Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Identifying the decision to be supported: A review of papers from environmental modelling and software

Two of the basic tenets of decision support system efforts are to help identify and structure the decisions to be supported, and to then provide analysis in how those decisions might be best made. One example from wetland management would be that wildlif

Scale decisions and good practices in socio-environmental systems modelling: guidance and documentation during problem scoping and model formulation

Models of socio-environmental or social-ecological systems (SES) commonly address problems requiring interdisciplinary scientific expertise and input from a heterogeneous group of stakeholders. In SES modelling multiple interactions occur on different scales among various phenomena. These scale phenomena include the technical, such as system variables, process detail, inputs and outputs, which most often require spatial, temporal, thematic and organisational choices. From a good practice and project efficiency perspective, the problem scoping and conceptual model formulation phase of modelling is the one to address well from the outset. During this phase, intense and substantive discussions should arise regarding appropriate scales at which to represent the different phenomena. Although the details of these discussions influence the path of model development, they are seldom documented and as a result often forgotten. We draw upon personal experience with existing protocols and communications in recent literature to propose preliminary guidelines for documenting these early discussions about the scale(s) of the studied phenomena. Our guidelines aim to aid modelling group members in building and capturing the richness of their rationale for scoping and scale decisions. The resulting transcripts are intended to promote transparency of modelling decisions and provide essential support for the justification of the final model for its intended use. They also facilitate adaptive modifications of the pathway of model development via retracing decisions and iterative reflection upon alternative scale options

Modelling for Managing the Complex Issue of Catchment-Scale surface and Groundwater Allocation

The management of surface and groundwater can be regarded as presenting resource dilemmas. These are situations where multiple users share a common resource pool, and make contested claims about their rights to access the resource, and the best use and distribution of the resource among competing needs. Overshadowed by uncertainties caused by limited data and lack of scientific knowledge, resource dilemmas are challenging to manage, often leading to controversies and disputes about policy issues and outcomes. In the case of surface and groundwater management, the design of collective policies needs to be informed by a holistic understanding of different water uses and outcomes under different water availability and sharing scenarios. In this paper, we present an integrated modelling framework for assessing the combined impacts of changes in climate conditions and water allocation policies on surface and groundwater-dependent economic and ecological systems. We are implementing the framework in the Namoi catchment, Australia. However, the framework can be transferred and adapted for uses, including water planning, in other agricultural catchments

Enabling assessment of distributive justice through models for climate change planning: A review of recent advances and a research agenda

Models for supporting climate adaptation and mitigation planning, mostly in the form of Integrated Assessment Models, are poorly equipped for aiding questions related to fairness of adaptation and mitigation strategies, because they often disregard distributional outcomes. When evaluating policies using such models, the costs and benefits are typically aggregated across all actors in the system, and over the entire planning horizon. While a policy may be beneficial when considering the aggregate outcome, it can be harmful to some people, somewhere, at some point in time. The practice of aggregating over all actors and over time thus gives rise to problems of justice; it could also exacerbate existing injustices. While the literature discusses some of these injustices in ad-hoc and case specific manner, a systematic approach for considering distributive justice in model-based climate change planning is lacking. This study aims to fill this gap by proposing 11 requirements that an Integrated Assessment Model should meet in order to enable the assessment of distributive justice in climate mitigation and adaptation policies. We derive the requirements from various ethical imperatives stemming from the theory of distributive justice. More specifically, we consider both intra-generational (among people within one generation) and intergenerational (between generations) distributive justice. We investigate to what extent the 11 requirements are being met in recent model-based climate planning studies, and highlight several directions for future research to advance the accounting for distributive justice in model-based support for climate change planning. This article is categorized under: Climate, Nature, and Ethics > Climate Change and Global Justice

Environmental decision support systems (EDSS) development - Challenges and best practices

Despite the perceived value of DSS in informing environmental and natural resource management, DSS tools often fail to be adopted by intended end users. By drawing together the experience of a global group of EDSS developers, we have identified and assessed key challenges in EDSS development and offer recommendations to resolve them. Challenges related to engaging end users in EDSS development emphasise the need for a participatory process that embraces end users and stakeholders throughout the design and development process. Adoption challenges concerned with individual and organisational capacities to use EDSS and the match between EDSS and organisational goals can be overcome through the use of an internal champion to promote the EDSS at different levels of a target organisation; co-ordinate and build capacity within the organisation, and; ensure that developers maintain focus on developing EDSS which are relatively easy and inexpensive to use and update (and which are perceived as such by the target users). Significant challenges exist in relation to ensuring EDSS longevity and financial sustainability. Such business challenges may be met through planning and design that considers the long-term costs of training, support, and maintenance; revenue generation and licensing by instituting processes which support communication and interactions; and by employing software technology which enables easy model expansion and re use to gain an economy of scale and reduce development costs. A final group of perhaps more problematic challenges relate to how the success of EDSS ought to be evaluated. Whilst success can be framed relatively easily in terms of interactions with end users, difficulties of definition and measurability emerge in relation to the extent to which EDSS achieve intended outcomes. To tackle the challenges described, the authors provide a set of best practice recommendations concerned with promoting design for ease of use, design for usefulness, establishing trust and credibility, promoting EDSS acceptance, and starting simple and small in functionality terms. Following these recommendations should enhance the achievement of successful EDSS adoption, but more importantly, help facilitate the achievement of desirable social and environmental outcomes

Selecting among five common modelling approaches for integrated environmental assessment and management

The design and implementation of effective environmental policies need to be informed by a holistic understanding of the system processes (biophysical, social and economic), their complex interactions, and how they respond to various changes. Models, integrating different system processes into a unified framework, are seen as useful tools to help analyse alternatives with stakeholders, assess their outcomes, and communicate results in a transparent way. This paper reviews five common approaches or model types that have the capacity to integrate knowledge by developing models that can accommodate multiple issues, values, scales and uncertainty considerations, as well as facilitate stakeholder engagement. The approaches considered are: systems dynamics, Bayesian networks, coupled component models, agent-based models and knowledge-based models (also referred to as expert systems). We start by discussing several considerations in model development, such as the purpose of model building, the availability of qualitative versus quantitative data for model specification, the level of spatio-temporal detail required, and treatment of uncertainty. These considerations and a review of applications are then used to develop a framework that aims to assist modellers and model users in the choice of an appropriate modelling approach for their integrated assessment applications and that enables more effective learning in interdisciplinary settings. © 2013 Elsevier Ltd.Rebecca A. Kelly (Letcher), Anthony J. Jakeman, Olivier Barreteau, Mark E. Borsuk, Sondoss ElSawah, Serena H. Hamilton, Hans Jørgen Henriksen, Sakari Kuikka, Holger R. Maier, Andrea Emilio Rizzoli, Hedwig van Delden and Alexey A. Voino