Informed substitution of hazardous chemicals through the lens of California's Safer Consumer Products Alternatives Analysis: Best practices, challenges, and opportunities.

California adopted the Safer Consumer Products (SCP) regulations in 2013, which mandate that companies that manufacture specific products containing designated chemicals of concern complete an Alternatives Analysis. Alternatives Analysis is a process to avoid regrettable substitution by identifying, comparing, and selecting safer alternatives based on technical functions, hazards, exposure pathways, life-cycle multimedia impacts, and economic impacts. The SCP Alternatives Analysis builds upon and expands existing frameworks for alternatives assessments (AAs). The aim of this study was to identify practices from AA that facilitate the robust assessment of alternatives and that align with SCP requirements and identify gaps in the practice. We evaluated completed AAs for methods regarding transparency and careful documentation of information sources, data gaps, uncertainty, criteria, and justification for decision-making. The AAs in this review demonstrate some of the challenges in the field. Most AAs have a constrained scope and only consider chemical substitutes rather than a broad array of functional alternatives. Their scopes were also limited in the hazard endpoints that were evaluated. This was most noted with ecotoxicity endpoints, which were generally confined to aquatic toxicity. The majority of AAs do not explicitly explain their decision-making methods or adequately discuss tradeoffs across the adverse impacts. The AAs also lack the analysis in the exposure, life-cycle impacts, and economic impacts that are required in the SCP Alternatives Analysis process. Further, we recommend strategies and research opportunities to address these challenges and strengthen the practice of AAs. Integr Environ Assess Manag 2022;18:1007-1019. © 2021 SETAC.

A conceptual framework to untangle the concept of urban ecosystem services.

Urban ecosystem service (UES) is becoming an influential concept to guide the planning, design, and management of urban landscapes towards urban sustainability. However, its use is hindered by definitional ambiguity, and the conceptual bases underpinning its application remain weak. This is exemplified by two different but equally valid interpretations of UES: "urban ecosystem services", referring to ecosystem services from analogs of natural and semi-natural ecosystems within urban boundaries, and "urban ecosystem services", a much broader term that includes the former group as well as urban services in a city. While we recognize that a single definition of UES is not possible nor necessary as its application is context-dependent, it is nevertheless useful to clarify the relationships between these interpretations to promote consistent use, and importantly, explore how a broader interpretation of UES might advance its applications in areas that have been neglected. We developed a conceptual framework that links UES to natural and human-derived capital to explain the relationships between the dual meanings of UES and proposed three normative propositions to guide its application: (1) integrate holistically multiple components of natural capital to provide UES, (2) reduce dependence on non-renewable abiotic resources and human-derived capital, and (3) enhance UES through technology. The framework we developed helps to resolve the current ambiguity in the meanings of UES, highlights the need to recognise neglected aspects of natural capital important for UES, and can be used to clarify relationships with related concepts conveying dependence of human well-being on nature.

Manufacturing biological medicines on demand: Safety and efficacy of granulocyte colony-stimulating factor in a mouse model of total body irradiation.

Protein therapeutics, also known as biologics, are currently manufactured at centralized facilities according to rigorous protocols. The manufacturing process takes months and the delivery of the biological products needs a cold chain. This makes it less responsive to rapid changes in demand. Here, we report on technology application for on-demand biologics manufacturing (Bio-MOD) that can produce safe and effective biologics from cell-free systems at the point of care without the current challenges of long-term storage and cold-chain delivery. The objective of the current study is to establish proof-of-concept safety and efficacy of Bio-MOD-manufactured granulocyte colony-stimulating factor (G-CSF) in a mouse model of total body irradiation at a dose estimated to induce 30% lethality within the first 30 days postexposure. To illustrate on-demand Bio-MOD production feasibility, histidine-tagged G-CSF was manufactured daily under good manufacturing practice-like conditions prior to administration over a 16-day period. Bio-MOD-manufactured G-CSF improved 30-day survival when compared with saline alone (p = .073). In addition to accelerating recovery from neutropenia, the platelet and hemoglobin nadirs were significantly higher in G-CSF-treated animals compared with saline-treated animals (p < .05). The results of this study demonstrate the feasibility of consistently manufacturing safe and effective on-demand biologics suitable for real-time release.

Real-time dissolved carbon dioxide monitoring II: Surface aeration intensification for efficient CO2 removal in shake flasks and mini-bioreactors leads to superior growth and recombinant protein yields.

Mass transfer is known to play a critical role in bioprocess performance and henceforth monitoring dissolved O2 (DO) and dissolved CO2 (dCO2 ) is of paramount importance. At bioreactor level these parameters can be monitored online and can be controlled by sparging air/oxygen or stirrer speed. However, traditional small-scale systems such as shake flasks lack real time monitoring and also employ only surface aeration with additional diffusion limitations imposed by the culture plug. Here we present implementation of intensifying surface aeration by sparging air in the headspace of the reaction vessel and real-time monitoring of DO and dCO2 in the bioprocesses to evaluate the impact of intensified surface aeration. We observed that sparging air in the headspace allowed us to keep dCO2 at low level, which significantly improved not only biomass growth but also protein yield. We expect that implementing such controlled smart shake flasks can minimize the process development gap which currently exists in shake flask level and bioreactor level results.

Corrigendum to "YaliBricks, a versatile genetic toolkit for streamlined and rapid pathway engineering in Yarrowia lipolytica".

[This corrects the article DOI: 10.1016/j.meteno.2017.09.001.].

Genetic Tools for Streamlined and Accelerated Pathway Engineering in Yarrowia lipolytica.

Yarrowia lipolytica is an industrial oleaginous yeast that has many attractive physiological and metabolic characteristics for various biotechnological applications. Although it has a long history of industrial applications, the number of genetic tools available to effectively and efficiently engineer Y. lipolytica still falls behind the vast number of tools available for common organisms such as Escherichia coli and Saccharomyces cerevisiae. In this protocol, we have developed a complete and versatile genetic toolkit tailored for facile genetic manipulation in Y. lipolytica. We created a versatile DNA assembly platform YaliBrick, which can streamline the cloning of large multigene pathways with reused genetic parts. We established a sensitive luciferase reporter assay to characterize a set of 12 native promoters. In addition, we used YaliBrick to generate different gene configurations in multigene constructs. The five-gene biosynthetic pathway of the anticancer, antimicrobial pigment violacein was rapidly assembled in 1 week to demonstrate the simplicity and effectiveness of integrating pathway-balancing strategies with our YaliBrick vectors. In the end, we incorporated CRISPR-Cas9 into our YaliBrick vectors and achieved indel mutation and frameshift gene deletion at the CAN1 (arginine permease) genomic loci of Yarrowia lipolytica. The reported protocol provides a standard procedure to streamline and accelerate metabolic pathway engineering in Yarrowia lipolytica.

Corrigendum to "Rapid evolution of regulatory element libraries for tunable transcriptional and translational control of gene expression" [Synth Syst Biotechnol 2 (4) (2017) 295-301].

[This corrects the article DOI: 10.1016/j.synbio.2017.10.003.].

YaliBricks, a versatile genetic toolkit for streamlined and rapid pathway engineering in Yarrowia lipolytica.

Effective metabolic engineering of microorganisms relies on balanced expression of both heterologous and endogenous genes to channel metabolic flux towards products of interest while achieving reasonable biomass buildup. To facilitate combinatorial pathway engineering and facile genetic operation, we engineered a set of modular cloning vectors compatible with BioBrick standards, called YaliBricks, to allow for rapid assembly of multigene pathways with customized genetic control elements (promoters, intronic sequences and terminators) in the oleaginous yeast Yarrowia lipolytica. We established a sensitive luciferase reporter and characterized a set of 12 native promoters to expand the oleaginous yeast genetic toolbox for transcriptional fine-tuning. We harnessed the intron alternative splicing mechanism and explored three unique gene configurations that allow us to encode genetic structural variations into metabolic function. We elucidated the role of how these genetic structural variations affect gene expression. To demonstrate the simplicity and effectiveness of streamlined genetic operations, we assembled the 12 kb five-gene violacein biosynthetic pathway in one week. We also expanded this set of vectors to accommodate self-cleavage ribozymes and efficiently deliver guide RNA (gRNA) for targeted genome-editing with a codon-optimized CRISPR-Cas9 nuclease. Taken together, the tools built in this study provide a standard procedure to streamline and accelerate metabolic pathway engineering and genetic circuits construction in Yarrowia lipolytica.

Design and application of genetically-encoded malonyl-CoA biosensors for metabolic engineering of microbial cell factories.

Malonyl-CoA is the basic building block for synthesizing a range of important compounds including fatty acids, phenylpropanoids, flavonoids and non-ribosomal polyketides. Centering around malonyl-CoA, we summarized here the various metabolic engineering strategies employed recently to regulate and control malonyl-CoA metabolism and improve cellular productivity. Effective metabolic engineering of microorganisms requires the introduction of heterologous pathways and dynamically rerouting metabolic flux towards products of interest. Transcriptional factor-based biosensors translate an internal cellular signal to a transcriptional output and drive the expression of the designed genetic/biomolecular circuits to compensate the activity loss of the engineered biosystem. Recent development of genetically-encoded malonyl-CoA sensor has stood out as a classical example to dynamically reprogram cell metabolism for various biotechnological applications. Here, we reviewed the design principles of constructing a transcriptional factor-based malonyl-CoA sensor with superior detection limit, high sensitivity and broad dynamic range. We discussed various synthetic biology strategies to remove pathway bottleneck and how genetically-encoded metabolite sensor could be deployed to improve pathway efficiency. Particularly, we emphasized that integration of malonyl-CoA sensing capability with biocatalytic function would be critical to engineer efficient microbial cell factory. Biosensors have also advanced beyond its classical function of a sensor actuator for in situ monitoring of intracellular metabolite concentration. Applications of malonyl-CoA biosensors as a sensor-invertor for negative feedback regulation of metabolic flux, a metabolic switch for oscillatory balancing of malonyl-CoA sink pathway and source pathway and a screening tool for engineering more efficient biocatalyst are also presented in this review. We envision the genetically-encoded malonyl-CoA sensor will be an indispensable tool to optimize cell metabolism and cost-competitively manufacture malonyl-CoA-derived compounds.

Rapid evolution of regulatory element libraries for tunable transcriptional and translational control of gene expression.

Engineering cell factories for producing biofuels and pharmaceuticals has spurred great interests to develop rapid and efficient synthetic biology tools customized for modular pathway engineering. Along the way, combinatorial gene expression control through modification of regulatory element offered tremendous opportunity for fine-tuning gene expression and generating digital-like genetic circuits. In this report, we present an efficient evolutionary approach to build a range of regulatory control elements. The reported method allows for rapid construction of promoter, 5'UTR, terminator and trans-activating RNA libraries. Synthetic overlapping oligos with high portion of degenerate nucleotides flanking the regulatory element could be efficiently assembled to a vector expressing fluorescence reporter. This approach combines high mutation rate of the synthetic DNA with the high assembly efficiency of Gibson Mix. Our constructed library demonstrates broad range of transcriptional or translational gene expression dynamics. Specifically, both the promoter library and 5'UTR library exhibits gene expression dynamics spanning across three order of magnitude. The terminator library and trans-activating RNA library displays relatively narrowed gene expression pattern. The reported study provides a versatile toolbox for rapidly constructing a large family of prokaryotic regulatory elements. These libraries also facilitate the implementation of combinatorial pathway engineering principles and the engineering of more efficient microbial cell factory for various biomanufacturing applications.

Data from a pre-publication independent replication initiative examining ten moral judgement effects.

We present the data from a crowdsourced project seeking to replicate findings in independent laboratories before (rather than after) they are published. In this Pre-Publication Independent Replication (PPIR) initiative, 25 research groups attempted to replicate 10 moral judgment effects from a single laboratory's research pipeline of unpublished findings. The 10 effects were investigated using online/lab surveys containing psychological manipulations (vignettes) followed by questionnaires. Results revealed a mix of reliable, unreliable, and culturally moderated findings. Unlike any previous replication project, this dataset includes the data from not only the replications but also from the original studies, creating a unique corpus that researchers can use to better understand reproducibility and irreproducibility in science.

Regression/eradication of gliomas in mice by a systemically-deliverable ATF5 dominant-negative peptide.

Malignant gliomas have poor prognosis and urgently require new therapies. Activating Transcription Factor 5 (ATF5) is highly expressed in gliomas, and interference with its expression/function precipitates targeted glioma cell apoptosis in vitro and in vivo. We designed a novel deliverable truncated-dominant-negative (d/n) form of ATF5 fused to a cell-penetrating domain (Pen-d/n-ATF5-RP) that can be intraperitoneally/subcutaneously administered to mice harboring malignant gliomas generated; (1) by PDGF-B/sh-p53 retroviral transformation of endogenous neural progenitor cells; and (2) by human U87-MG xenografts. In vitro Pen-d/n-ATF5-RP entered into glioma cells and triggered massive apoptosis. In vivo, subcutaneously-administered Pen-d/n-ATF5-RP passed the blood brain barrier, entered normal brain and tumor cells, and then caused rapid selective tumor cell death. MRI verified elimination of retrovirus-induced gliomas within 8-21 days. Histopathology revealed growth-suppression of intracerebral human U87-MG cells xenografts. For endogenous PDGF-B gliomas, there was no recurrence or mortality at 6-12 months versus 66% mortality in controls at 6 months. Necropsy and liver-kidney blood enzyme analysis revealed no adverse effects on brain or other tissues. Our findings thus identify Pen-d/n-ATF5-RP as a potential therapy for malignant gliomas.

Development of a Recombinant Escherichia coli Strain for Overproduction of the Plant Pigment Anthocyanin.

Anthocyanins are water-soluble colored pigments found in terrestrial plants and are responsible for the red, blue, and purple coloration of many flowers and fruits. In addition to the plethora of health benefits associated with anthocyanins (cardioprotective, anti-inflammatory, antioxidant, and antiaging properties), these compounds have attracted widespread attention due to their promising potential as natural food colorants. Previously, we reported the biotransformation of anthocyanin, specifically cyanidin 3-O-glucoside (C3G), from the substrate (+)-catechin in Escherichia coli. In the present work, we set out to systematically improve C3G titers by enhancing substrate and precursor availability, balancing gene expression level, and optimizing cultivation and induction parameters. We first identified E. coli transporter proteins that are responsible for the uptake of catechin and secretion of C3G. We then improved the expression of the heterologous pathway enzymes anthocyanidin synthase (ANS) and 3-O-glycosyltransferase (3GT) using a bicistronic expression cassette. Next, we augmented the intracellular availability of the critical precursor UDP-glucose, which has been known as the rate-limiting precursor to produce glucoside compounds. Further optimization of culture and induction conditions led to a final titer of 350 mg/liter of C3G. We also developed a convenient colorimetric assay for easy screening of C3G overproducers. The work reported here constitutes a promising foundation to develop a cost-effective process for large-scale production of plant-derived anthocyanin from recombinant microorganisms.

Modular optimization of multi-gene pathways for fatty acids production in E. coli.

Microbial fatty acid-derived fuels have emerged as promising alternatives to petroleum-based transportation fuels. Here we report a modular engineering approach that systematically removed metabolic pathway bottlenecks and led to significant titre improvements in a multi-gene fatty acid metabolic pathway. On the basis of central pathway architecture, E. coli fatty acid biosynthesis was re-cast into three modules: the upstream acetyl coenzyme A formation module; the intermediary acetyl-CoA activation module; and the downstream fatty acid synthase module. Combinatorial optimization of transcriptional levels of these three modules led to the identification of conditions that balance the supply of acetyl-CoA and consumption of malonyl-CoA/ACP. Refining protein translation efficiency by customizing ribosome binding sites for both the upstream acetyl coenzyme A formation and fatty acid synthase modules enabled further production improvement. Fed-batch cultivation of the engineered strain resulted in a final fatty acid production of 8.6 g l(-1). The modular engineering strategies demonstrate a generalized approach to engineering cell factories for valuable metabolites production.

Trans and saturated fat on food labels in Canada: fact or fiction?

OBJECTIVE: Food labels are the number one source for nutrition information for Canadians, but are food labels accurate? This study aims to provide an assessment of the accuracy of the reported trans fatty acid and saturated fatty acid values on food labels in selected foods. METHODS: Over 380 samples of cookies, crackers, granola bars, breakfast bars and a variety of frozen foods were collected between 2005 and 2008 in the Greater Toronto Area, Ottawa and Vancouver, as part of Health Canada's Trans Fat Monitoring Program. The food categories chosen were based on earlier studies indicating that they were significant sources of trans fatty acids and the individual samples were chosen based on market share data. The trans fatty acid and saturated fatty acid contents of the samples were determined by gas chromatography and the laboratory results were compared to the values reported in the Nutrition Facts tables. CONCLUSIONS: Statistical analysis indicated no significant difference between laboratory and food label values for cookies, crackers, granola bars, breakfast bars and frozen foods for trans fat or saturated fat. The results demonstrate that Canadians can rely on food labels for making informed dietary choices with respect to trans fat and saturated fat content.

Differential cellular responses to protein adducts of naphthoquinone and monocrotaline pyrrole.

Protein-xenobiotic adducts are byproducts of xenobiotic metabolism. While there is a correlation between protein adduction and target organ toxicity, a cause and effect relationship is not often clear. Naphthoquinone (NQ) and monocrotaline pyrrole (MCTP) are two pneumotoxic electrophiles that form covalent adducts with a similar select group of proteins rich in reactive thiols. In this study, we treated human pulmonary artery endothelial cells (HPAEC) with NQ, MCTP, or preformed NQ or MCTP adducts to the protein galectin-1 (gal-1) and examined indicators of reactive oxygen species (ROS) oxidative injury, markers of apoptosis (caspase-3 and annexin V), and gene responses of cellular stress. ROS production was assayed fluorescently using CM-H(2)DCFDA. NQ adducts to gal-1 (NQ-gal) produced 183% more intracellular ROS than gal-1 alone (p < 0.0001). Caspase-3 activity and annexin V staining of phosphatidylserine were used to assess apoptotic activity in treated cells. HPAEC exposed to MCTP-gal had increases in both caspase-3 activation and membrane translocation of annexin V relative to gal-1 alone (p < 0.0001). Direct application of NQ produced significantly more ROS and induced significant caspase-3 activation, whereas MCTP did not. Human bronchial epithelial cells were also exposed to MCTP-gal and found to have significant increases in both caspase-3 activation and annexin V staining in comparison to that of gal-1 (p < 0.05). Western blot analysis showed that both NQ and MCTP significantly induced the Nrf2 mediated stress response pathway despite differences in ROS generation. ER stress was not induced by either adducts or parent compounds as seen by quantitative RT-PCR, but HOX-1 expression was significantly induced by NQ-gal and MCTP alone. Electrophile adduction to gal-1 produces different cytotoxic effects specific to each reactive intermediate.

Trans fatty acids: current contents in Canadian foods and estimated intake levels for the Canadian population.

Research conducted in the mid-1990s indicated that the levels of trans fats in Canadian diets were among the highest in the world. The consumption of trans fats raises blood levels of low-density lipoprotein (LDL)-cholesterol, while reducing levels of high-density lipoprotein (HDL)-cholesterol. In June 2007, Health Canada called on the food industry to voluntarily reduce levels of trans fats in vegetable oils and soft (tub)-margarines to < 2% of total fat, and in all other foods, to < 5%. Industry must show satisfactory progress by June 2009, or Health Canada might have to introduce legislation to ensure that recommended limits are achieved. Since 2005, Health Canada has been performing a national assessment of prepackaged and restaurant foods that likely contain trans fats. From 2005 to 2009, 1120 samples were analyzed, of which 852 or approximately 76% met the recommended trans fat limits. As a result of reformulation, most of the products had decreased trans + saturated fat content. The estimated average intake of trans fatty acids (TFA) in Canada significantly dropped from the high value of 8.4 g/day in the mid-1990s to 3.4 g/day (or 1.4% food energy) in 2008. However, this TFA intake of 1.4% of energy is still above the World Health Organization recommended limit of TFA intake of < 1% of energy, which suggests that the Canadian food industry needs to put more effort into reducing the TFA content in its products, especially in tub-margarines, donuts, and bakery products.

Effects of on-board and dockside handling on the formation of biogenic amines in mahimahi (Coryphaena hippurus), skipjack tuna (Katsuwonus pelamis), and yellowfin tuna (Thunnus albacares).

Consumer illnesses by scombroid poisonings have been a continuing problem for many years. The intoxications follow the ingestion of fish such as tuna and mahimahi that have undergone bacterial decomposition, leading to the formation of biogenic amines. Research studies have concluded that histamine is one of the indicators of scombrotoxic fish and that other amines, such as cadaverine, could be involved in the illnesses. Guidance for the handling of fish on board fishing vessels to prevent the production of scombrotoxic fish has been limited by a lack of data addressing changes that occur in fish from the water to delivery at dockside. In this study, the changes in selected biogenic amines were determined in mahimahi and tuna, which were captured and held in seawater at 25 to 35 degrees C for incubation times up to 18 h. The fillets from the treated fish were sectioned by transverse cuts and analyzed for histamine, cadaverine, and putrescine. Results showed that at 26 degrees C, more than 12 h of incubation were required before a histamine concentration of 50 ppm was reached in mahimahi. At 35 degrees C, 50 ppm histamine formed within 9 h. Similar results were found for skipjack and yellowfin tuna. Histamine concentrations exceeded 500 ppm within an additional 3 h of incubation in mahimahi. At both temperatures, an increase in the concentration of cadaverine preceded an increase in histamine levels. Changes in putrescine concentrations in the fish were less pronounced. The study also demonstrated that histidine decarboxylase activity was retained in some frozen samples of fish and could result in further increases in histamine on thawing.