceed using ammonia as an assimilatory substrate.

Laparoscopic anterior lumbar interbody fusion precipitating pituitary apoplexy

OBJECTIVE

Pituitary apoplexy may be the first presentation of a previously undiagnosed pituitary adenoma. Although many mechanisms of pituitary apoplexy have been proposed in the literature, the exact pathogenesis remains unclear. Many predisposing events have been implicated in the pathogenesis, however, the role of laparoscopy precipitating pituitary apoplexy has not been previously described. The authors present a case of pituitary apoplexy in a previously undiagnosed pituitary adenoma, which presented in the immediate post-operative period after a laparoscopic anterior lumbar interbody fusion.

CLINICAL PRESENTATION

A 45-year-old man presented with a sudden onset of headache, photophobia, diplopia, visual field deficits, and decreased visual acuity in the immediate post-operative period after an uneventful laparoscopic anterior lumbar interbody fusion. Results of computed tomography of the brain revealed a hyperdense suprasellar mass without any signs of subarachnoid blood. The patient underwent magnetic resonance imaging, which revealed a hemorrhagic pituitary tumor with lateral and suprasellar extension, with compression of the cavernous sinus and optic chiasm, respectively. An urgent transsphenoidal decompression of the hemorrhagic pituitary adenoma was performed. Post-operatively, the patient demonstrated marked neurological improvement with recovery of visual acuity and extraocular movements.

CONCLUSION

To the authors' knowledge, this is the first case reported in the literature of a laparoscopic procedure precipitating pituitary apoplexy. Recognition of this rare complication of laparoscopic surgery, and the importance of rapid diagnosis and urgent surgical treatment are emphasized.

Reversal of radiographically impending stroke with multiple intraarterial papaverine infusions in severe diffuse cerebral vasospasm induced by subarachnoid hemorrhage

BACKGROUND

Selective intraarterial infusion of papaverine is used in the treatment of symptomatic cerebral vasospasm induced by aneurysmal subarachnoid hemorrhage (SAH). Delays in instituting therapy for vasospasm can lead to irreversible cerebral infarction and a devastating outcome. Endovascular papaverine treatment of vasospasm in the presence of low-attenuation lesions on computed tomography (CT) is controversial, because of the fear of reperfusion hemorrhage in completed infarcts.

METHOD

Two patients with aneurysmal SAH who subsequently developed severe diffuse vasospasm were identified. In both patients, large areas of low-attenuation change suggesting impending cerebral infarction were seen on CT scans. The patients received multiple infusions of intraarterial papaverine in an effort to treat vasospasm refractory to medical management.

FINDINGS

After multiple intermittent administrations of papaverine, which initially appeared to increase the low-attenuation changes, there was dramatic reversal of the radiographic findings. There was also improvement in circulation time, transcranial Doppler velocities, and clinical outcome.

INTERPRETATION

These findings suggest that in some patients, intraarterial infusions of papaverine initiated in the earliest stages of ischemia may exacerbate the radiographic appearance of low-attenuation changes, but may ultimately reverse the evolution of cerebral infarction.

A new trihydroxy fatty acid from the ascomycete, Chinese truffle Tuber indicum

From the chloroform/methanol extract of the fruiting bodies of the ascomycete Chinese truffle Tuber indicum Cooke et Massee, a new trihydroxylated monounsaturated fatty acid (1) has been isolated. The structure of this new linoleic acid-derived metabolite was established as 9,10,11-trihydroxy-(12Z)-12-octadecenoic acid by means of spectroscopic and chemical methods. The fatty acid composition of the chloroform-soluble fraction of this fungus was analyzed by gas chromatography-mass spectrometry. The content of the predominant unsaturated fatty acids (oleic and linoleic acids) is as high as 68%. The use of dimethyl disulfide adduct was effective in the determination of the position of the double bond, and the glycol oxidation fission reaction with sodium metaperiodate supported on silica gel was helpful in establishing the location of the trihydroxylic groups in the new fatty acid.

Armillaramide, a new sphingolipid from the fungus Armillaria mellea

A new C(18)-phytosphingosine ceramide containing non-hydroxy fatty acid, armillaramide (1), has been isolated together with ergosterol peroxide from the fruiting bodies of the basidiomycete Armillaria mellea. Its structure was established as (2S,3S,4R)-2-hexadecanoylamino-octadecane-1,3,4-triol by spectroscopic and chemical methods.

The history and evolution of transsphenoidal surgery

Initial attempts at transcranial approaches to the pituitary gland in the late 1800s and early 1900s resulted in a mortality rate that was generally considered prohibitive. Schloffer suggested the use of a transsphenoidal route as a safer, alternative approach to the sella turcica. He reported the first successful removal of a pituitary tumor via the transsphenoidal approach in 1906. His procedure underwent a number of modifications by interested surgeons, the culmination of which was A. E. Halstead's description in 1910 of a sublabial gingival incision for the initial stage of exposure. From 1910 to 1925, Cushing, combining a number of suggestions made by previous authors, refined the transsphenoidal approach and used it to operate on 231 pituitary tumors, with a mortality rate of 5.6%. As he developed increasing expertise with transcranial surgery, however, Cushing reduced his mortality rate to 4.5%. With the transcranial approach, he was able to verify suprasellar tumors and achieve better decompression of the optic apparatus, resulting in better recovery of vision and a lower recurrence rate. As a result he and most other neurosurgeons at the time abandoned the transnasal in favor of the transcranial approaches. Norman Dott, a visiting scholar who studied with Cushing in 1923, returned to Edinburgh, Scotland, and continued to use the transsphenoidal procedure while others pursued transcranial approaches. Dott introduced the procedure to Gerard Guiot, who published excellent results with the transsphenoidal approach and revived the interest of many physicians throughout Europe in the early 1960s. Jules Hardy, who used intraoperative fluoroscopy while learning the transsphenoidal approach from Guiot, then introduced the operating microscope to further refine the procedure; he thereby significantly improved its efficacy and decreased surgical morbidity. With the development of antibiotic drugs and modern microinstrumentation, the transsphenoidal approach became the preferred route for the removal of lesions that were confined to the sella turcica. The evolution of the transsphenoidal approaches and their current applications and modifications are discussed.

Evaluation of TCDD biodegradability under different redox conditions

Polychlorinated dibenzo-p-dioxins have been generated as unwanted by-products in many industrial processes. Although their widespread distribution in different environmental compartments has been recognized, little is known about their fate in the ultimate environment sinks. The highly stable dioxin isomer 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) has been called the most toxic compound known to man. In this laboratory microcosm study, TCDD bioavailability was evaluated under five reduction/oxidation (redox) conditions including aerobic biodegradation, aerobic cometabolism, methanogenesis, iron reduction, and reductive dechlorination. Activated sludge and aquifer sediments from a TCDD and a pentachlorophenol (PCP) contaminated site were used as the inocula. Acetate, sludge cake, and cane molasses were used as the primary substrates (carbon sources) in cometabolism and reductive dechlorination microcosms. After a 90-day incubation period, microcosms constructed under reductive dechlorination conditions were the only treatment showing promising remediation results. The highest TCDD degradation rate [up to 86% of TCDD removal (with an initial concentration of 96 microg/kg of soil)] was observed in the microcosms with anaerobic activated sludge as the microbial inocula and sludge cakes as the primary substrates. Except for reductive dechlorination microcosms, no significant TCDD removal was observed in the microcosms prepared under other conditions. Thus, application of an effective primary substrate to enhance the reductive dechlorination process is a feasible method for TCDD bioremediation. Bioremediation expense can be significantly reduced by the supplement of some less expensive alternative substrates (e.g., sludge cakes, cane molasses). Results would be useful in designing a scale-up in situ or on-site bioremediation system such as bioslurry reactor for field application.

Application of microbial enumeration technique to evaluate the occurrence of natural bioremediation

Natural bioremediation is believed to be the major processes that account for both containment of the petroleum-hydrocarbon plume and reduction of the contaminant concentrations. In this study, the feasibility of applying the microbial enumeration technique was assessed for natural biodegradation evaluation at three selected gasoline spill sites. At each site, two monitor wells were installed along the groundwater flow, and one multilevel sampler (MLS) was installed to delineate the vertical distribution of the contaminant plume. Two continuous soil cores were collected at each site to evaluate the horizontal distribution of the microbial activity. Soil samples were used for microbial enumeration, grain-size distribution analysis, and sediment extraction. In situ tracer study was performed using 1,2,4-trimethylbenzene (1,2,4-TMB) as the tracer to study the efficiency of contaminant biodegradation. Investigation results demonstrate the agreement between microbial enumeration and other evaluation techniques for natural bioremediation (e.g., geochemical indicator analysis, tracer study). Results suggest that the microbial enumeration is useful in assessing the occurrence, efficiency, and status of the bioremediation. Because this technique provides insight into factors controlling contaminant biodegradation, it could be performed as the supplemental method for natural bioremediation evaluation at petroleum-hydrocarbon spill sites.

Serum antioxidant status of civil aircrew

Objective. To study the serum antioxidant status in civil aircrew members who had more than 4000 h of cumulative flight hours, therefore exposed to a higher dose of cosmic radiation comparing to the dose received by ground residents. Method. Differences in the serum levels of total antioxidant capacity (TAOC), superoxide dismutase (SOD) and malondialdehyde (MDA) were investigated in 230 crew members, 37 local ground residents in Xinjiang, and 37 ground residents in Tianjin. Result. Significantly higher levels of all the three serum indexes were found in civil aircrew members. Serum levels of TAOC and SOD were higher in Xinjiang than in Tianjin ground residents, although no difference was found for MDA. Positive correlations were observed among the three serum indexes in this study. Conclusion. The elevated serum level of MDA in civil aircrew members deserves a proper attention by health care policy makers.

Development of a biobarrier for the remediation of PCE-contaminated aquifer

The industrial solvent tetrachloroethylene (PCE) is among the most ubiquitous chlorinated compounds found in groundwater contamination. The objective of this study was to develop a biobarrier system, which includes a peat layer to enhance the anaerobic reductive dechlorination of PCE in situ. Peat was used to supply primary substrate (electron donor) continuously. A laboratory-scale column experiment was conducted to evaluate the feasibility of this proposed system or PCE removal. This experiment was performed using a series of continuous-flow glass columns including a soil column, a peat column, followed by two consecutive soil columns. Anaerobic acclimated sludges were inoculated in all three soil columns to provide microbial consortia for PCE biodegradation. Simulated PCE-contaminated groundwater with a flow rate of 0.25 l/day was pumped into this system. Effluent samples from each column were analyzed for PCE and its degradation byproducts (trichloroethylene (TCE), cis-dichloroethylene (cis-DCE), vinyl chloride (VC), ethylene (ETH), and ethane). Results show that the decrease in PCE concentrations and production of PCE byproducts were observed over a 65-day operating period. Up to 98%, of PCE removal efficiency was obtained in this passive system. Results indicate that the continuously released organics from peat column enhanced PCE biotransformation. Thus, the developed biobarrier treatment scheme has the potential to be developed into a cost-effective in situ PCE-remediation technology, and can be utilized as an interim step to aid in system scale-up.

New glycosphingolipid containing an unusual sphingoid base from the basidiomycete Polyporus ellisii

A new 9-methyl-sphinga-4,8-dienine-containing glucocerebroside (1), together with two additional known analogs, cerebrosides B and D, was isolated from the chloroform-soluble lipid fraction of the ethanol and chloroform/methanol extract of the fruiting bodies of the basidiomycete Polyporus ellisii Berk. and characterized. The structure and relative stereochemistry of the new compound were identified as (2S,3R,4E,8E-1-(beta-D-glucopyranosyl)-3-hydroxy-2-[(R)-2'-hydroxyheptadecanoyl]amino-9-methyl-4,8-octadecadiene by means of spectroscopic (1H,13C, and two-dimensional nuclear magnetic resonance; mass spectrometry) and chemical methods.

Posterior fusion of the subaxial cervical spine: indications and techniques

The biomechanical stability of the subaxial cervical spine (C3–7) can be compromised by numerous pathological processes, and the restoration of stability may ultimately require fusion and placement of rigid internal fixation devices. A posterior fusion and stabilization procedure is often used to treat cervical instability secondary to traumatic injury, rheumatoid arthritis, ankylosing spondylitis, neoplastic disease, infections, and previous laminectomy. Numerous techniques and advances in spinal instrumentation have evolved over the last 30 years. The authors review the indications and the various methods for stabilizing and fusing the subaxial cervical spine via posterior approaches.