Effects of sunflower oil infusions of Asparagopsis taxiformis on in vitro ruminal methane production and biohydrogenation of polyunsaturated fatty acids

Asparagopsis taxiformis inhibits ruminal methane (CH4) production due to its bromoform (CHBr3) content. The immersion of A. taxiformis in edible vegetable oils allows the extraction and stabilization of the highly volatile CHBr3 in the oil phase. The objectives of this study were to explore the effects of adding sunflower oils with increasing concentrations of CHBr3 on in vitro ruminal methanogenesis and biohydrogenation. Five batches of 48-h in vitro incubations were performed in 14 fermentation bottles, using rumen inocula collected shortly after the slaughter of young crossbred bulls and 1 g of dry matter (DM) from a total diet of mixed feed without added oil (control) or with 60 μL of sunflower oil per gram of DM as the substrate. The treatments were the CHBr3 content in the oil added: 0 μg (B0), 25 μg (B25), 50 μg (B50), 75 μg (B75), 100 μg (B100), and 150 μg (B150) of CHBr3 per gram of substrate DM. Organic matter (OM) degradability, total gas, CH4, volatile fatty acids (VFA), long-chain fatty acids, and dimethyl acetals (DMA) were analyzed at the end of each incubation. Data were analyzed with a model considering the treatments as the fixed effect and the run as a random block and using orthogonal contrasts. Degradability of OM was higher in the control group and was unaffected by CHBr3 concentration. Total gas production per gram of degraded OM was unaffected by treatments and averaged 205 ± 29.8 mL/g. Methane (mL) production decreased linearly with increasing CHBr3 concentrations, with 33%, 47%, and 87% reductions for B75, B100, and B150, respectively. Total VFA concentration was unaffected by oil inclusion but was reduced by 20% in CHBr3-containing treatments, although without any dose-response pattern. The molar percentage of acetate decreased linearly, whereas propionate and butyrate increased linearly with the increasing CHBr3 dosage. Including oil in the diet decreased the branched-chain fatty acids and DMA content. Increasing CHBr3 concentrations did not affect branched-chain fatty acids, but linearly increased most of the identified DMA. Adding oil to the control diet increased the 18:2n-6, whereas increasing the concentration of CHBr3 had no effect on 18:2n-6 but decreased linearly the 18:0 and increased the trans-18:1 isomers. The results obtained provide evidence that oil immersions of A. taxiformis can successfully inhibit ruminal production of CH4 in vitro at doses of 100 and 150 μg/g DM, and simultaneously modulate biohydrogenation.

In vitro activity of cefiderocol and other newly approved antimicrobials against multi-drug resistant Gram-negative pathogens recovered in intensive care units in Spain and Portugal

OBJECTIVE

The antimicrobial resistance is a significant public health threat, particularly for healthcare-associated infections caused by carbapenem-resistant Gram-negative pathogens which are increasingly reported worldwide. The aim of this study was to provide data on the in vitro antimicrobial activity of cefiderocol and that of commercially available comparator antibiotics against a defined collection of recent clinical multi-drug resistant (MDR) microorganisms, including carbapenem resistant Gram-negative bacteria collected from different regions in Spain and Portugal.

METHODS

A total of 477 clinical isolates of Enterobacterales, Pseudomonas aeruginosa, Acinetobacter baumannii and Stenotrophomonas maltophilia were prospectively (n=265) and retrospectively (n=212) included (2016-2019). Susceptibility testing was performed using standard broad microdilution and results were interpreted using CLSI-2021 and EUCAST-2021 criteria.

RESULTS

Overall, cefiderocol showed a good activity against Enterobacterales isolates, being 99.5% susceptible by CLSI and 94.5% by EUCAST criteria. It also demonstrated excellent activity against P. aeruginosa and S. maltophilia isolates, all being susceptible to this compound considering CLSI breakpoints. Regarding A. baumannii (n=64), only one isolate was resistant to cefiderocol.

CONCLUSIONS

Our results are in agreement with other studies performed outside Spain and Portugal highlighting its excellent activity against MDR gram-negative bacteria. Cefiderocol is a therapeutic alternative to those available for the treatment of infections caused by these MDR bacteria.

Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study

BACKGROUND

No effective pharmacological or non-pharmacological interventions exist for patients with long COVID. We aimed to describe recovery 1 year after hospital discharge for COVID-19, identify factors associated with patient-perceived recovery, and identify potential therapeutic targets by describing the underlying inflammatory profiles of the previously described recovery clusters at 5 months after hospital discharge.

METHODS

The Post-hospitalisation COVID-19 study (PHOSP-COVID) is a prospective, longitudinal cohort study recruiting adults (aged ≥18 years) discharged from hospital with COVID-19 across the UK. Recovery was assessed using patient-reported outcome measures, physical performance, and organ function at 5 months and 1 year after hospital discharge, and stratified by both patient-perceived recovery and recovery cluster. Hierarchical logistic regression modelling was performed for patient-perceived recovery at 1 year. Cluster analysis was done using the clustering large applications k-medoids approach using clinical outcomes at 5 months. Inflammatory protein profiling was analysed from plasma at the 5-month visit. This study is registered on the ISRCTN Registry, ISRCTN10980107, and recruitment is ongoing.

FINDINGS

2320 participants discharged from hospital between March 7, 2020, and April 18, 2021, were assessed at 5 months after discharge and 807 (32·7%) participants completed both the 5-month and 1-year visits. 279 (35·6%) of these 807 patients were women and 505 (64·4%) were men, with a mean age of 58·7 (SD 12·5) years, and 224 (27·8%) had received invasive mechanical ventilation (WHO class 7-9). The proportion of patients reporting full recovery was unchanged between 5 months (501 [25·5%] of 1965) and 1 year (232 [28·9%] of 804). Factors associated with being less likely to report full recovery at 1 year were female sex (odds ratio 0·68 [95% CI 0·46-0·99]), obesity (0·50 [0·34-0·74]) and invasive mechanical ventilation (0·42 [0·23-0·76]). Cluster analysis (n=1636) corroborated the previously reported four clusters: very severe, severe, moderate with cognitive impairment, and mild, relating to the severity of physical health, mental health, and cognitive impairment at 5 months. We found increased inflammatory mediators of tissue damage and repair in both the very severe and the moderate with cognitive impairment clusters compared with the mild cluster, including IL-6 concentration, which was increased in both comparisons (n=626 participants). We found a substantial deficit in median EQ-5D-5L utility index from before COVID-19 (retrospective assessment; 0·88 [IQR 0·74-1·00]), at 5 months (0·74 [0·64-0·88]) to 1 year (0·75 [0·62-0·88]), with minimal improvements across all outcome measures at 1 year after discharge in the whole cohort and within each of the four clusters.

INTERPRETATION

The sequelae of a hospital admission with COVID-19 were substantial 1 year after discharge across a range of health domains, with the minority in our cohort feeling fully recovered. Patient-perceived health-related quality of life was reduced at 1 year compared with before hospital admission. Systematic inflammation and obesity are potential treatable traits that warrant further investigation in clinical trials.

FUNDING

UK Research and Innovation and National Institute for Health Research.

Small for gestational age very preterm infants present a higher risk of developing bronchopulmonary dysplasia

INTRODUCTION

Several studies assessed the influence of a low birth weight on bronchopulmonary dysplasia (BPD), but not all could find a significant association. Our aim was to assess the association between low birth weight and BPD in preterm infants, prospectively recruited at 11 level III Portuguese neonatal centers.

METHODS

Obstetrical and neonatal data on mothers and preterm infants with gestational ages between 24 and 30 weeks, born during 2015 and 2016 after a surveilled pregnancy, were analyzed. Neonates were considered small for gestational age (SGA) when their birthweight was below the 10th centile of Fenton's growth chats and BPD was defined as the dependency for oxygen therapy until 36 weeks of corrected age. Statistical analysis was performed using IBM SPSS® statistics 23 and a p-value <0.05 was considered statistically significant.

RESULTS

Out of 614, a total of 494 preterm infants delivered from 410 women were enrolled in the study; 40 (8.0%) infants with SGA criteria. SGA were more often associated with a single pregnancy, had greater use of antenatal corticosteroids, increased prevalence of gestational hypertensive disorders, C-section, rupture of membranes below 18 hours, rate of intubation in the delivery room, use of surfactant treatment, oxygen therapy, mechanical ventilation need, BPD, cystic periventricular leukomalacia, nosocomial sepsis and pneumonia; had lower prevalence of chorioamnionitis, and lower Apgar scores. The multivariate analysis by logistic regression, adjusted for BPD risk factors revealed a significant association between SGA and BPD: OR = 5.2 [CI: 1.46-18.58]; p = 0.01.

CONCLUSION

The results of this study increase the scientific evidence that SGA is an independent risk factor for BPD.

Laboratory information management software for engineered mini-protein therapeutic workflow

Background

Protein based therapeutics are one of the fastest growing classes of novel medical interventions in areas such as cancer, infectious disease, and inflammation. Protein engineering plays an important role in the optimization of desired therapeutic properties such as reducing immunogenicity, increasing stability for storage, increasing target specificity, etc. One category of protein therapeutics is nature-inspired bioengineered cystine-dense peptides (CDPs) for various biological targets. These engineered proteins are often further modified by synthetic chemistry. For example, candidate mini-proteins can be conjugated into active small molecule drugs. We refer to modified mini-proteins as “Optides” (Optimized peptides). To efficiently serve the multidisciplinary lab scientists with varied therapeutic portfolio research goals in a non-commercial setting, a cost effective extendable laboratory information management system (LIMS) is/was needed.

Results

We have developed a LIMS named Optide-Hunter for a generalized engineered protein compounds workflow that tracks entities and assays from creation to preclinical experiments. The implementation and custom modules are built using LabKey server, which is an Open Source platform for scientific data integration and analysis. Optide-Hunter contains a compound registry, in-silico assays, high throughput production, large-scale production, in vivo assays and data extraction from a specimen-tracking database. It is used to store, extract, and view data for various therapeutics projects. Optide-Hunter also includes external processing stand-alone software (HPLCPeakClassifierApp) for automated chromatogram classification. The HPLCPeakClassifierApp is used for pre-processing of HPLC data prior to loading to Optide-Hunter. The custom implementation is done using data transformation modules in R, SQL, javascript, and java and is Open Source to assist new users in customizing it for their unique workflows. Instructions for exploring a deployed version of Optide-Hunter can be found at https://www.labkey.com/case%20study/optide-hunter

Conclusion

The Optide-Hunter LIMS system is designed and built to track the process of engineering, producing and prioritizing protein therapeutic candidates. It can be easily adapted and extended for use in small or large research laboratories where multidisciplinary scientists are collaborating to engineer compounds for potential therapeutic or protein science applications. Open Source exploration of Optide-Hunter can help any bioinformatics scientist adapt, extend, and deploy an equivalent system tailored to each laboratory’s workflow.

Low-cost Method for Obtaining Medical Rapid Prototyping Using Desktop 3D printing: A Novel Technique for Mandibular Reconstruction Planning

BACKGROUND

Three-dimensional (3D) printing is relatively a new technology with clinical applications, which enable us to create rapid accurate prototype of the selected anatomic region, making it possible to plan complex surgery and pre-bend hardware for individual surgical cases. This study aimed to express our experience with the use of medical rapid prototype (MRP) of the maxillofacial region created by desktop 3D printer and its application in maxillofacial reconstructive surgeries.

MATERIAL AND METHODS

Three patients with benign mandible tumors were included in this study after obtaining informed consent. All patient's maxillofacial CT scan data was processed by segmentation and isolation software and mandible MRP was printed using our desktop 3D printer. These models were used for preoperative surgical planning and prebending of the reconstruction plate.

CONCLUSIONS

MRP created by desktop 3D printer is a cost-efficient, quick and easily produced appliance for the planning of reconstructive surgery. It can contribute in patient orientation and helping them in a better understanding of their condition and proposed surgical treatment. It helps surgeons for pre-operative planning in the resection or reconstruction cases and represent an excellent tool in academic setting for residents training. The pre-bended reconstruction plate based on MRP, resulted in decreased surgery time, cost and anesthesia risks on the patients. Key words:3D printing, medical modeling, rapid prototype, mandibular reconstruction, ameloblastoma.

Elucidating constraints for differentiation of major human Klebsiella pneumoniae clones using MALDI-TOF MS

The establishment of matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS) in routine microbial identification boosted many developments towards high-throughput applications, including bacterial typing. However, results are still controversial for different bacterial species. We aim to evaluate the suitability of MALDI-TOF MS for typing clinically relevant multidrug resistant (MDR) Klebsiella pneumoniae subsp. pneumoniae clones using routine conditions and a previously validated chemometric analysis workflow. Mass spectra of 83 K. pneumoniae clinical isolates representing major human MDR clones [11 sequence types (STs), 22 PFGE-types] recovered in Portugal and Spain during outbreaks and non-outbreak situations (2003-2012) were obtained from cell extracts (CE) and intact cells (IC), and analysed with different chemometric tools. We observed a highly consistent peak pattern among isolates from different clones either with CE or IC, suggesting a high degree of conservation of biomolecules analysed (a large part corresponding to ribosomal proteins). Moreover, the low degree of agreement between MALDI-TOF MS and other methods (from 34.9 % to 43.4 % of correct assignments for CE and from 40.8 % to 70.1 % for IC) corroborates the low discriminatory potential of the technique at infraspecies level. Our results suggest a low discriminatory power of MALDI-TOF MS for clinically relevant MDR K. pneumoniae clones and highlight the need of developing tools for high-resolution typing in this species.

MALDI-TOF mass spectrometry as a tool for the discrimination of high-risk Escherichia coli clones from phylogenetic groups B2 (ST131) and D (ST69, ST405, ST393)

Reliable, quick and low-cost methods are needed for the early detection of multidrug-resistant and highly virulent high-risk B2 and D Escherichia coli clones or clonal complexes (HiRCC). Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) seems to have a good discriminatory potential at different subspecies levels, but it was never evaluated for the discrimination of E. coli clones. We assessed the potential of MALDI-TOF MS coupled to multivariate data analysis to discriminate representative E. coli B2 and D HiRCC. Seventy-three E. coli isolates from B2 (including ST131 and B2 non-ST131 clones) and D (ST69, ST393, ST405) with variable pulsed-field gel electrophoresis (PFGE) patterns, origins and dates (1980-2010) were tested. MS spectra were acquired from independent extracts obtained from different plate cultures in two different Microflex LT MALDI-TOF devices (Bruker) after a standard extraction procedure. MALDI-TOF MS fingerprinting analysis revealed a good discriminatory ability between the four HiRCC analysed (ST131, ST69, ST405, ST393) and between B2 ST131 and other B2 non-ST131 isolates. Clusters defined by MALDI-TOF MS were consistent with the clonal complexes assigned by multilocus sequence typing (MLST), although differences were detected regarding the composition of clusters obtained by the comparison of PFGE profiles. We demonstrate, for the first time, that characteristic mass fingerprints of different E. coli HiRCC are sufficiently discriminatory and robust to enable their differentiation by MALDI-TOF MS, which might represent a promising tool for the optimisation of infection control, individual patient management and large-scale epidemiological studies of public health relevance. The good correlation between phenotypic and genotypic features further corroborates phylogenetic relationships delineated by MLST.

Rapid detection of urinary tract infections caused by Proteus spp. using PNA-FISH

We developed a fluorescence in situ hybridization (FISH) method for the rapid detection of Proteus spp. in urine, using a novel peptide nucleic acid (PNA) probe. Testing on 137 urine samples from patients with urinary tract infections has shown specificity and sensitivity values of 98 % (95 % CI, 93.2-99.7) and 100 % (95 % CI, 80,8-100), respectively, when compared with CHROMagar Orientation medium. Results indicate that PNA-FISH is a reliable alternative to traditional culture methods and can reduce the diagnosis time to approximately 2 h.

The "knucklehead" approach and what matters in terms of health for formerly incarcerated Latino men

In terms of the examination of the relationship between masculinity and health, there has been limited exploration of how the ways in which formerly incarcerated Latino men (FILM) construct their masculinities may conflict with public health messages. Using information gained from three years of ethnographic research that was conducted with formerly incarcerated Puerto Rican males in three urban communities in New York City, the authors examine what matters to FILM in terms of their health and well-being and what conflicts exist between public health prevention messages and FILM masculinity. Our results indicate the following: (1) major threats to the health of FILM, such as HIV risk behavior, alcohol and drug use and high caloric intake, are perceived as irrelevant to most of the FILM in the study; (2) young FILM believe that they engage in risky behaviors because of their "knucklehead" mentality and diminish their risks by becoming "street-smart;" and (3) social isolation, loneliness and general risk-taking behavior among FILM are salient issues that have yet to be effectively addressed. Of our sample of 32 FILM, we identified 7 individuals who have transitioned from having a "knucklehead" approach in their lives to possessing a greater sense of awareness of health and social matters. These seven individuals followed either or both of the following pathways: (1) pursuing a college education or (2) becoming community leaders.

FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis

SUMMARY

Images containing spatial expression patterns illuminate the roles of different genes during embryogenesis. In order to generate initial clues to regulatory interactions, biologists frequently need to know the set of genes expressed at the same time at specific locations in a developing embryo, as well as related research publications. However, text-based mining of image annotations and research articles cannot produce all relevant results, because the primary data are images that exist as graphical objects. We have developed a unique knowledge base (FlyExpress) to facilitate visual mining of images from Drosophila melanogaster embryogenesis. By clicking on specific locations in pictures of fly embryos from different stages of development and different visual projections, users can produce a list of genes and publications instantly. In FlyExpress, each queryable embryo picture is a heat-map that captures the expression patterns of more than 4500 genes and more than 2600 published articles. In addition, one can view spatial patterns for particular genes over time as well as find other genes with similar expression patterns at a given developmental stage. Therefore, FlyExpress is a unique tool for mining spatiotemporal expression patterns in a format readily accessible to the scientific community.

AVAILABILITY

http://www.flyexpress.net

CONTACT

s.kumar@asu.edu.

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

BACKGROUND

Since its inception, proteomics has essentially operated in a discovery mode with the goal of identifying and quantifying the maximal number of proteins in a sample. Increasingly, proteomic measurements are also supporting hypothesis-driven studies, in which a predetermined set of proteins is consistently detected and quantified in multiple samples. Selected reaction monitoring (SRM) is a targeted mass spectrometric technique that supports the detection and quantification of specific proteins in complex samples at high sensitivity and reproducibility. Here, we describe ATAQS, an integrated software platform that supports all stages of targeted, SRM-based proteomics experiments including target selection, transition optimization and post acquisition data analysis. This software will significantly facilitate the use of targeted proteomic techniques and contribute to the generation of highly sensitive, reproducible and complete datasets that are particularly critical for the discovery and validation of targets in hypothesis-driven studies in systems biology.

RESULT

We introduce a new open source software pipeline, ATAQS (Automated and Targeted Analysis with Quantitative SRM), which consists of a number of modules that collectively support the SRM assay development workflow for targeted proteomic experiments (project management and generation of protein, peptide and transitions and the validation of peptide detection by SRM). ATAQS provides a flexible pipeline for end-users by allowing the workflow to start or end at any point of the pipeline, and for computational biologists, by enabling the easy extension of java algorithm classes for their own algorithm plug-in or connection via an external web site.This integrated system supports all steps in a SRM-based experiment and provides a user-friendly GUI that can be run by any operating system that allows the installation of the Mozilla Firefox web browser.

CONCLUSIONS

Targeted proteomics via SRM is a powerful new technique that enables the reproducible and accurate identification and quantification of sets of proteins of interest. ATAQS is the first open-source software that supports all steps of the targeted proteomics workflow. ATAQS also provides software API (Application Program Interface) documentation that enables the addition of new algorithms to each of the workflow steps. The software, installation guide and sample dataset can be found in http://tools.proteomecenter.org/ATAQS/ATAQS.html.

The Protein Information and Property Explorer 2: gaggle-like exploration of biological proteomic data within one webpage

The Protein Information and Property Explorer 2 (PIPE2) is an enhanced software program and updated web application that aims at providing the proteomic researcher a simple, intuitive user interface through which to begin inquiry into the biological significance of a list of proteins typically produced by MS/MS proteomic processing software. PIPE2 includes an improved interface, new data visualization options, and new data analysis methods for combining disparate, but related, data sets. In particular, PIPE2 has been enhanced to handle multi-dimensional data such as protein abundance, gene expression, and/or interaction data. The current architecture of PIPE2, modeled after that of Gaggle (a programming infrastructure for interoperability between separately developed software tools), contains independent functional units that can be instantiated and pieced together at the user's discretion to form a pipelined analysis workflow. Among these functional units is the Network Viewer component, which adds rich network analysis capabilities to the suite of existing proteomic web resources. Additionally, PIPE2 implements a framework within which new analysis procedures can be easily deployed and distributed over the World Wide Web. PIPE2 is available as a web service at http://pipe2.systemsbiology.net/.

Effectiveness of rotavirus vaccination against childhood diarrhoea in El Salvador: case-control study

OBJECTIVE

To evaluate the effectiveness of a monovalent rotavirus vaccine against severe rotavirus disease and to assess its impact on diarrhoea in children aged less than 2 years after national introduction in El Salvador, a low-middle income country in Central America.

DESIGN

Matched case-control study.

SETTING

Seven hospitals in cities across El Salvador, January 2007 to June 2009.

PARTICIPANTS

323 children aged less than 2 years admitted with laboratory confirmed rotavirus diarrhoea and 969 healthy controls matched for age and neighbourhood.

MAIN OUTCOME MEASURE

Effectiveness of rotavirus vaccination ((1-adjusted odds ratio of vaccination)x100) against rotavirus diarrhoea requiring hospital admission.

RESULTS

Cases and controls were similar for breast feeding, premature birth, maternal education, and socioeconomic variables. G1P[8] strains were identified in 92% of rotavirus cases. Effectiveness of two doses of vaccination against diarrhoea requiring hospital admission was 76% (95% confidence interval 64% to 84%). Protection was significantly lower (P=0.046) among children aged 12 months or more (59%, 27% to 77%) compared with children aged 6-11 months (83%, 68% to 91%). One dose of vaccine was 51% (26% to 67%) effective. At the sentinel hospitals, all admissions for diarrhoea among children under 5 declined by 40% in 2008 and by 51% in 2009 from the prevaccine year 2006.

CONCLUSIONS

A monovalent rotavirus vaccine was highly effective against admissions for rotavirus diarrhoea in children aged less than 2 years in El Salvador and substantially reduced the number of such admissions in this low-middle income setting. The impact on disease epidemiology after vaccination, particularly among older children, warrants future attention.

The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data

MOTIVATION

Mass spectrometry experiments in the field of proteomics produce lists containing tens to thousands of identified proteins. With the protein information and property explorer (PIPE), the biologist can acquire functional annotations for these proteins and explore the enrichment of the list, or fraction thereof, with respect to functional classes. These protein lists may be saved for access at a later time or different location. The PIPE is interoperable with the Firegoose and the Gaggle, permitting wide-ranging data exploration and analysis. The PIPE is a rich-client web application which uses AJAX capabilities provided by the Google Web Toolkit, and server-side data storage using Hibernate.

AVAILABILITY

http://pipe.systemsbiology.net.

The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism

Purple aerobic anoxygenic phototrophs (AAPs) are the only organisms known to capture light energy to enhance growth only in the presence of oxygen but do not produce oxygen. The highly adaptive AAPs compose more than 10% of the microbial community in some euphotic upper ocean waters and are potentially major contributors to the fixation of the greenhouse gas CO2. We present the complete genomic sequence and feature analysis of the AAP Roseobacter denitrificans, which reveal clues to its physiology. The genome lacks genes that code for known photosynthetic carbon fixation pathways, and most notably missing are genes for the Calvin cycle enzymes ribulose bisphosphate carboxylase (RuBisCO) and phosphoribulokinase. Phylogenetic evidence implies that this absence could be due to a gene loss from a RuBisCO-containing alpha-proteobacterial ancestor. We describe the potential importance of mixotrophic rather than autotrophic CO2 fixation pathways in these organisms and suggest that these pathways function to fix CO2 for the formation of cellular components but do not permit autotrophic growth. While some genes that code for the redox-dependent regulation of photosynthetic machinery are present, many light sensors and transcriptional regulatory motifs found in purple photosynthetic bacteria are absent.

Comparison of transarterial chemoembolization in patients with unresectable, diffuse vs focal hepatocellular carcinoma

HYPOTHESIS

Transarterial chemoembolization (TACE) is beneficial for selected patients with unresectable hepatocellular carcinoma (HCC).

DESIGN AND SETTING

A prospective comparison study in a tertiary hospital.

STUDY PERIOD

November 21, 1995, to May 2, 2001, with a mean follow-up of 939 days.

PATIENTS

A total of 157 TACE treatments were performed in 88 patients with unresectable HCC: 132 treatments in 69 patients with focal HCC (F-HCC) and 25 treatments in 19 patients with diffuse HCC (D-HCC).

INTERVENTIONS

Transarterial chemoembolization consisted of selective catheterization and intra-arterial infusion of a mixture of doxorubicin hydrochloride, cisplatin, and mitomycin followed by embolization. Sequential treatments were performed for bilobar HCC.

MAIN OUTCOME MEASURES

Child-Pugh classification and clinical outcomes, including alpha-fetoprotein (AFP) response, length of hospital stay, readmission rate, and survival, were compared between patients with F-HCC and D-HCC following TACE using the chi(2) test, Fisher exact test, or t test (2-tailed, unpaired).

RESULTS

Fifty-eight patients (84%) in the F-HCC group and 18 patients (95%) in the D-HCC group had cirrhosis. For those patients with cirrhosis, 58 (100%) in the F-HCC group and 14 (78%) in the D-HCC group had a Child-Pugh score of A or B (P =.002). The mean baseline AFP was higher in the D-HCC group: 55 577 vs 7815 ng/mL in the F-HCC group (P =.001). Of the patients secreting AFP, 4 (29%) of 14 in the D-HCC group and 30 (68%) of 44 in the F-HCC group had a significant decrease in AFP 1 month following TACE (P =.01). The mean hospital stay was longer (3 vs 1.9 days; P =.001), and readmissions occurred more frequently (44% vs 9%; P<.001) in the D-HCC group. The mean survival rate was significantly higher in the F-HCC group: 425 vs 103 days (P<.001).

CONCLUSIONS

In patients with F-HCC, TACE is well tolerated and provides a survival benefit. However, there is no apparent benefit for patients with D-HCC. Importantly, tumor characteristics and hepatic reserve are essential criteria for successful TACE.

Multicentre evaluation of the VITEK 2 Advanced Expert System for interpretive reading of antimicrobial resistance tests

Interpretive reading analyses the complete resistance profiles of bacteria to multiple antibiotics and infers the resistance mechanisms present; it aids therapeutic choice and enhances surveillance data. We evaluated the Advanced Expert System (AES), which interprets MICs generated by the VITEK 2. Ten European laboratories tested 42 reference strains and 76-106 of their own strains, representing important resistance genotypes. Interpretive reading by the VITEK 2 AES achieved full agreement with genotype data for 88-89% of strains, with the correct mechanism identified as one of two possibilities for a further 5-6%. Mechanisms inferred with 90% agreement with reference data included methicillin resistance in staphylococci, glycopeptide resistance in enterococci, quinolone resistance in staphylococci and Enterobacteriaceae, AAC(6')-APH(2")-mediated aminoglycoside resistance in Gram-positive cocci, erm-mediated macrolide resistance in pneumococci, extended-spectrum beta-lactamases (ESBLs) in Enterobacteriaceae and Pseudomonas aeruginosa, and acquired penicillinases in Enterobacteriaceae. VanA, VanB and VanC phenotypes of enterococci were distinguished reliably, and ESBL production was accurately inferred in AmpC-inducible species as well as Escherichia coli and Klebsiella spp. Mechanisms identified, but only as possibilities among several, included IRT-type beta-lactamases and individual aminoglycoside-modifying enzymes in Enterobacteriaceae. Most disagreements with reference data concerned pneumococci found to have high-level penicillin resistance by the VITEK 2 AES but previously determined, phenotypically, to have intermediate resistance. When ESBL production was inferred in E. coli and klebsiellae, the VITEK 2 AES edited susceptible results for cephalosporins (except cefoxitin) to resistant; when an acquired penicillinase was inferred in Enterobacteriaceae, piperacillin results were edited to resistant; and when staphylococci were found methicillin resistant, resistance was reported for all beta-lactams. Further editing may be desirable (e.g. of cephalosporin results for salmonellas inferred to have ESBLs).

Amphotericin B kills unicellular leishmanias by forming aqueous pores permeable to small cations and anions

The polyene antibiotic amphotericin B (AmB) is known to form two types of ionic channels across sterol-containing liposomes, depending on its concentration and time after mixing (Cohen, 1992). In the present study, it is shown that AmB only kills unicellular Leishmania promastigotes (LPs) when aqueous pores permeable to small cations and anions are formed. Changes of membrane potential across ergosterol-containing liposomes and LPs were followed by fluorescence changes of 3,3' dipropylthiadicarbocyanine (DiSC3(5)). In KCl-loaded liposomes suspended in an iso-osmotic sucrose solution, low AmB concentrations (</=0.1 microM) induced a polarization potential, indicating K+ leakage, but no movement of cations and anions was allowed until AmB concentrations greater than 0.1 microM were added. In agreement with these data, it was found that AmB altered the negative membrane potential held across LPs in a manner consistent with the differential cation/anion selectivity exhibited by the channels formed in liposomes. Thus, LPs suspended in an iso-osmotic sucrose solution did not exhibit any AmB-induced membrane depolarization effect brought about by efflux of anions until 0.1 microM or higher AmB concentrations were added. By contrast, LPs suspended in an iso-osmotic NaCl solution and exposed to 0.05 microM AmB exhibited a nearly total collapse of the negative membrane potential, indicating Na+ entry into the cells. The concentration dependence of the AmB-induced permeability to different salts was also measured across vesicles derived from the plasma membrane of leishmanias (LMVs), by using a rapid mixing technique. At concentrations above 0.1 microM, AmB induced the formation of aqueous pores across LMVs with a positive cooperativity, yielding Hill coefficients between 2 to 3. Measured anion selectivity across such aqueous pores followed the sequence: SCN > NO3 > Cl > I > Br > acetate (SO2-4 being impermeable). Cell killing by AmB was followed by fluorescence changes of the DNA-binding compound ethidium bromide (EB). At low concentrations (</=0.1 microM), AmB was found to be nonlethal against LPs but, above this concentration, leishmanias were rapidly killed. The rate and extent of such an effect were found to be dependent on the type of cation and anion present in the external aqueous solution. For both NH+4 and Na+ salts, the measured rank order of AmB cell killing followed the same sequence that was determined for AmB-induced salt permeation across LMVs. Further, replacement of either extracellular Na+ by choline or Cl- by SO2-4, or its partial substitution by sucrose, in iso-osmotic conditions, led to a complete inhibition of the killing effect exerted by otherwise lethal AmB concentrations. Finally, it was shown that tetraethylammonium (TEA+), an organic cation that is known to block AmB-induced salt permeation across LMVs was able to retard the time lag observed for EB incorporation across LPs, indicating that this parameter can be taken to represent the time taken for salt accumulation inside the parasites. The present results thus indicate clearly that low AmB concentrations (</=0.1 microM) were able to form across LPs, cation channels that collapsed the parasite membrane potential but are not lytic. At high concentrations (>/=0.1 microM), a salt influx via the aqueous pores formed by the antibiotic was followed by osmotic changes leading to cell lysis. This last stage is supported by electron microscopy observations of the changes of parasite morphology immediately upon addition of AmB, which indicated that the typical elongated promastigote cell forms became rounded and the flagella swells and round up. The present work is the first demonstration of the in vitro sensitivity of Leishmania promastigotes to osmotic lysis by AmB.

Structural integrity and identification of causes of liver allograft dysfunction occurring more than 5 years after transplantation

The clinicopathologic features of liver allograft dysfunction occurring in 51 symptomatic recipients after more than 5 years' survival (mean 7.1 years) with the same hepatic allograft were compared with those of a similar group of 14 asymptomatic patients (mean survival, 9.9 years) who underwent a nonclinically indicated protocol liver biopsy evaluation. Predictably, patients who had clinically indicated biopsies more frequently showed histopathologic alterations (76% versus 36%, p < 0.002). After detailed clinicopathologic correlation, the changes in the symptomatic patients were attributed primarily to definite or presumed viral hepatitis in 17 of 51 (33%) patients, 11 of whom had recurrent viral disease; seven of 51 (14%) had nonviral recurrent original disease, three (6%) had obstructive cholangiopathy, and 11 (22%) had acute and/or chronic rejection. In 13 of 51 (25%) of the symptomatic patients, the clinical and pathologic abnormalities were minimal. Long-term liver allograft survival in nine of 14 (64%) of the asymptomatic patients was associated with minimally abnormal histologic alterations. Two of the asymptomatic patients had obstructive cholangiopathy; two others has recurrence of the original disease and one has possible viral hepatitis. Viral hepatitis types B and C, alcoholic liver disease, autoimmune hepatitis, granulomatous hepatitis (not otherwise specified), and probably primary biliary cirrhosis and primary sclerosing cholangitis were shown to recur after hepatic transplantation. The histopathologic changes associated with acute and chronic rejection frequently overlapped with other syndromes causing late dysfunction, such as chronic viral or autoimmune hepatitis, primary biliary cirrhosis, or primary sclerosing cholangitis; more than one insult could be identified in 15 cases, which made the differential diagnosis of causes of late liver allograft dysfunction much more difficult than early after hepatic transplantation. It is important to correlate the biopsy findings with the liver injury tests, the results of viral and autoimmune antibody serologic studies, and review of previous biopsies and to be aware of the original disease, recent changes in immunosuppression, and results of therapeutic intervention(s) to identify correctly the causes of liver allograft dysfunction in this patient population.

Early tolerance in pediatric liver allograft recipients

The authors report on six pediatric liver transplant recipients for whom allograft tolerance occurred shortly after transplantation (ie, less than 1.5 years). All the patients had associated life-threatening viral complications. They are currently immunocompetent. The tolerant state may be related to the development of a TH2 cytokine pattern.

Effect of ketoconazole on lethal action of amphotericin B on Leishmania mexicana promastigotes

The effect of ergosterol depletion by ketoconazole on the leishmanicidal activity of the pore-forming antibiotic amphotericin B (AmB) was investigated. Leishmania mexicana promastigotes were lysed within minutes by the addition of micromolar concentrations of AmB (0.5 microM) but became insensitive to AmB after growth in the presence of ketoconazole (0.25 microM, 90 h). Lipid chromatographic analysis indicated that under such conditions, ketoconazole depleted the major Leishmania sterols, dehydroepisterol and ergosterol. Plasma membrane vesicles prepared from ketoconazole-treated promastigotes exhibited a much reduced enhancement of their salt permeability after the addition of AmB at concentrations as high as 5 microM. This finding clearly indicates that upon ketoconazole treatment, the capacity of pore formation by the antibiotic is substantially impaired. The reduction of desmethyl sterols by ketoconazole was accompanied by a significant increase of 14-alpha-methyl sterols, but exogenous cholesterol remained unchanged. This ability of Leishmania promastigotes to incorporate cholesterol from the external medium may explain why ketoconazole-treated cells exhibited a much decreased but significative response to AmB when they were exposed to high AmB concentrations (2.5 or 5.0 microM). Parallel measurements by using a fluorescence energy transfer method indicated that binding of AmB to ketoconazole-treated Leishmania promastigotes and heat-transformed leishmanias was also decreased but to different extents, a finding that may be related to the differences in their sterol content. The results obtained clearly indicate that the specific interaction of AmB with desmethyl sterols, such as dehydroepisterol, ergosterol, and even exogenous cholesterol, is an absolute requirement for the lethal action exerted by this polyene antibiotic on L. mexicana promastigotes.

Combined liver-kidney transplantation and the effect of preformed lymphocytotoxic antibodies

Thirty-eight sequentially placed liver and kidney allografts were evaluated with respect to patient and graft survival, and the influence of preformed lymphocytotoxic antibodies was analysed. The results suggest that the survival rate of combined liver and kidney transplantation is similar to the survival rate of liver transplantation alone. Sequentially placed kidney allografts may be protected from hyperacute rejection in the presence of donor specific lymphocytotoxic antibodies, but not in all instances. Both patient and kidney allograft survival was lower in positive crossmatch patients (33% and 17% respectively) than in negative crossmatch patients (78% and 75%). High levels of panel reactive antibodies (> 10%) also appeared to have a deleterious effect on survival, although the majority of the patients who failed also had a positive crossmatch. Although performed lymphocytotoxic antibodies are not an absolute contraindication to combined liver-kidney transplantation, they do appear to have a deleterious effect on long-term graft survival. However, more correlation with clinical parameters is needed.