Applying neutral drift to the directed molecular evolution of a β-glucuronidase into a β-galactosidase: Two different evolutionary pathways lead to the same variant

<p>Abstract</p> <p>Background</p> <p>Directed protein evolution has been used to modify protein activity and research has been carried out to enhance the production of high quality mutant libraries. Many theoretical approaches suggest that allowing a population to undergo neutral selection may be valuable in directed evolution experiments.</p> <p>Findings</p> <p>Here we report on an investigation into the value of neutral selection in a classical model system for directed evolution, the conversion of the <it>E. coli </it>β-glucuronidase to a β-galactosidase activity. We find that neutral selection, i.e. selection for retaining glucuronidase activity, can efficiently identify the majority of sites of mutation that have been identified as beneficial for galactosidase activity in previous experiments. Each variant demonstrating increased galactosidase activity identified by our neutral drift experiments contained a mutation at one of four sites, T509, S557, N566 or W529. All of these sites have previously been identified using direct selection for beta galactosidase activity.</p> <p>Conclusions</p> <p>Our results are consistent with others that show that a neutral selection approach can be effective in selecting improved variants. However, we interpret our results to show that neutral selection is, in this case, not a more efficient approach than conventional directed evolution approaches. However, the neutral approach is likely to be beneficial when the resulting library can be screened for a range of related activities. More detailed statistical studies to resolve the apparent differences between this system and others are likely to be a fruitful avenue for future research.</p

Advanced monitoring of high-rate anaerobic reactors through quantitative image analysis of granular sludge and multivariate statistical analysis

Four organic loading disturbances were performed in lab-scale EGSB reactors fed with ethanol. In load disturbance 1 (LD1) and 2 (LD2), the organic loading rate (OLR) was increased between 5 and 18.5 kg COD m-3 day-1, through the influent ethanol concentration increase, and the hydraulic retention time decrease from 7.8 to 2.5 h, respectively. Load disturbances 3 (LD3) and 4 (LD4) were applied by increasing the OLR to 50 kg COD m-3 day-1 during 3 days and 16 days, respectively. The granular sludge morphology was quantified by image analysis and was related to the reactor performance, including effluent volatile suspended solids, indicator of washout events. In general, it was observed the selective washout of filamentous forms associated to granules erosion/fragmentation and to a decrease in the specific acetoclastic activity. These phenomena induced the transitory deterioration of reactor performance in LD2, LD3, and LD4, but not in LD1. Extending the exposure time in LD4 promoted acetogenesis inhibition after 144 h. The application of Principal Components Analysis determined a latent variable that encompasses a weighted sum of performance, physiological and morphological information. This new variable was highly sensitive to reactor efficiency deterioration, enclosing variations between 27% and 268% in the first hours of disturbances. The high loadings raised by image analysis parameters, especially filaments length per aggregates area (LfA), revealed that morphological changes of granular sludge, should be considered to monitor and control load disturbances in high rate anaerobic (granular) sludge bed digesters.Fundação para a Ciência e a Tecnologia (FCT) - Bolsa SFRH/BD/13317/2003, POCI/AM/60141/2004, POCTI/BIO/37934/200

Dengue-1 Envelope Protein Domain III along with PELC and CpG Oligodeoxynucleotides Synergistically Enhances Immune Responses

The major weaknesses of subunit vaccines are their low immunogenicity and poor efficacy. Adjuvants can help to overcome some of these inherent defects with subunit vaccines. Here, we evaluated the efficacy of the newly developed water-in-oil-in-water multiphase emulsion system, termed PELC, in potentiating the protective capacity of dengue-1 envelope protein domain III. Unlike aluminum phosphate, dengue-1 envelope protein domain III formulated with PELC plus CpG oligodeoxynucleotides induced neutralizing antibodies against dengue-1 virus and increased the splenocyte secretion of IFN-γ after in vitro re-stimulation. The induced antibodies contained both the IgG1 and IgG2a subclasses. A rapid anamnestic neutralizing antibody response against a live dengue virus challenge was elicited at week 26 after the first immunization. These results demonstrate that PELC plus CpG oligodeoxynucleotides broaden the dengue-1 envelope protein domain III-specific immune responses. PELC plus CpG oligodeoxynucleotides is a promising adjuvant for recombinant protein based vaccination against dengue virus

Features of home and neighbourhood and the liveability of older South Africans

While older people live in developing countries, little is known about the relative importance of features of their communities in influencing their liveability. We examinecomponents of home and neighbourhood among older South Africans. Linear regression analyses revealed that features of home (basic amenities, household composition, financial status and safety) and neighbourhood (ability to shop for groceries, participate in organizations and feel safe from crime) are significantly associated with life satisfaction. Approaches to liveability that are person-centred and also set within contexts beyond home and neighbourhood are needed to addressboundaries between home and neighbourhood; incorporate personal resources into liveability models and import broader environmental contexts such as health and social policy

The search for the ideal biocatalyst

While the use of enzymes as biocatalysts to assist in the industrial manufacture of fine chemicals and pharmaceuticals has enormous potential, application is frequently limited by evolution-led catalyst traits. The advent of designer biocatalysts, produced by informed selection and mutation through recombinant DNA technology, enables production of process-compatible enzymes. However, to fully realize the potential of designer enzymes in industrial applications, it will be necessary to tailor catalyst properties so that they are optimal not only for a given reaction but also in the context of the industrial process in which the enzyme is applied

Quantifying the Adaptive Potential of an Antibiotic Resistance Enzyme

For a quantitative understanding of the process of adaptation, we need to understand its “raw material,” that is, the frequency and fitness effects of beneficial mutations. At present, most empirical evidence suggests an exponential distribution of fitness effects of beneficial mutations, as predicted for Gumbel-domain distributions by extreme value theory. Here, we study the distribution of mutation effects on cefotaxime (Ctx) resistance and fitness of 48 unique beneficial mutations in the bacterial enzyme TEM-1 β-lactamase, which were obtained by screening the products of random mutagenesis for increased Ctx resistance. Our contributions are threefold. First, based on the frequency of unique mutations among more than 300 sequenced isolates and correcting for mutation bias, we conservatively estimate that the total number of first-step mutations that increase Ctx resistance in this enzyme is 87 [95% CI 75–189], or 3.4% of all 2,583 possible base-pair substitutions. Of the 48 mutations, 10 are synonymous and the majority of the 38 non-synonymous mutations occur in the pocket surrounding the catalytic site. Second, we estimate the effects of the mutations on Ctx resistance by determining survival at various Ctx concentrations, and we derive their fitness effects by modeling reproduction and survival as a branching process. Third, we find that the distribution of both measures follows a Fréchet-type distribution characterized by a broad tail of a few exceptionally fit mutants. Such distributions have fundamental evolutionary implications, including an increased predictability of evolution, and may provide a partial explanation for recent observations of striking parallel evolution of antibiotic resistance

Innovation, low energy buildings and intermediaries in Europe: systematic case study review

As buildings throughout their lifecycle account for circa 40% of total energy use in Europe, reducing energy use of the building stock is a key task. This task is, however, complicated by a range of factors, including slow renewal and renovation rates of buildings, multiple non- coordinated actors, conservative building practices, and limited competence to innovate. Drawing from academic literature published during 2005-2015, this article carries out a systematic review of case studies on low energy innovations in the European residential building sector, analysing their drivers. Specific attention is paid to intermediary actors in facilitating innovation processes and creating new opportunities. The study finds that qualitative case study literature on low energy building innovation has been limited, particularly regarding the existing building stock. Environmental concerns, EU, national and local policies have been the key drivers; financial, knowledge and social sustainability and equity drivers have been of modest importance; while design, health and comfort, and market drivers have played a minor role. Intermediary organisations and individuals have been important through five processes: (1) facilitating individual building projects, (2) creating niche markets, (3) implementing new practices in social housing stock, (4) supporting new business model creation, and (5) facilitating building use post construction. The intermediaries have included both public and private actors, while local authority agents have acted as intermediaries in several cases

Directing the evolution of Rubisco and Rubisco activase: first impressions of a new tool for photosynthesis research

During the last decade the practice of laboratory-directed protein evolution has become firmly established as a versatile tool in biochemical research by enabling molecular evolution toward desirable phenotypes or detection of novel structure–function interactions. Applications of this technique in the field of photosynthesis research are still in their infancy, but recently first steps have been reported in the directed evolution of the CO2-fixing enzyme Rubisco and its helper protein Rubisco activase. Here we summarize directed protein evolution strategies and review the progressive advances that have been made to develop and apply suitable selection systems for screening mutant forms of these enzymes that improve the fitness of the host organism. The goal of increasing photosynthetic efficiency of plants by improving the kinetics of Rubisco has been a long-term goal scoring modest successes. We discuss how directed evolution methodologies may one day be able to circumvent the problems encountered during this venture

Strengthening pharmaceutical systems for palliative care services in resource limited settings: Piloting an mhealth application across a rural and urban setting in Uganda

Background: Medicine availability is improving in sub-Saharan Africa for palliative care services. There is a need to develop strong and sustainable pharmaceutical systems to enhance the proper management of palliative care medicines, some of which are controlled. One approach to addressing these needs is the use of mobile technology to support data capture, storage and retrieval. Utilizing mobile technology in healthcare (mHealth) has recently been highlighted as an approach to enhancing palliative care services but development is at an early stage. Methods: An electronic application was implemented into palliative care services at two settings in Uganda; a rural hospital and an urban hospice. Measures of the completeness of data capture, time efficiency of activities and the changes to medicines stock and waste management were taken pre- and post-implementation to identify changes to practice arising from the introduction of the application. Results: Improvements in all measures were identified at both sites. The application supported the registration and management of 455 patients and a total of 565 consultations. Improvements in both time efficiency and medicines management were noted. Time taken to collect and report pharmaceuticals data was reduced from 7 days to 30 minutes and 10 days to 1 hour at the urban hospice and rural hospital respectively. Stock expiration reduced from 3% to 0.5% at the urban hospice and from 58% to 0% at the rural hospital. Additional observations relating to the use of the application across the two sites are reported. Conclusions: A mHealth approach adopted in this study was shown to improve existing processes for patient record management, pharmacy forecasting and supply planning, procurement, and distribution of essential health commodities for palliative care services. An important next step will be to identify where and how such mHealth approaches can be implemented more widely to improve pharmaceutical systems for palliative care services in resource limited settings