Ramón Gonzalez

• Federal University of Rio de Janeiro

2-Hydroxyacyl-CoA lyase/synthase (HACL/S) is a thiamine diphosphate (ThDP)-dependent versatile enzyme originally discovered in the mammalian α-oxidation pathway. HACL/S natively cleaves 2-hydroxyacyl-CoAs and, in its reverse direction, condenses formyl-CoA with aldehydes or ketones. The one-carbon elongation biochemistry based on HACL/S has enabled...

2-Hydroxyacyl-CoA lyase/synthase (HACL/S) is a thiamine diphosphate (ThDP)-dependent versatile enzyme originally discovered in the mammalian α-oxidation pathway. HACL/S natively cleaves 2-hydroxyacyl-CoAs and, in its reverse direction, condenses formyl-CoA with aldehydes or ketones. The one-carbon elongation biochemistry based on HACL/S has enabled...

From the view of a circular economy, the bioconversion of methane into cell protein and carbohydrates could provide alternative food resources while cutting greenhouse gases, considering renewable gases from anaerobic...

One-carbon (C1) compounds are emerging as cost-effective and potentially carbon-negative feedstocks for biomanufacturing, which require efficient, versatile metabolic platforms for the synthesis of value-added products. Synthetic formyl-CoA elongation (FORCE) pathways allow diverse product synthesis from C1 compounds via iterative C1 elongation, op...

Formate can be envisioned at the core of a carbon-neutral bioeconomy, where it is produced from CO2 by (electro-)chemical means and converted into value-added products by enzymatic cascades or engineered microbes. A key step in expanding synthetic formate assimilation is its thermodynamically challenging reduction to formaldehyde. Here, we develop...

Carbon-negative synthesis of biochemical products has the potential to mitigate global CO2 emissions. An attractive route to do this is the reverse β-oxidation (r-BOX) pathway coupled to the Wood-Ljungdahl pathway. Here, we optimize and implement r-BOX for the synthesis of C4-C6 acids and alcohols. With a high-throughput in vitro prototyping workfl...

C1 gaseous substrates (CH4, CO2, and CO) derived from natural gas, biogas, and syngas, are of interest due to their threats to the environment or inefficient utilization. Benefiting from advanced genetic editing tools and bioconversion strategies, metabolically engineered C1-gas-utilizing microorganisms (CGUM), such as methanotrophs, cyanobacteria,...

Arnold L. Demain passed away on April 3, 2020, just shy of his 93rd birthday, from complications due to COVID-19 infection. He led an exemplary life as a scientist and humanitarian. In 2017, the Journal of Industrial Microbiology and Biotechnology (JIMB) published a special issue entitled “Arnold Demain—Industrial microbiologist extraordinaire” to...

Most microorganisms can metabolize glycerol when external electron acceptors are available (i.e. under respiratory conditions). However, few can do so under fermentative conditions owing to the unique redox constraints imposed by the high degree of reduction of glycerol. Here, we utilize in silico analysis combined with in vivo genetic and biochemi...

Metabolic engineering often entails concurrent engineering of substrate utilization, central metabolism and product synthesis pathways, inevitably creating interdependency with native metabolism. Here we report an alternative approach using synthetic pathways for C1 bioconversion that generate multicarbon products directly from C1 units and hence a...

One of the biggest challenges to realize a circular carbon economy is the synthesis of complex carbon compounds from one-carbon (C1) building blocks. Since the natural solution space of C1−C1 condensations is limited to highly complex enzymes, the development of more simple and robust biocatalysts may facilitate the engineering of C1 assimilation r...

Purpose: Upper airway surgery comprises a set of techniques that modify the anatomy of the vocal tract, including tonsillectomy and septoplasty. The objective of this work is to study the changes in acoustic parameters and the effects on the identification or verification of the speaker through the speech produced after the vocal tract surgeries,...

Polyketides found in nature originate from backbones synthesized through iterative decarboxylative Claisen condensations catalysed by polyketide synthases (PKSs). However, PKSs suffer from complicated architecture, energy inefficiencies, complex regulation, and competition with essential metabolic pathways for extender unit malonyl-CoA, all combini...

This paper shows the performance of various traction control strategies that aim to minimize slippage and wheel fighting by properly adjusting the velocity of each traction wheel in a planetary rover. These strategies are validated through simulations performed in ANVEL (Quantum Signal LLC) and using two rovers currently employed by NASA. These exp...

Despite the potential of biotechnological processes for one-carbon (C1) bioconversion, efficient biocatalysts required for their implementation are yet to be developed. To address intrinsic limitations of native C1 biocatalysts, here we report that 2-hydroxyacyl CoA lyase (HACL), an enzyme involved in mammalian α-oxidation, catalyzes the ligation o...

Significance We have demonstrated the design, prototyping, and implementation of a non-natural route to isoprenoid biosynthesis, termed the isoprenoid alcohol (IPA) pathway. Opposed to working within the confines of native metabolic pathways, our approach of utilizing all available biochemical reactions identified a synthetic route to isoprenoid co...

This paper presents a comprehensive comparison of well-known machine learning algorithms for estimating discrete slip events associated with individual wheels in planetary exploration rovers. This analysis is performed with various tuning configurations for each algorithm (55 setups). This research also shows the key role that environment plays in...

Prenylated aromatics (PAs) are an important class of natural products with valuable pharmaceutical applications. To address current limitations of their sourcing from plants, here, we present a microbial platform for the in vivo synthesis of PAs based on the aromatic prenyltransferase NphB from Streptomyces sp. strain CL190. As proof of concept, we...

Methane is considered a “dream energy package” for chemical production. The large amount of energy stored in methane (CH4) and the current market trend toward lower CH4 price make the use of CH4 as a carbon and energy source for higher-value chemical production desirable. With a substantial stored energy capacity of 47 MJ/kg as determined by the lo...

Convergence of market drivers such as abundant availability of inexpensive natural gas and increasing awareness of its global warming effects have created new opportunities for the development of small-scale gas-to-liquid (GTL) conversion technologies that can efficiently utilize methane, the primary component of natural gas. Leveraging the unique...

Synthetic biology, encompassing the design and construction of novel artificial biological pathways and organisms and the redesign of existing natural biological systems, is rapidly expanding the number of applications for which biological systems can play an integral role. In the context of chemical production, the combination of synthetic biology...

Decanoic acid is a valuable compound used as precursor for industrial chemicals, pharmaceuticals and biofuels. Despite efforts to produce it from renewables, only limited achievements have been reported. Here, we report an engineered cell factory able to produce decanoic acid as a major product from glycerol, and abundant and renewable feedstock. W...

An engineered reversal of the β-oxidation cycle (r-BOX) and the fatty acid biosynthesis (FAB) pathway are promising biological platforms for advanced fuel and chemical production in part due to their iterative nature supporting the synthesis of various chain length products. While diverging in their carbon-carbon elongation reaction mechanism, iter...

This paper introduces an unsupervised method for the classification of discrete rovers' slip events based on proprioceptive signals. In particular, the method is able to automatically discover and track various degrees of slip (i.e. low slip, moderate slip, high slip). The proposed method is based on aggregating the data over time, since high level...

Background: To determine the clinical outcomes and morbidity of endoscopic medial wall combined with transcutaneous lateral orbital wall decompression in Graves’ orbitopathy. Methodology: A retrospective noncomparative case series of patients who underwent surgical decompression for Graves’ orbitopathy at Hospital Universitario de Fuenlabrada betwe...

This paper describes an initial investigation that shows the major impact that moisture and vegetation produce on a soil and how that effect may be measured using a thermal camera. In particular, those two variables influence how the soil compacts and, hence, the traversability of a vehicle. A broad set of experiments, under different weather condi...

This paper describes a simple and efficient methodology to generate a mobility map accounting for two sources of uncertainty, namely measurement errors (RMSE of a Digital Elevation Model) and interpolation error (kriging method). The proposed methodology means a general-purpose solution since it works with standard and publicly-available Digital El...

This paper describes a stochastic approach to vehicle mobility prediction over large spatial regions [>\(5 \times 5\) (km\(^2\))]. The main source of uncertainty considered in this work derives from uncertainty in terrain elevation, which arises from sampling (at a finer resolution) a Digital Elevation Model. In order to account for such uncertaint...

The next era of chemical manufacturing Producing mass quantities of chemicals has its roots in the industrial revolution. But industrial synthesis leads to sizeable sustainability and socioeconomic challenges. The rapid advances in biotechnology suggest that biological manufacturing may soon be a feasible alternative, but can it produce chemicals a...

This paper presents an efficient method for increasing the accuracy of one key step regarding the process of determining a mobility map. That is, the interpolation of the original Digital Elevation Model (DEM) to a finer resolution before running multi-body-dynamics simulations. Specifically, this paper explores the use of fractal dimension and ele...

Fatty acid oxidation pathways are attractive for metabolic engineering purposes due to their cyclic nature as well as their reactions that allow for the selective functionalization of alkyl chains. These characteristics allow for the production of various chemicals, such as alcohols, alkanes, ketones and hydroxyacids, in a wide range of carbon numb...

Anabolic metabolism can produce an array of small molecules, but yields and productivities are low owing to carbon and energy inefficiencies and slow kinetics. Catabolic and fermentative pathways, on the other hand, are carbon and energy efficient but support only a limited product range. We used carbon- and energy-efficient non-decarboxylative Cla...

Concerns over sustained availability of fossil resources along with environmental impact of their use have stimulated the development of alternative methods for fuel and chemical production from renewable resources. In this work, we present a new approach to produce α,β-unsaturated carboxylic acids (α,β-UCAs) using an engineered reversal of the β-o...

Background: Chinese hamster ovary (CHO) cells are the main host for producing recombinant proteins with human therapeutic applications mainly because of their capability to perform proper folding and glycosylation processes. In addition, mild hypothermia is one of the main strategies for maximising the productivity of these systems. However, littl...

This work presents a teaching experience of Robotics in Computer Science & Engineering studies at the University of Almería (Spain). The teaching methodology is mainly based on the use of ICT. In particular, interactive software tools, virtual and remote laboratories, and an e-learning content management are used. Such technologies have significant...

We describe the case of a 13-year-old girl with paradoxical vocal fold motion (PVFM) who failed to improve with repeated medical treatment, speech therapy and psychotherapy, but was successfully treated with botulinum toxin A (BTX-A) injection to the vocal folds. For delivering the BTX-A we used a channeled fiber-optic laryngoscope under local anes...

Unlabelled: Given their simple and easy-to-manipulate chemical structures, short-chain fatty acids (SCFAs) are valuable feedstocks for many industrial applications. While the microbial production of SCFAs by engineered Escherichia coli has been demonstrated recently, productivity and yields are limited by their antimicrobial properties. In this wo...

One of the most significant research field in mobile robotics deals with robots operating in off-road conditions (planetary rovers, agriculture robots, search and rescue operations, military robots, etc.). However, obtaining a successful result is not an easy task. One primary point is the locomotion system. In this case, tracks constitute a well-k...

The recently engineered reversal of the β-oxidation cycle has been proposed as a potential platform for the efficient synthesis of longer chain (C ≥ 4) fuels and chemicals. Here, we demonstrate the utility of this platform for the synthesis of medium-chain length (C6–C10) products through the manipulation of key components of the pathway. Deletion...

We recently used a synthetic/bottom-up approach to establish the identity of the four enzymes composing an engineered functional reversal of the β-oxidation cycle for fuel and chemical production in Escherichia coli (Clomburg et al. 2012. ACS Synth. Biol. 1:541-554). While native enzymes that catalyze the first three steps of the pathway were ident...

An engineered reversal of the β-oxidation cycle was exploited to demonstrate its utility for the synthesis of medium chain (6- to 10-carbons) ω-hydroxyacids and dicarboxylic acids from glycerol as the only carbon source. A redesigned β-oxidation reversal facilitated the production of medium chain carboxylic acids, which were converted to ω-hydroxya...

We report on the growth of non-stoichiometric nanocrystalline hydroxyapatite (nHAp) with a composition similar to natural bone by a wet-chemical in-situ precipitation route on carbon nanotubes (CNTs) with different degrees of oxygen functionalities and on graphene oxide (GO). Both, functionalization degree and morphology of CNTs and GO appear as cr...

This paper discusses the formulation of an optimal control framework for a two time-scale system modeled in terms of singular perturbation theory. The fast dynamics subsystem is controlled online by means of a robust receding horizon control approach considering economic objectives in the performance function and fulfilling state and input constrai...

Bimetallic PdAu catalysts are more active than monometallic ones for the selective oxidation of alcohols, but the reasons for improvement remain insufficiently detailed. A metal-on-metal material can probe the structure–catalysis relationship more clearly than conventionally prepared bimetallics. In this study, Pd-on-Au nanoparticles with variable...

The modularity and versatility of an engineered functional reversal of the β-oxidation cycle make it a promising platform for the synthesis of longer-chain (C≥4) products. While the pathway has recently been exploited for the production of n-alcohols and carboxylic acids, fully capitalizing on its potential for the synthesis of a diverse set of pro...

If methane, the main component of natural gas, can be efficiently converted to liquid fuels, world reserves of methane could satisfy the demand for transportation fuels in addition to use in other sectors. However, the direct activation of strong C-H bonds in methane and conversion to desired products remains a difficult technological challenge. Th...

Mild hypothermia condition in mammalian cell culture technology has been one of the main focuses of research for the development of breeding strategies to maximize productivity of these production systems. Despite the large number of studies that show positive effects of mild hypothermia on specific productivity of r-proteins, no experimental appro...

This paper presents the development of an energy management strategy of a Plug-in Hybrid Electric Vehicle (PHEV). In this case, a rule-based optimal controller selects the appropriate operation mode. Furthermore, advantages and drawbacks of such vehicles are compared with respect to other vehicles powered by the most popular powertrain architecture...

When a tracked mobile robot operates in off-road conditions many disturbances and inconveniences can lead to a unsuccessful result. Some of these inconveniences deal with robot-terrain interaction, such as slip and sinkage phenomena, and with inaccurate robot localization. In this context, both a careful and precise design and a strict testing proc...

Mobile robots must have effective motion controllers that handle the properties of the surrounding environment. In this context, motion control is defined as a layer in the navigation architecture that generates the proper control actions to successfully steer the mobile robot through a desired trajectory. Particularly, motion controllers should be...

As commented in previous chapters, when a mobile robot moves in off-road conditions some undesirable effects, such as noisy measurements and inaccurate robot location, are intensified. Additionally, simplified models are usually used for control design purposes. Thus, these factors can lead to uncertainties in the robot motion that may entail inapp...

Robot localization is defined as the process in which a mobile robot determines its current position and orientation relative to an inertial reference frame [124]. In the context of off-road mobile robots, localization techniques have to deal with the particular features of off-road conditions, such as a noisy environment (vibrations when the robot...

In the context of robotics, a model is defined as a set of mathematical differential equations that represents the behaviour of a robot. In this sense, kinematic and dynamic modelling constitutes a key issue related to off-road mobile robotics, since such models may be used to design appropriate mechanical structures [117, 125]; to design planning...

Glycerol, a by-product from biodiesel manufacture, is a highly functionalized renewable raw material. Supported precious metal catalysts have been studied extensively for selective oxidation as a means to upgrade glycerol. Bimetallic PdAu catalysts are shown to be more active than monometallic ones, but the reasons for the enhancement are not well...

The use of plasmonic nanoparticle complexes for biomedical applications such as imaging, gene therapy, and cancer treatment is a rapidly emerging field expected to significantly improve conventional medical practices. In contrast, the use of these types of nanoparticles to noninvasively trigger biochemical pathways has been largely unexplored. Here...

Fatty acids (FAs) are essential components of cellular structure and energy‐generating routes in living organisms. They exist in a variety of chemical configurations and functionalities and are catabolized by different oxidative routes, according to their structure. α‐ and ω‐Oxidation are minor routes that occur only in eukaryotes, while β‐oxidatio...

This manuscript evaluates through physical experiments a navigation architecture for off-road mobile robots. It has been implemented taking into account low-cost components and computational requirements while still being able to robustly address the required tasks. The visual odometry approach uses two consumer-grade cameras for estimating robot d...

Glycerol has attracted the attention of scientific and industrial communities due to its generation in bulk quantities as a byproduct of biofuel industries. With the rapid growth of these industries in recent years, glycerol is frequently treated as a very low-value byproduct or even a waste product with a disposal cost associated to it. Glycerol i...

Metabolic engineering was formally defined more than two decades ago (Bailey, 1991) and it is now an established discipline. Metabolic engineering is generally defined as the directed improvement of product formation or cellular properties through the modification of specific biochemical reactions or the introduction of new ones with the use of rec...

Eight fermentative bacterial strains were isolated from mixed enrichment cultures of a composite soil sample collected at 1.34 km depth from the former Homestake gold mine in Lead, SD, USA. Phylogenetic analysis of their 16S rRNA gene sequences revealed that these isolates were affiliated with the phylum Firmicutes belonging to genera Bacillus and...

Background Due to its abundance and low-price, glycerol has become an attractive carbon source for the industrial production of value-added fuels and chemicals. This work reports the engineering of E. coli for the efficient conversion of glycerol into L-lactic acid (L-lactate). Results Escherichia coli strains have previously been metabolically en...

This paper presents a novel approach for guiding mobile robots inside greenhouses demonstrated by promising preliminary physical experiments. It represents a comprehensive attempt to use the successful principles of AGVs (auto-guided vehicles) inside greenhouses, but avoiding the necessity of modifying the crop layout, and avoiding having to bury m...

The use of plasmonic nanoparticle complexes for biomedical applications such as imaging, gene therapy, and cancer treatment is a rapidly emerging field expected to significantly improve conventional medical practices. In contrast, the use of these types of nanoparticles to noninvasively trigger biochemical pathways has been largely unexplored. Here...

To ensure the long-term viability of biorefineries, it is essential to go beyond the carbohydrate-based platform and develop complementing technologies capable of producing fuels and chemicals from a wide array of available materials. Glycerol, a readily available and inexpensive compound, is generated during biodiesel, oleochemical, and bioethanol...

While we have recently constructed a functional reversal of the β-oxidation cycle as a platform for the production of fuels and chemicals by engineering global regulators and eliminating native fermentative pathways, the system-level approach used makes it difficult to determine which of the many deregulated enzymes are responsible for product synt...

In this paper, we present the work related to the application of a visual odometry approach to estimate the location of mobile robots operating in off-road conditions. The visual odometry approach is based on template matching, which deals with estimating the robot displacement through a matching process between two consecutive images. Standard vis...

Methyl ketones are a group of highly reduced platform chemicals with widespread applications in the fragrance, flavor and pharmacological industries. Current methods for the industrial production of methyl ketones include oxidation of hydrocarbons, but recent advances in the characterization of methyl ketone synthases from wild tomato have sparked...

Availability, low price, and high degree of reduction have made glycerol a highly attractive and exploited carbon source for the production of fuels and reduced chemicals. Here we report the quantitative analysis of the fermentative metabolism of glycerol in Escherichia coli through the use of kinetic modeling and metabolic control analysis (MCA) t...

Coralline calcium-hydroxyapatite and calcium carbonate from Porites Porites coral were added to a polymeric matrix based on polyvinyl acetate (POVIAC(®)), to obtain a novel bone substitute composite as well as a system for the controlled drug (cephalexin) release. Composite samples with different compositions were characterized by physical-chemical...

Systems metabolic engineering has made the renewable production of industrial chemicals a feasible alternative to modern operations. One major example of a renewable process is the production of carboxylic acids, such as octanoic acid (C8), from Escherichia coli, engineered to express thioesterase enzymes. C8, however, is toxic to E. coli above a c...

This paper focuses on the design of a tube-based Model Predictive Control law for the control of constrained mobile robots in off-road conditions with longitudinal slip while ensuring robustness and stability. A time-varying trajectory tracking error model is used, where uncertainties are assumed to be bounded and additive. The robust tube-based MP...

Advanced (long-chain) fuels and chemicals are generated from short-chain metabolic intermediates through pathways that require carbon-chain elongation. The condensation reactions mediating this carbon-carbon bond formation can be catalysed by enzymes from the thiolase superfamily, including β-ketoacyl-acyl-carrier protein (ACP) synthases, polyketid...

Escherichia coli K-12 strain MG1655 was engineered to coproduce acetaldehyde and hydrogen during glucose fermentation by the use of exogenous acetyl-coenzyme A (acetyl-CoA) reductase (for the conversion of acetyl-CoA to acetaldehyde) and the native formate hydrogen lyase. A putative acetaldehyde dehydrogenase/acetyl-CoA reductase from Salmonella en...

Improved design of metabolic flux estimation using mixed label 13C labeling experiments and identifiability analysis motivated re-examination of metabolic fluxes during anaerobic fermentation in the Escherichia coli. Comprehensive metabolic flux maps were determined by using a mixture of differently labeled glucose and compared to conventional flux...

The replacement of glucose by mannose as a means to improve recombinant protein productivity was studied for the first time in continuous cultures of Chinese hamster ovary (CHO) cells producing human recombinant tissue plasminogen activator (t-PA). Steady-state operation at two hexose levels in the inlet (2.5 and 10mM) allowed comparing the effect...

En este trabajo se comentan las principales expe-riencias adquiridas por miembros del grupo de investigación Automática, Electrónica y Robótica (TEP-197) de la Universi-dad de Almería en la robotización de tareas en invernaderos. En particular, en la aplicación de robots manipuladores en estaciones de trabajo capaces de realizar varias tareas y rob...

Due to its availability, low-price, and high degree of reduction, glycerol has become an attractive carbon source for the production of fuels and reduced chemicals. Using the platform we have established from the identification of key pathways mediating fermentative metabolism of glycerol, this work reports the engineering of Escherichia coli for t...

Coralina® HAP-200 (coralline hydroxyapatite obtained by hydrothermal treatment of marine corals) and POVIAC® (polymeric matrix based on PVAc), commercial trade marks were mixed with a natural product from the Cuban sea costs, i.e. calcium carbonate from Porites Porites coral, to obtain a novel bioactive composite with potential use as bone restorat...

This paper presents a control law for the trajectory tracking of mobile robots under slip conditions and subject to both system constraints and varying dynamics. First, a control law is obtained based on a Lyapunov function to guarantee closed-loop asymptotic stability, resulting in a set of feedback gains, one for each extreme model realization. O...

As we aim to increase the number of fuels and chemicals produced by biocatalysts in an economically competitive process, biocatalyst inhibition by these products becomes an ever-increasing problem. Here we discuss our strategy to increase the tolerance of Escherichia coli to short-chain fatty acids. Our approach is two-pronged: analysis of the inhi...

The fermentative metabolism of Escherichia coli has been extensively studied and represents the primary metabolic mode of interest for industrial applications. However, most of this knowledge originates from the study of metabolic components in isolation and is rather incomplete. In contrast to previous studies, we have used a system-level approach...

Pyruvate is located at a metabolic junction of assimilatory and dissimilatory pathways and represents a switch point between respiratory and fermentative metabolism. In Escherichia coli, the pyruvate dehydrogenase complex (PDHC) and pyruvate formate-lyase are considered the primary routes of pyruvate conversion to acetyl-CoA for aerobic respiration...

This study explored the potential of polyvinyl acetate/CaCO 3/coralline hydroxyapatite composites to act as a controlled drug delivery system. Firstly, a composite biomaterial was prepared and cephalexin was added as a model drug. Physical chemical characterization showed that the incorporation of CaCO3 causes morphological changes in the biomateri...

Glycerol has become an ideal feedstock for the microbial production of bio-based chemicals due to its abundance, low cost, and high degree of reduction. We have previously reported the pathways and mechanisms for the utilization of glycerol by Escherichia coli in minimal salts medium under microaerobic conditions. Here we capitalize on such results...

Glycerol (or glycerin) is a byproduct of biodiesel, oleo - chemical, and bioethanol production processes. Due to the tremendous growth of the biofuel industry, glycerol is now regarded as a waste product, often with a disposal cost associated with it. Glycerol is abundant and inexpensive, and it is also a highly reduced molecule, which offers the o...

Although lignocellulosic sugars have been proposed as the primary feedstock for the biological production of renewable fuels and chemicals, the availability of fatty acid (FA)-rich feedstocks and recent progress in the development of oil-accumulating organisms make FAs an attractive alternative. In addition to their abundance, the metabolism of FAs...

The instability caused by fluctuations in oil prices and the undesirable damage that greenhouse gas emissions cause to the environment have encouraged the investigation of alternative platforms for the sustainable production of fuels from renewable sources. Recent advances in synthetic biology, metabolic engineering and plant and microbial genomics...