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Plate readers are commonly used to measure cell growth and fluorescence, yet the utility and reproducibility of plate reader data is limited by the fact that it is typically reported in arbitrary or relative units. We have previously established a robust serial dilution protocol for calibration of plate reader measurements of absorbance to estimated bacterial cell count and for green fluorescence from proteins expressed in bacterial cells to molecules of equivalent fluorescein. We now extend these protocols to calibration of red fluorescence to the sulforhodamine-101 fluorescent dye and blue fluorescence to Cascade Blue. Evaluating calibration efficacy via an interlaboratory study, we find that these calibrants do indeed provide comparable precision to the prior calibrants and that they enable effective cross-laboratory comparison of measurements of red and blue fluorescence from proteins expressed in bacterial cells.

Biologically derived materials have numerous applications in biomedical fields and beyond. Yet, the properties of these materials are difficult to alter because the natural biosynthetic mechanisms are difficult to elucidate, imitate, or adjust. Thus, many bio-derived materials are isolated from natural tissues, or substitutes are recombinantly produced and then modified ex vivo. A major shift in this paradigm is being driven by the maturing field of synthetic biology, which is innovating a ‘tool box’ of methods to tune biomolecules and biosynthetic mechanisms in vivo. In the context of materials, this has led to higher production titers due to reprogrammed natural biosynthesis and has enabled design of novel materials by combining desired domains in vivo. Here, we highlight recent applications of synthetic biology to bio-derived ribosomal and nonribosomal polymer materials for biomedical applications. We then describe state-of-the-art techniques that will impact bio-derived material production and engineering in the near future. Continued innovation at the convergence of synthetic biology and materials science promises to begin a new era of biomaterial design and synthesis.

Compared to grounded force feedback, providing tactile feedback via a wearable device can free the user and broaden the potential applications of simulated physical interactions. However, neither the limitations nor the full potential of tactile-only feedback have been precisely examined. Here we investigate how the dimensionality of cutaneous fingertip feedback affects user movements and virtual object recognition. We combine a recently invented 6-DOF fingertip device with motion tracking, a head-mounted display, and novel contact-rendering algorithms to enable a user to tactilely explore immersive virtual environments. We evaluate rudimentary 1-DOF, moderate 3-DOF, and complex 6-DOF tactile feedback during shape discrimination and mass discrimination, also comparing to interactions with real objects. Results from 20 naive study participants show that higher-dimensional tactile feedback may indeed allow completion of a wider range of virtual tasks, but that feedback dimensionality surprisingly does not greatly affect the exploratory techniques employed by the user.

Yeast genomes can be assembled from sequencing data, but genome integrations and episomal plasmids often fail to be resolved with accuracy, completeness, and contiguity. Resolution of these features is critical for many synthetic biology applications, including strain quality control and identifying engineering in unknown samples. Here, we report an integrated workflow, named Prymetime, that uses sequencing reads from inexpensive NGS platforms, assembly and error correction software, and a list of synthetic biology parts to achieve accurate whole genome sequences of yeasts with engineering annotated. To build the workflow, we first determined which sequencing methods and software packages returned an accurate, complete, and contiguous genome of an engineered S. cerevisiae strain with two similar plasmids and an integrated pathway. We then developed a sequence feature annotation step that labels synthetic biology parts from a standard list of yeast engineering sequences or from a custom sequence list. We validated the workflow by sequencing a collection of 15 engineered yeasts built from different parent S. cerevisiae and nonconventional yeast strains. We show that each integrated pathway and episomal plasmid can be correctly assembled and annotated, even in strains that have part repeats and multiple similar plasmids. Interestingly, Prymetime was able to identify deletions and unintended integrations that were subsequently confirmed by other methods. Furthermore, the whole genomes are accurate, complete, and contiguous. To illustrate this clearly, we used a publicly available S. cerevisiae CEN.PK113 reference genome and the accompanying reads to show that a Prymetime genome assembly is equivalent to the reference using several standard metrics. Finally, we used Prymetime to resequence the nonconventional yeasts Y. lipolytica Po1f and K. phaffii CBS 7435, producing an improved genome assembly for each strain. Thus, our workflow can achieve accurate, complete, and contiguous whole genome sequences of yeast strains before and after engineering. Therefore, Prymetime enables NGS-based strain quality control through assembly and identification of engineering features.

Pharmaceutical production hosts may be derived from almost any organism, from Chinese Hamster Ovary (CHO) cell lines to isolated actinomycetes. Each host can be improved, historically only through adaptive evolution. Recently, the maturation of organism engineering has expanded the available models, methods, and tools for altering host phenotypes. New tools like CRISPR-associated endonucleases promise to enable precise cellular reprogramming and to access previously intractable hosts. In this review, we discuss the most recent advances in engineering several types of pharmaceutical production hosts. These include model organisms, potential platform hosts with advantageous metabolism or physiology, specialized producers capable of unique biosynthesis, and CHO, the most widely used recombinant protein production host. To realize improved engineered hosts, an increasing number of approaches involving DNA sequencing and synthesis, host rewriting technologies, computational methods, and organism engineering strategies must be used. Integrative workflows that enable application of the right combination of methods to the right production host could enable economical production solutions for emerging human health treatments.

Yeast whole genome sequencing (WGS) lacks end-to-end workflows that identify genetic engineering. Here we present Prymetime, a tool that assembles yeast plasmids and chromosomes and annotates genetic engineering sequences. It is a hybrid workflow—it uses short and long reads as inputs to perform separate linear and circular assembly steps. This structure is necessary to accurately resolve genetic engineering sequences in plasmids and the genome. We show this by assembling diverse engineered yeasts, in some cases revealing unintended deletions and integrations. Furthermore, the resulting whole genomes are high quality, although the underlying assembly software does not consistently resolve highly repetitive genome features. Finally, we assemble plasmids and genome integrations from metagenomic sequencing, even with 1 engineered cell in 1000. This work is a blueprint for building WGS workflows and establishes WGS-based identification of yeast genetic engineering., The cost and complexity of whole genome sequencing limits its use in identifying and validating sequences used for genetic engineering and synthetic biology. Here the authors present Prymetime, an integrated workflow to sequence engineered strains and identify engineering in metagenomes.

International audience; Fingertip haptic feedback offers advantages in many applications , including robotic teleoperation, gaming, and training. However, fingertip size and shape vary significantly across humans, making it difficult to design fingertip interfaces and rendering techniques suitable for everyone. This paper starts with an existing data-driven haptic rendering algorithm that ignores fingertip size, and it then develops two software-based approaches to personalize this algorithm for fingertips of different sizes using either additional data or geometry. We evaluate our algorithms in the rendering of pre-recorded tactile sensations onto rubber casts of six different fingertips as well as onto the real fingertips of 13 human participants. Results on the casts show that both approaches significantly improve performance, reducing force error magnitudes by an average of 78% with respect to the standard non-personalized rendering technique. Congruent results were obtained for real fingertips, with subjects rating each of the two personalized rendering techniques significantly better than the standard non-personalized method.

International audience; Small size and low weight are critical requirements for wearable and portable haptic interfaces, making it essential to work toward the optimization of their sensing and actuation systems. This paper presents a new approach for task-driven design optimization of fingertip cutaneous haptic devices. Given one (or more) target tactile interactions to render and a cutaneous device to optimize, we evaluate the minimum number and best configuration of the device's actuators to minimize the estimated haptic rendering error. First, we calculate the motion needed for the original cutaneous device to render the considered target interaction. Then, we run a principal component analysis (PCA) to search for possible couplings between the original motor inputs, looking also for the best way to reconfigure them. If some couplings exist, we can redesign our cutaneous device with fewer motors, optimally configured to render the target tactile sensation. The proposed approach is quite general and can be applied to different tactile sensors and cutaneous devices. We validated it using a BioTac tactile sensor and custom plate-based 3-DoF and 6-DoF fingertip cutaneous devices, considering six representative target tactile interactions. The algorithm was able to find couplings between each device's motor inputs, proving it to be a viable approach to optimize the design of wearable and portable cutaneous devices. Finally, we present two examples of optimized designs for our 3-DoF fingertip cutaneous device.

Centralized facilities for genetic engineering, or "biofoundries", offer the potential to design organisms to address emerging needs in medicine, agriculture, industry, and defense. The field has seen rapid advances in technology, but it is difficult to gauge current capabilities or identify gaps across projects. To this end, our foundry was assessed via a timed "pressure test", in which 3 months were given to build organisms to produce 10 molecules unknown to us in advance. By applying a diversity of new approaches, we produced the desired molecule or a closely related one for six out of 10 targets during the performance period and made advances toward production of the others as well. Specifically, we increased the titers of 1-hexadecanol, pyrrolnitrin, and pacidamycin D, found novel routes to the enediyne warhead underlying powerful antimicrobials, established a cell-free system for monoterpene production, produced an intermediate toward vincristine biosynthesis, and encoded 7802 individually retrievable pathways to 540 bisindoles in a DNA pool. Pathways to tetrahydrofuran and barbamide were designed and constructed, but toxicity or analytical tools inhibited further progress. In sum, we constructed 1.2 Mb DNA, built 215 strains spanning five species ( Saccharomyces cerevisiae, Escherichia coli, Streptomyces albidoflavus, Streptomyces coelicolor, and Streptomyces albovinaceus), established two cell-free systems, and performed 690 assays developed in-house for the molecules.

Autism spectrum disorder (ASD) impacts 1 in 68 children in the U.S., with tremendous individual and societal costs. Technology-aided intervention, more specifically robotic intervention, has gained momentum in recent years due to the inherent affinity of many children with ASD towards technology. In this paper we present a novel robot-mediated intervention system for imitation skill learning, which is considered a core deficit area for children with ASD. The Robot-mediated Imitation Skill Training Architecture (RISTA) is designed in such a manner that it can operate either completely autonomously or in coordination with a human therapist depending on the intervention need. Experimental results are presented from small user studies validating system functionality, assessing user tolerance, and documenting subject performance. Preliminary results show that this novel robotic system draws more attention from the children with ASD and teaches gestures more effectively as compared to a human therapist. While no broad generalized conclusions can be made about the effectiveness of RISTA based on our small user studies, initial results are encouraging and justify further exploration in the future.

Increasingly researchers are attempting to develop robotic technologies for children with autism spectrum disorder (ASD). This pilot study investigated the development and application of a novel robotic system capable of dynamic, adaptive, and autonomous interaction during imitation tasks with embedded real-time performance evaluation and feedback. The system was designed to incorporate both a humanoid robot and a human examiner. We compared child performance within system across these conditions in a sample of preschool children with ASD (n = 8) and a control sample of typically developing children (n = 8). The system was well-tolerated in the sample, children with ASD exhibited greater attention to the robotic system than the human administrator, and for children with ASD imitation performance appeared superior during the robotic interaction.

Utilization of exogenous sugars found in lignocellulosic biomass hydrolysates, such as xylose, must be improved before yeast can serve as an efficient biofuel and biochemical production platform. In particular, the first step in this process, the molecular transport of xylose into the cell, can serve as a significant flux bottleneck and is highly inhibited by other sugars. Here we demonstrate that sugar transport preference and kinetics can be rewired through the programming of a sequence motif of the general form G-G/F-XXX-G found in the first transmembrane span. By evaluating 46 different heterologously expressed transporters, we find that this motif is conserved among functional transporters and highly enriched in transporters that confer growth on xylose. Through saturation mutagenesis and subsequent rational mutagenesis, four transporter mutants unable to confer growth on glucose but able to sustain growth on xylose were engineered. Specifically, Candida intermedia gxs1 Phe(38)Ile(39)Met(40), Scheffersomyces stipitis rgt2 Phe(38) and Met(40), and Saccharomyces cerevisiae hxt7 Ile(39)Met(40)Met(340) all exhibit this phenotype. In these cases, primary hexose transporters were rewired into xylose transporters. These xylose transporters nevertheless remained inhibited by glucose. Furthermore, in the course of identifying this motif, novel wild-type transporters with superior monosaccharide growth profiles were discovered, namely S. stipitis RGT2 and Debaryomyces hansenii 2D01474. These findings build toward the engineering of efficient pentose utilization in yeast and provide a blueprint for reprogramming transporter properties.

Molecular transport is a key process in cellular metabolism. This step is often limiting when using a nonnative carbon source, as exemplified by xylose catabolism in Saccharomyces cerevisiae . As a step toward addressing this limitation, this study seeks to characterize monosaccharide transport preference and efficiency. A group of 26 known and putative monosaccharide transport proteins was expressed in a recombinant Saccharomyces cerevisiae host unable to transport several monosaccharides. A growth-based assay was used to detect transport capacity across six different carbon sources (glucose, xylose, galactose, fructose, mannose, and ribose). A mixed glucose-and-xylose cofermentation was performed to determine substrate preference. These experiments identified 10 transporter proteins that function as transporters of one or more of these sugars. Most of these proteins exhibited broad substrate ranges, and glucose was preferred in all cases. The broadest transporters confer the highest growth rates and strongly prefer glucose. This study reports the first molecular characterization of the annotated XUT genes of Scheffersomyces stipitis and open reading frames from the yeasts Yarrowia lipolytica and Debaryomyces hansenii. Finally, a phylogenetic analysis demonstrates that transporter function clusters into three distinct groups. One particular group comprised of D. hansenii XylHP and S. stipitis XUT1 and XUT3 demonstrated moderate transport efficiency and higher xylose preferences.

The general central dogma frames the emergent properties of life, which make biology both necessary and difficult to engineer. In a process engineering paradigm, each biological process stream and process unit is heavily influenced by regulatory interactions and interactions with the surrounding environment. Synthetic biology is developing the tools and methods that will increase control over these interactions, eventually resulting in an integrative synthetic biology that will allow ground-up cellular optimization. In this review, we attempt to contextualize the areas of synthetic biology into three tiers: (1) the process units and associated streams of the central dogma, (2) the intrinsic regulatory mechanisms, and (3) the extrinsic physical and chemical environment. Efforts at each of these three tiers attempt to control cellular systems and take advantage of emerging tools and approaches. Ultimately, it will be possible to integrate these approaches and realize the vision of integrative synthetic biology when cells are completely rewired for biotechnological goals. This review will highlight progress towards this goal as well as areas requiring further research.

Hexose and pentose cofermentation is regarded as one of the chief obstacles impeding economical conversion of lignocellulosic biomass to biofuels. Over time, successful application of traditional metabolic engineering strategy has produced yeast strains capable of utilizing the pentose sugars (especially xylose and arabinose) as sole carbon sources, yet major difficulties still remain for engineering simultaneous, exogenous sugar metabolism. Beyond catabolic pathways, the focus must shift towards non-traditional aspects of cellular engineering such as host molecular transport capability, catabolite sensing and stress response mechanisms. This review highlights the need for an approach termed 'panmetabolic engineering', a new paradigm for integrating new carbon sources into host metabolic pathways. This approach will concurrently optimize the interdependent processes of transport and metabolism using novel combinatorial techniques and global cellular engineering. As a result, panmetabolic engineering is a whole pathway approach emphasizing better pathways, reduced glucose-induced repression and increased product tolerance. In this paper, recent publications are reviewed in light of this approach and their potential to expand metabolic engineering tools. Collectively, traditional approaches and panmetabolic engineering enable the reprogramming of extant biological complexity and incorporation of exogenous carbon catabolism.

Background: While pulmonary hypertension (PHT) contributes significantly to the morbidity and mortality of adults with sickle cell disease (SCD), it has not been studied in pediatric SCD patients. We sought to evaluate the prevalence and significance of PHT in pediatric SCD population. Methods: From May 1999 to July 2004, 123 echocardiograms were performed in SCD patients. Utilizing the tricuspid valve regurgitant jet, right ventricular systolic pressure (RVSP) was estimated in 56 studies (47 patients, aged 0 to 18 years). PHT was defined as RVSP >30 mmHg. Mean steady-state as well as the most recent white blood count (WBC), hemoglobin (Hb) level, reticulocyte count, ferritin level, and number of red cell units transfused in the year prior to the study were noted. In addition, all chest X-ray readings were reviewed to determine the number and type of life-time pulmonary events (effusions, infiltrates, pneumonia, atelectasis or CHF) in each patient. Acute chest syndrome (ACS) was determined to be any effusion, infiltrate or pneumonia. Statistical analysis included Fisher’s exact test and Spearman’s correlation coefficients. Results: Eleven patients were acutely ill at the time of the echocardiogram and were excluded from the analysis. Of the remaining 36 patients, pulmonary hypertension was present in 24 (66%). There was a significant difference in RVSP between younger (0 to 9 years) and older (10 to 18 years) groups of patient (p A significant negative correlation was shown between RVSP and most recent Hb (r = −0.41; p = 0.012) as well as RVSP and the mean steady state platelet count (r = −0.35; p = 0.035). A positive correlation was found between RVSP and the number of ACS episodes (r = 0.37; p = 0.024), RVSP and mean steady state reticulocyte count (r = 0.51; p = 0.002) as well as the most recent reticulocyte count (r = 0.42; p = 0.012). There was however, no correlation found between RVSP and the number of episodes of CHF, collapse or atelectasis separately or grouped together. No correlation was found between RVSP and the number of units transfused or ferritin level. Conclusion: Pulmonary Hypertension is highly prevalent in the pediatric SCD population and its prevalence increases with age. It correlates with indicators of acute and chronic hemolysis as well as the number of ACS events. Our study did not demonstrate correlations between PHT and iron overload indices. Prospective clinical trials monitoring PHT in SCD pediatric patients are indicated.