Metabolic Deficiences Revealed in the Biotechnologically Important Model Bacterium Escherichia coli BL21(DE3)

The Escherichia coli B strain BL21(DE3) has had a profound impact on biotechnology through its use in the production of recombinant proteins. Little is understood, however, regarding the physiology of this important E. coli strain. We show here that BL21(DE3) totally lacks activity of the four [NiFe]-hydrogenases, the three molybdenum- and selenium-containing formate dehydrogenases and molybdenum-dependent nitrate reductase. Nevertheless, all of the structural genes necessary for the synthesis of the respective anaerobic metalloenzymes are present in the genome. However, the genes encoding the high-affinity molybdate transport system and the molybdenum-responsive transcriptional regulator ModE are absent from the genome. Moreover, BL21(DE3) has a nonsense mutation in the gene encoding the global oxygen-responsive transcriptional regulator FNR. The activities of the two hydrogen-oxidizing hydrogenases, therefore, could be restored to BL21(DE3) by supplementing the growth medium with high concentrations of Ni2+ (Ni2+-transport is FNR-dependent) or by introducing a wild-type copy of the fnr gene. Only combined addition of plasmid-encoded fnr and high concentrations of MoO42− ions could restore hydrogen production to BL21(DE3); however, to only 25–30% of a K-12 wildtype. We could show that limited hydrogen production from the enzyme complex responsible for formate-dependent hydrogen evolution was due solely to reduced activity of the formate dehydrogenase (FDH-H), not the hydrogenase component. The activity of the FNR-dependent formate dehydrogenase, FDH-N, could not be restored, even when the fnr gene and MoO42− were supplied; however, nitrate reductase activity could be recovered by combined addition of MoO42− and the fnr gene. This suggested that a further component specific for biosynthesis or activity of formate dehydrogenases H and N was missing. Re-introduction of the gene encoding ModE could only partially restore the activities of both enzymes. Taken together these results demonstrate that BL21(DE3) has major defects in anaerobic metabolism, metal ion transport and metalloprotein biosynthesis

Computerized advice on drug dosage to improve prescribing practice

International audienceComputerized advice on drug dosage to improve prescribing practice (Review) 1 Copyright © 2013 The Cochrane Collaboration. Published by JohnWiley & Sons, Ltd. Data collection and analysis Two review authors independently extracted data and assessed study quality.We grouped the results from the included studies by drug used and the effect aimed at for aminoglycoside antibiotics, amitriptyline, anaesthetics, insulin, anticoagulants, ovarian stimulation, anti-rejection drugs and theophylline. We combined the effect sizes to give an overall effect for each subgroup of studies, using a random-effects model. We further grouped studies by type of outcome when appropriate (i.e. no evidence of heterogeneity). Main results Forty-six comparisons (from 42 trials) were included (as compared with 26 comparisons in the last update) including a wide range of drugs in inpatient and outpatient settings. All were randomized controlled trials except two studies. Interventions usually targeted doctors, although some studies attempted to influence prescriptions by pharmacists and nurses. Drugs evaluated were anticoagulants, insulin, aminoglycoside antibiotics, theophylline, anti-rejection drugs, anaesthetic agents, antidepressants and gonadotropins. Although all studies used reliable outcome measures, their quality was generally low. This update found similar results to the previous update and managed to identify specific therapeutic areas where the computerized advice on drug dosage was beneficial compared with routine care: 1. it increased target peak serum concentrations (standardized mean difference (SMD) 0.79, 95% CI 0.46 to 1.13) and the proportion of people with plasma drug concentrations within the therapeutic range after two days (pooled risk ratio (RR) 4.44, 95% CI 1.94 to 10.13) for aminoglycoside antibiotics; 2. it led to a physiological parameter more often within the desired range for oral anticoagulants (SMD for percentage of time spent in target international normalized ratio +0.19, 95% CI 0.06 to 0.33) and insulin (SMD for percentage of time in target glucose range: +1.27, 95% CI 0.56 to 1.98); 3. it decreased the time to achieve stabilization for oral anticoagulants (SMD -0.56, 95% CI -1.07 to -0.04); 4. it decreased the thromboembolism events (rate ratio 0.68, 95% CI 0.49 to 0.94) and tended to decrease bleeding events for anticoagulants although the difference was not significant (rate ratio 0.81, 95%CI 0.60 to 1.08). It tended to decrease unwanted effects for aminoglycoside antibiotics (nephrotoxicity: RR 0.67, 95% CI 0.42 to 1.06) and anti-rejection drugs (cytomegalovirus infections: RR 0.90, 95% CI 0.58 to 1.40); 5. it tended to reduce the length of time spent in the hospital although the difference was not significant (SMD -0.15, 95% CI -0.33 to 0.02) and to achieve comparable or better cost-effectiveness ratios than usual care; 6. there was no evidence of differences in mortality or other clinical adverse events for insulin (hypoglycaemia), anaesthetic agents, antirejection drugs and antidepressants. For all outcomes, statistical heterogeneity quantified by I2 statistics was moderate to high. Authors’ conclusions This review update suggests that computerized advice for drug dosage has some benefits: it increases the serum concentrations for aminoglycoside antibiotics and improves the proportion of people for which the plasma drug is within the therapeutic range for aminoglycoside antibiotics. It leads to a physiological parameter more often within the desired range for oral anticoagulants and insulin. It decreases the time to achieve stabilization for oral anticoagulants. It tends to decrease unwanted effects for aminoglycoside antibiotics and anti-rejection drugs, and it significantly decreases thromboembolism events for anticoagulants. It tends to reduce the length of hospital stay compared with routine care while comparable or better cost-effectiveness ratios were achieved. However, there was no evidence that decision support had an effect on mortality or other clinical adverse events for insulin (hypoglycaemia), anaesthetic agents, anti-rejection drugs and antidepressants. In addition, there was no evidence to suggest that some decision support technical features (such as its integration into a computer physician order entry system) or aspects of organization of care (such as the setting) could optimize the effect of computerized advice. Taking into account the high risk of bias of, and high heterogeneity between, studies, these results must be interpreted with caution. P L A I N L A N G U A G E S U M M A R Y Computerized advice on drug dosage to improve prescribing practice (Review) 2 Copyright © 2013 The Cochrane Collaboration. Published by JohnWiley & Sons, Ltd. Computerized advice on drug dosage to improve prescribing practice Background Physicians and other healthcare professionals often prescribe drugs that will only work at certain concentrations. These drugs are said to have a narrow therapeutic window. This means that if the concentration of the drug is too high or too low, they may cause serious side effects or not provide the benefits they should. For example, blood thinners (anticoagulants) are prescribed to thin the blood to prevent clots. If the concentration is too high, people may experience excessive bleeding and even death. In contrast, if the concentration is too low, a clot could form and cause a stroke. For these types of drugs, it is important that the correct amount of the drug be prescribed. Calculating and prescribing the correct amount can be complicated and time-consuming for healthcare professionals. Sometimes determining the correct dose can take a long time since healthcare professionals may not want to prescribe high doses of the drugs initially because they make mistakes in calculations. Several computer systems have been designed to do these calculations and assist healthcare professionals in prescribing these types of drugs. Study characteristics We sought clinical trial evidence from scientific databases to evaluate the effectiveness of these computer systems. The evidence is current to January 2012. We found data from 42 trials (40 randomized controlled trials (trials that allocate people at random to receive one of a number of drugs or procedures) and two non-randomized controlled trials). Key results Computerized advice for drug dosage can benefit people taking certain drugs compared with empiric dosing (where a dose is chosen based on a doctor’s observations and experience)without computer assistance.When using the computer system, healthcare professionals prescribed appropriately higher doses of the drugs initially for aminoglycoside antibiotics and the correct drug dose was reached more quickly for oral anticoagulants. It significantly decreased thromboembolism (blood clotting) events for anticoagulants and tended to reduce unwanted effects for aminoglycoside antibiotics and anti-rejection drugs (although not an important difference). It tended to reduce the length of hospital stay compared with routine care with comparable or better cost-effectiveness. There was no evidence of effects on death or clinical side events for insulin (low blood sugar (hypoglycaemia)), anaesthetic agents, anti-rejection drugs (drugs taken to prevent rejection of a transplanted organ) and antidepressants. Quality of evidence The quality of the studies was low so these results must be interpreted with caution

Stock structure of blue threadfin Eleutheronema tetradactylum across northern Australia, as indicated by parasites

The parasite fauna of the blue threadfin Eleutheronema tetradactylum, collected from 14 sites across northern Australia, was examined to evaluate the degree of movement and subsequent stock structure of the fish. Univariate and multivariate analysis of nine 'permanent' parasite species [the nematodes Anisakis (type I) and Terranova (type II), the cestodes Otobothrium australe, Pterobothrium pearsoni, Pterobothrium sp. A, Callitetrarhynchus gracilis, Parotobothrium balli and Nybelinia sp., and the acanthocephalan Pomphorhynchus sp.] demonstrated little similarity between sites, indicating limited mixing and therefore long-term separation of post-juvenile fish. As such, the effects of fishing are likely to be localized within the current administrative boundaries, implying little need for interstate co-operative management. Within each jurisdiction, management of E. tetradactylum populations, including the establishment of harvest strategies and fishery regulations, should be conducted in a way that recognizes the resident nature of the fish. © 2011 The Authors. Journal of Fish Biolog

Stock structure of blue threadfin Eleutheronema tetradactylum on the Queensland east coast, as determined by parasites and conventional tagging

Blue threadfin Eleutheronema tetradactylum (Polynemidae) were examined from four areas (Princess Charlotte Bay, Trinity Inlet, Halifax Bay and Upstart Bay) in eastern Queensland covering a distance of c. 950 km of coastline. Parasites were used as biological markers to infer stock structure of E. tetradactylum. Parasites designated as 'temporary' biological markers were the copepod Thysanote eleutheronemi, the acanthocephalan Neoechinorhynchus topseyi, the nematode Philometra rajani and hemiurid trematodes. The larval nematodes Anisakis sp. Type 1 and Terranova sp. Type 2; and the larval cestodes Pterobothrium pearsoni and Callitetrarhynchus gracilis were considered 'permanent' biological markers. Both univariate and multivariate analyses demonstrated that there was little difference in temporary parasite abundance between the four areas. In contrast, the same analyses revealed that most areas had two or more significant differences in permanent parasite abundance, with the exception of Halifax Bay and Upstart Bay, which were significantly different only in the multivariate analysis. Biological markers predicted that Princess Charlotte Bay and Trinity Inlet consisted of distinct populations, whereas Halifax Bay and Upstart Bay were not clearly differentiated. Tag recapture data supported this hypothesis; the majority of recaptures were within 100 km of the initial tagging location. Geographical movement of E. tetradactylum may be limited due to their biology and ecology, as well as the distances and oceanographic boundaries that separate habitats. Contrary to current management definitions, the stock structure of E. tetradactylum on the east coast of Queensland appears to be geographically differentiated at a small spatial scale

Stock identification of wahoo (Acanthocybium solandri) in the Pacific and Indian Oceans using morphometrics and parasites

The wahoo (Acanthocybium solandri) is an increasingly important by-product species of tropical pelagic fisheries worldwide. However, specific management of the species is currently hindered by a dearth of information on basic biology and stock structure. This study examined the stock structure of wahoo using morphometric characters and parasite fauna from fish collected in three regions of the western Pacific, and one region in each of the eastern Pacific and eastern Indian Oceans. Similar morphometric measurements and parasite abundance of wahoo collected off eastern Australia suggest they may form part of a single phenotypic stock in the western Pacific Ocean. Morphometric measurements and parasite fauna were significantly different among wahoo from the western Pacific and eastern Pacific Oceans, suggesting multiple discrete phenotypic stocks despite genetic homogeneity. Assessing fish from a range of regions throughout the Pacific Ocean may help discriminate stock boundaries in this region. Future research using complementary techniques, such as otolith microchemistry and genetic microsatellites, may improve our understanding of the global stock structure of wahoo to suitably inform regional fishery management organizations

Parasites as indicators of movement and population connectivity of a non-diadromous, tropical estuarine teleost: King threadfin Polydactylus macrochir

Temporal and spatial patterns in parasite assemblages were examined to evaluate the degree of movement and connectivity of post-recruitment life-history stages of a large, non-diadromous tropical estuarine teleost, king threadfin Polydactylus macrochir, collected from 18 locations across northern Australia. Ten parasites types (juvenile stages of two nematodes and seven cestodes, and adults of an acanthocephalan) were deemed to be suitable for use as biological tags, in that they were considered to have a long residence time in the fish, were relatively easy to find and were morphologically very different to each other which aided discrimination. Univariate and discriminant function analysis of these parasites revealed little difference in temporal replicates collected from five locations, suggesting that the parasite communities were stable over the timeframes explored. Univariate, discriminant function, and Bray-Curtis similarity analyses indicated significant spatial heterogeneity, with Bray-Curtis classification accuracies ranging from 55 to 100% for locations in north-western and northern Australia, 24 to 88% in the Gulf of Carpentaria, and 39 to 88% on the east coast of Queensland. Few differences were observed among locations separated b

Integrating different approaches in the definition of biological stocks: A northern Australian multi-jurisdictional fisheries example using grey mackerel, Scomberomorus semifasciatus

A holistic approach to stock structure studies utilises multiple different techniques on the same individuals sampled from selected populations and combines results across spatial and temporal scales to produce a weight of evidence conclusion. It is the most powerful and reliable source of information to use in formulating resource management and monitoring plans. Few examples of the use of a holistic approach in stock structure studies exist, although more recently this is changing. Using such an approach makes integration of results from each technique challenging. An integrated stock definition (ISD) approach for holistic stock structure studies was developed in this study to aid in the appropriate interpretation of stock structure results to guide the determination of fishery management units. The ISD approach is applied herein to a study of the northern Australian endemic grey mackerel, Scomberomorus semifasciatus (Scombridae). Analyses of genetic (mitochondrial DNA and microsatellites), parasite, otolith stable isotope, and growth data are synthesised to determine the stock structure of S. semifasciatus across northern Australia. Integration of the results from all techniques identified at least six S. semifasciatus stocks for management purposes. Further, the use of the ISD approach provided a simple basis for integrating multiple techniques and for their interpretation. The use of this holistic approach was a powerful tool in providing greater certainty about the appropriate management units for S. semifasciatus. Future stock structure studies investigating spatial management questions in the fisheries context should adopt a holistic approach and apply the ISD approach for a more accurate definition of biological stocks to improve fisheries management