Standards. The building blocks of complexity

Without standards, the world as we know it would not be possible. International and supra-cultural standards and norms have been a key factor in engineering, as well as in the development of industrial societies. Despite the obvious successes in electronic and mechanical design, other technological areas present difficulties for the application of standards. In the field of biotechnology and synthetic biology – which aims at studying living things from an engineering perspective – standards are desirable, but whether they can be widely adopted remains to be proved.
 This monograph reviews the sociological and scientific aspects of standardisation and delves into the more problematic fa…

Controversies on the origin of life

Different viewpoints, many with deep philosophical and historical roots, have shaped the scientific study of the origin of life. Some of these argue that primeval life was based on simple anaerobic microorganisms able to use a wide inventory of abiotic organic materials (i.e. a heterotrophic origin), whereas others invoke a more sophisticated organization, one that thrived on simple inorganic molecules (i.e. an autotrophic origin). While many scientists assume that life started as a self-replicative molecule, the first gene, a primitive self-catalytic metabolic network has also been proposed as a starting point. Even the emergence of the cell itself is a contentious issue: did boundaries an…

Metabolic complementation in bacterial communities: Necessary conditions and optimality

Bacterial communities may display metabolic complementation, in which different members of the association partially contribute to the same biosynthetic pathway. In this way, the end product of the pathway is synthesized by the community as a whole. However, the emergence and the benefits of such complementation are poorly understood. Herein, we present a simple model to analyze the metabolic interactions among bacteria, including the host in the case of endosymbiotic bacteria. The model considers two cell populations, with both cell types encoding for the same linear biosynthetic pathway. We have found that, for metabolic complementation to emerge as an optimal strategy, both product inhib…

Microbial Diversity in the Midguts of Field and Lab-Reared Populations of the European Corn Borer Ostrinia nubilalis

Background: Insects are associated with microorganisms that contribute to the digestion and processing of nutrients. The European Corn Borer (ECB) is a moth present world-wide, causing severe economical damage as a pest on corn and other crops. In the present work, we give a detailed view of the complexity of the microorganisms forming the ECB midgut microbiota with the objective of comparing the biodiversity of the midgut-associated microbiota and explore their potential as a source of genes and enzymes with biotechnological applications. Methodological/Principal Findings: A high-throughput sequencing approach has been used to identify bacterial species, genes and metabolic pathways, parti…

A reconciliation with Darwin? Divergent views on evolutionism in Erich Wasmann and Jaime Pujiula, biologists and Jesuits

A diferencia del cas Galileu, l’esglesia Catolica ha gestionat amb discrecio el pensament evolucionista i les obres de Charles Darwin. Entre els cientifics catolics, hi trobem defensors d’un evolucionisme amanit amb remarcables excepcions relacionades amb l’origen divi de la vida i de l’especie humana. L’entomoleg i jesuita Erich Wasmann arriba a la conclusio que la teoria evolutiva podia donar explicacio a les seues observacions sobre els mirmecofils i adopta un evolucionisme catolicament matisat que Ernst Haeckel considerava fraudulent pero molt perillos. El bioleg i jesuita catala Jaume Pujiula segui l’obra de Wasmann tot i prenent posicions ideologiques mes radicals que la de l’entomole…

Comparative biochemistry of CO2 fixation and the evolution of autotrophy

Carbon dioxide fixation is a polyphyletic trait that has evolved in widely separated prokaryotic branches. The three principal CO2-assimilation pathways are (i) the reductive pentose-phosphate cycle, i. e. the Calvin-Benson cycle; (ii) the reductive citric acid (or Arnon) cycle; and (iii) the net synthesis of acetyl-CoA from CO/CO2, or Wood pathway. Sequence analysis and the comparative biochemistry of these routes suggest that all of them were shaped to a considerable extent by the evolutionary recruitment of enzymes. Molecular phylogenetic trees show that the Calvin-Benson cycle was a relatively late development in the (eu)bacterial branch, suggesting that some form(s) of carbon assimilat…

The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii

Background Bacterial symbioses are widespread among insects. The early establishment of such symbiotic associations has probably been one of the key factors for the evolutionary success of insects, since it may have allowed access to novel ecological niches and to new imbalanced food resources, such as plant sap or blood. Several genomes of bacterial endosymbionts of different insect species have been recently sequenced, and their biology has been extensively studied. Recently, the complete genome sequence of Candidatus Carsonella ruddii, considered the primary endosymbiont of the psyllid Pachpsylla venusta, has been published. This genome consists of a circular chromosome of 159,662 bp and…

Microbial communities of the Mediterranean rocky coast: ecology and biotechnological potential

AbstractMicrobial communities from harsh environments hold great promise as sources of biotechnologically-relevant strains. In the present work, we have deeply characterized the microorganisms from three different rocky locations of the Mediterranean coast, an environment characterised by being subjected to harsh conditions such as high levels of irradiation and large temperature and salinity fluctuations. Through culture-dependent and culture-independent techniques, we have retrieved a complete view of the ecology and functional aspects of these communities and assessed the biotechnological potential of the cultivable microorganisms. A culture-independent approach through high-throughput 1…

Evolutionary theory: it's on the school syllabus in Mexico

Kineococcus vitellinus sp. nov., Kineococcus indalonis sp. nov. and Kineococcus siccus sp. nov., isolated nearby the Tabernas desert (Almería, Spain)

This article belongs to the Section Environmental Microbiology.

Serratia symbiotica from the aphid Cinara cedri: a missing link from facultative to obligate insect endosymbiont.

The genome sequencing of Buchnera aphidicola BCc from the aphid Cinara cedri, which is the smallest known Buchnera genome, revealed that this bacterium had lost its symbiotic role, as it was not able to synthesize tryptophan and riboflavin. Moreover, the biosynthesis of tryptophan is shared with the endosymbiont Serratia symbiotica SCc, which coexists with B. aphidicola in this aphid. The whole-genome sequencing of S. symbiotica SCc reveals an endosymbiont in a stage of genome reduction that is closer to an obligate endosymbiont, such as B. aphidicola from Acyrthosiphon pisum, than to another S. symbiotica, which is a facultative endosymbiont in this aphid, and presents much less gene decay…

CONCEPTS IN BIOLOGY

Professor Henry C. Rebsamen, General Director of Normal Education, as proof of his great efforts for the advancement of the youth education, started the class in Concepts in Biology, doing us the honor of proposing a class in this interesting subject, and obtaining from the Ministry of Justice and Public Instruction their gracious respective appointment.

Standards. : The building blocks of complexity

Without standards, the world as we know it would not be possible. International and supra-cultural standards and norms have been a key factor in engineering, as well as in the development of industrial societies. Despite the obvious successes in electronic and mechanical design, other technological areas present difficulties for the application of standards. In the field of biotechnology and synthetic biology ??which aims at studying living things from an engineering perspective?? standards are desirable, but whether they can be widely adopted remains to be proved. This monograph reviews the sociological and scientific aspects of standardisation and delves into the more problematic facets o…

A genome-scale study of metabolic complementation in endosymbiotic consortia: the case of the cedar aphid

AbstractBacterial endosymbionts and their insect hosts establish an intimate metabolic relationship. Bacteria offer a variety of essential nutrients to their hosts, whereas insect cells provide the necessary sources of matter and energy to their tiny metabolic allies. These nutritional complementations sustain themselves on a diversity of metabolite exchanges between the cell host and the reduced yet highly specialized bacterial metabolism –which, for instance, overproduces a small set of essential amino acids and vitamins. A well-known case of metabolic complementation is provided by the cedar aphidCinara cedrithat harbors two co-primary endosymbionts,Buchnera aphidicolaBCc andCa.Serratia …

On the origin of life : an incomplete scientific story

La ciencia nunca se acaba

Transmetabolism: the non‐conformist approach to biotechnology

Research work of the author is funded by Agencia Estatal de Investigación (AEI), Ministerio de Ciencia e Innovación (grant SETH ref. RTI2018-095584-B-C41-42-43-44 co-financed by ERDF) and the European Union H2020 (BioRobooST project ID 210491758; MIPLACE project ref. PCI2019-111845-2, Programación Conjunta Internacional 2019, AEI).

Polar solar panels: Arctic and Antarctic microbiomes display similar taxonomic profiles

Solar panels located on high (Arctic and Antarctic) latitudes combine the harshness of the climate with that of the solar exposure. We report here that these polar solar panels are inhabited by similar microbial communities in taxonomic terms, dominated by Hymenobacter spp., Sphingomonas spp. and Ascomycota. Our results suggest that solar panels, even on high latitudes, can shape a microbial ecosystem adapted to irradiation and desiccation.

Belnapia mucosa sp. nov. and Belnapia arida sp. nov., isolated from desert biocrust

Two novel Gram-staining-negative, aerobic, cocci-shaped, non-motile, non-spore forming, pink-pigmented bacteria designated strains T6T and T18T, were isolated from a biocrust (biological soil crust) sample from the vicinity of the Tabernas Desert (Spain). Both strains were catalase-positive and oxidase-negative, and grew under mesophilic, neutrophilic and non-halophilic conditions. According to the 16S rRNA gene sequences, strains T6T and T18T showed similarities with Belnapia rosea CGMCC 1.10758T and Belnapia moabensis CP2CT (98.11 and 98.55% gene sequence similarity, respectively). The DNA G+C content was 69.80 and 68.96% for strains T6T and T18T, respectively; the average nucleotide iden…

Darwinism and the Origin of Life

Abstract Historically, ideas on the origins of life have been mingled with evolutionary explanations. Darwin avoided discussing the origin of the very first species in public although he acknowledged the possibility that life originated by natural causes. Some of his followers adopted this materialistic position and advocated some sort of spontaneous generation in the distant past. Nevertheless, Pasteur’s experiments were a major obstacle for scientific acceptance of the sudden emergence of life. The scientific study of the origin of life, established in the 1920s, required abandoning the idea of a unique chance event and considering a view of life emerging as the result of a long evolution…

Structural analyses of a hypothetical minimal metabolism

By integrating data from comparative genomics and large-scale deletion studies, we previously proposed a minimal gene set comprising 206 protein-coding genes. To evaluate the consistency of the metabolism encoded by such a minimal genome, we have carried out a series of computational analyses. Firstly, the topology of the minimal metabolism was compared with that of the reconstructed networks from natural bacterial genomes. Secondly, the robustness of the metabolic network was evaluated by simulated mutagenesis and, finally, the stoichiometric consistency was assessed by automatically deriving the steady-state solutions from the reaction set. The results indicated that the proposed minimal …

The source of gibberellins in the parthenocarpic development of ovaries on topped pea plants.

The role and source of gibberellins (GAs) involved in the development of parthenocarpic fruits of Pisum sativum L. has been investigated. Gibberellins applied to the leaf adjacent to an emasculated ovary induced parthenocarpic fruit development on intact plants. The application of gibberellic acid (GA3) had to be done within 1 d of anthesis to be fully effective and the response was concentration-dependent. Gibberellin A1 and GA3 worked equally well and GA20 was less efficient. [(3)H]Gibberellin A1 applied to the leaf accumulated in the ovary and the accumulation was related to the growth response. These experiments show that GA applied to the leaf in high enough concentration is translocat…

Nature lessons: the whitefly bacterial endosymbiont is a minimal amino acid factory with unusual energetics

Reductive genome evolution is a universal phenomenon observed in endosymbiotic bacteria in insects. As the genome reduces its size and irreversibly losses coding genes, the functionalities of the cell system, including the energetics processes, are more restricted. Several energetic pathways can also be lost. How do these reduced metabolic networks sustain the energy needs of the system? Among the bacteria with reduced genomes Candidatus Portiera aleyrodidarum, obligate endosymbiont of whiteflies, represents an extreme case since lacks several key mechanisms for ATP generation. Thus, to analyze the cell energetics in this system, a genome-scale metabolic model of this endosymbiont was const…

Determinism and contingency shape metabolic complementation in an endosymbiotic consortium

Bacterial endosymbionts and their insect hosts establish an intimate metabolic relationship. Bacteria offer a variety of essential nutrients to their hosts, whereas insect cells provide the necessary sources of matter and energy to their tiny metabolic allies. These nutritional complementations sustain themselves on a diversity of metabolite exchanges between the cell host and the reduced yet highly specialized bacterial metabolism-which, for instance, overproduces a small set of essential amino acids and vitamins. A well-known case of metabolic complementation is provided by the cedar aphid Cinara cedri that harbors two co-primary endosymbionts, Buchnera aphidicola BCc and Ca. Serratia sym…

Metabolic stasis in an ancient symbiosis: genome-scale metabolic networks from two Blattabacterium cuenoti strains, primary endosymbionts of cockroaches

Abstract Background Cockroaches are terrestrial insects that strikingly eliminate waste nitrogen as ammonia instead of uric acid. Blattabacterium cuenoti (Mercier 1906) strains Bge and Pam are the obligate primary endosymbionts of the cockroaches Blattella germanica and Periplaneta americana, respectively. The genomes of both bacterial endosymbionts have recently been sequenced, making possible a genome-scale constraint-based reconstruction of their metabolic networks. The mathematical expression of a metabolic network and the subsequent quantitative studies of phenotypic features by Flux Balance Analysis (FBA) represent an efficient functional approach to these uncultivable bacteria. Resul…

Genome Economization in the Endosymbiont of the Wood Roach Cryptocercus punctulatus Due to Drastic Loss of Amino Acid Synthesis Capabilities

Cockroaches (Blattaria: Dictyoptera) harbor the endosymbiont Blattabacterium sp. in their abdominal fat body. This endosymbiont is involved in nitrogen recycling and amino acid provision to its host. In this study, the genome of Blattabacterium sp. of Cryptocercus punctulatus (BCpu) was sequenced and compared with those of the symbionts of Blattella germanica and Periplaneta americana, BBge and BPam, respectively. The BCpu genome consists of a chromosome of 605.7 kb and a plasmid of 3.8 kb and is therefore approximately 31 kb smaller than the other two aforementioned genomes. The size reduction is due to the loss of 55 genes, 23 of which belong to biosynthetic pathways for amino acids. The …

The Software Crisis of Synthetic Biology

In fifteen years, Synthetic Biology (SB) has moved from proof-of-concept designs to several flagship achievements. Standardisation efforts are still under way, basic engineering concepts such as modularity and orthogonality are still controversial in biology, and making predictions from computer models is still unreliable. A deep characterization in the pattern of re-use of biological blocks in SB has not been attempted to date. We have compared the topological organisation of two different technological networks, one associated to a standard, large-scale software repository and the second provided by the Registry of Standard Biological Parts (RSBP). Our results strongly suggest that softwa…

Charles Darwin and the Origin of Life

When Charles Darwin published The Origin of Species 150 years ago he consciously avoided discussing the origin of life. However, analysis of some other texts written by Darwin, and of the correspondence he exchanged with friends and colleagues demonstrates that he took for granted the possibility of a natural emergence of the first life forms. As shown by notes from the pages he excised from his private notebooks, as early as 1837 Darwin was convinced that “the intimate relation of Life with laws of chemical combination, & the universality of latter render spontaneous generation not improbable”. Like many of his contemporaries, Darwin rejected the idea that putrefaction of preexisting organ…

Goethe's dream

The German philosopher Immanuel Kant (1724–1804) defined living organisms as objects with an intrinsic purpose, which are self‐organized in such a way that every part is a function of the whole and the whole is a function of every part, and in which “nothing is for nothing”. Kant already anticipated the tension between agency and structure, and between forward and backward causation. He also perceived living beings as entities that, being extremely complex, are not amenable to descriptions based on laws that are similar to the fundamental laws of physics: “There will never be a Newton of a grass blade,” he wrote. Less metaphorically, Kant believed that science would not be able to understan…

The young Ramón y Cajal as a cell-theory dissenter

Pereto Magraner, Juli, Juli.Pereto@uv.es

Blueprint for a minimal photoautotrophic cell: conserved and variable genes in Synechococcus elongatus PCC 7942.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License.-- et al.

Strategies for Making Life

Synthetic biology is a multifaceted discipline and the pathways towards an artificial cell are diverse. Top-down strategies seek simplification of genomes, their chemical synthesis and transplantation into a cell chassis. In the long term, scientists hope to have genomic platforms to reinvent metabolic networks capable of producing molecules of biotechnological interest. On the other hand, a bottom-up strategy relies on the chemical implementation of fundamental concepts such as self-reproduction, self-replication and self-maintaining systems. In addition to the artificial synthesis of simplified genomes and protocells, some scientists explore xenobiology, or making life as we do not know i…

ChemInform Abstract: Out of Fuzzy Chemistry: From Prebiotic Chemistry to Metabolic Networks

The origin of life on Earth was a chemical affair. So how did primitive biochemical systems originate from geochemical and cosmochemical processes on the young planet? Contemporary research into the origins of life subscribes to the Darwinian principle of material causes operating in an evolutionary context, as advocated by A. I. Oparin and J. B. S. Haldane in the 1920s. In its simplest form (e.g., a bacterial cell) extant biological complexity relies on the functional integration of metabolic networks and replicative genomes inside a lipid boundary. Different research programmes have explored the prebiotic plausibility of each of these autocatalytic subsystems and combinations thereof: sel…

Out of fuzzy chemistry: from prebiotic chemistry to metabolic networks

The origin of life on Earth was a chemical affair. So how did primitive biochemical systems originate from geochemical and cosmochemical processes on the young planet? Contemporary research into the origins of life subscribes to the Darwinian principle of material causes operating in an evolutionary context, as advocated by A. I. Oparin and J. B. S. Haldane in the 1920s. In its simplest form (e.g., a bacterial cell) extant biological complexity relies on the functional integration of metabolic networks and replicative genomes inside a lipid boundary. Different research programmes have explored the prebiotic plausibility of each of these autocatalytic subsystems and combinations thereof: sel…

What Is Life?

Despite the difficulty of defining a living being, biological sciences have considerably advanced. Today many authors feel the need to revisit the issue of the definition of life, among other reasons, because we are very close to have a second example of life. This life will not be the direct result of more than 3,500 million years of evolution, but the outcome of a project of synthetic biology in a laboratory. The fact that evolution has explored only a small part of the possible may pave the way towards alternative artificial lives. Focusing on the nature of life makes us more critical with the Cartesian comparisons between cells and machines. At the same time, progress in synthetic biolo…

The cockroach Blattella germanica obtains nitrogen from uric acid through a metabolic pathway shared with its bacterial endosymbiont.

Uric acid storedin the fat bodyof cockroaches is a nitrogen reservoirmobilized in times of scarcity. The discovery of urease in Blattabacterium cuenoti, the primary endosymbiont of cockroaches, suggests that the endosymbiont may participate in cockroach nitrogen economy. However, bacterial urease may only be one piece in the entire nitrogen recycling process from insect uric acid. Thus, in addition to the uricolytic pathway to urea, there must be glutamine synthetase assimilating the released ammonia by the urease reaction to enable the stored nitrogen to be metabolically usable. None of the Blattabacterium genomes sequenced to date possess genes encoding for those enzymes. To test the host…

Metabolic Networks of Sodalis glossinidius: A Systems Biology Approach to Reductive Evolution

BackgroundGenome reduction is a common evolutionary process affecting bacterial lineages that establish symbiotic or pathogenic associations with eukaryotic hosts. Such associations yield highly reduced genomes with greatly streamlined metabolic abilities shaped by the type of ecological association with the host. Sodalis glossinidius, the secondary endosymbiont of tsetse flies, represents one of the few complete genomes available of a bacterium at the initial stages of this process. In the present study, genome reduction is studied from a systems biology perspective through the reconstruction and functional analysis of genome-scale metabolic networks of S. glossinidius.ResultsThe functiona…

Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach.

Genome-scale metabolic models usually contain inconsistencies that manifest as blocked reactions and gap metabolites. With the purpose to detect recurrent inconsistencies in metabolic models, a large-scale analysis was performed using a previously published dataset of 130 genome-scale models. The results showed that a large number of reactions (~22%) are blocked in all the models where they are present. To unravel the nature of such inconsistencies a metamodel was construed by joining the 130 models in a single network. This metamodel was manually curated using the unconnected modules approach, and then, it was used as a reference network to perform a gap-filling on each individual genome-s…

Phylogenomic evidence for the presence of a flagellum and cbb(3) oxidase in the free-living mitochondrial ancestor.

The initiation of the intracellular symbiosis that would give rise to mitochondria and eukaryotes was a major event in the history of life on earth. Hypotheses to explain eukaryogenesis fall into two broad and competing categories: those proposing that the host was a phagocytotic proto-eukaryote that preyed upon the free-living mitochondrial ancestor (hereafter FMA), and those proposing that the host was an archaebacterium that engaged in syntrophy with the FMA. Of key importance to these hypotheses are whether the FMA was motile or nonmotile, and the atmospheric conditions under which the FMA thrived. Reconstructions of the FMA based on genome content of Rickettsiales representatives-gener…

La vida artificial abrirá las puertas a una nueva biología

Sphingomonas solaris sp. nov., isolated from a solar panel in Boston, Massachusetts

Solar panel surfaces, although subjected to a range of extreme environmental conditions, are inhabited by a diverse microbial community adapted to solar radiation, desiccation and temperature fluctuations. This is the first time a new bacterial species has been isolated from this environment. Strain R4DWNT belongs to the genus Sphingomonas and was isolated from a solar panel surface in Boston, MA, USA. Strain R4DWNT is a Gram-negative, non-motile and rod-shaped bacteria that tested positive for oxidase and catalase and forms round-shaped, shiny and orange-coloured colonies. It is mesophilic, neutrophilic and non-halophilic, and presents a more stenotrophic metabolism than its closest neighb…

The iGEM Competition

The international Genetically Engineered Machine (iGEM) competition is a well-known example of synthetic biology and a workbench for the development of heterodox, multidisciplinary and frontier work made by undergraduate students. We review the origin, organization and structure of the competition; we describe how an iGEM team can be set in place, and briefly summarize some of the main milestones and challenges of a competition that is only one decade old. We discuss the links of the competition with the Registry of Standard Biological Parts and the flagship role of iGEM as a very trench of the synthetic biology revolution.

A universal definition of life: autonomy and open-ended evolution.

Life is a complex phenomenon that not only requires individual self-producing and self- sustaining systems but also a historical-collective organization of those individual systems, which brings about characteristic evolutionary dynamics. On these lines, we propose to define univer- sally living beings as autonomous systems with open-ended evolution capacities, and we claim that all such systems must have a semi-permeable active boundary (membrane), an energy trans- duction apparatus (set of energy currencies) and, at least, two types of functionally interdependent macromolecular components (catalysts and records). The latter is required to articulate a 'phenotype- genotype' decoupling that…

Synthetic Biology in Action

Last decade has witnessed remarkable advances towards the engineering of life. The examples range from the design of an efficient cellular factory for the semi-synthesis of the antimalarial drug artemisinin, to the chemical synthesis of chromosomes, both bacterial and eukaryotic. In parallel, advances in the deep characterization of cell machineries in the simplest cells show that we are very far of fully understanding the regulation of metabolic and genetic circuits. Biological emergent properties and noise may suppose an obstacle for predictive design. Besides the obvious biotechnological benefits of synthetic biology, the path towards the artificial cell will report new insights on the e…

Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti

Abstract Background Metabolic reconstruction is the computational-based process that aims to elucidate the network of metabolites interconnected through reactions catalyzed by activities assigned to one or more genes. Reconstructed models may contain inconsistencies that appear as gap metabolites and blocked reactions. Although automatic methods for solving this problem have been previously developed, there are many situations where manual curation is still needed. Results We introduce a general definition of gap metabolite that allows its detection in a straightforward manner. Moreover, a method for the detection of Unconnected Modules, defined as isolated sets of blocked reactions connect…

Prokaryotic symbiotic consortia and the origin of nucleated cells: A critical review of Lynn Margulis hypothesis.

The publication in the late 1960s of Lynn Margulis endosymbiotic proposal is a scientific milestone that brought to the fore of evolutionary discussions the issue of the origin of nucleated cells. Although it is true that the times were ripe, the timely publication of Lynn Margulis' original paper was the product of an intellectually bold 29-years old scientist, who based on the critical analysis of the available scientific information produced an all-encompassing, sophisticated narrative scheme on the origin of eukaryotic cells as a result of the evolution of prokaryotic consortia and, in bold intellectual stroke, put it all in the context of planetary evolution. A critical historical reas…

Extremophilic microbial communities on photovoltaic panel surfaces: a two‐year study

Solar panel surfaces can be colonized by microorganisms adapted to desiccation, temperature fluctuations and solar radiation. Although the taxonomic and functional composition of these communities has been studied, the microbial colonization process remains unclear. In the present work, we have monitored this microbial colonization process during 24 months by performing weekly measurements of the photovoltaic efficiency, carrying out 16S rRNA gene high‐throughput sequencing, and studying the effect of antimicrobial compounds on the composition of the microbial biocenosis. This is the first time a long‐term study of the colonization process of solar panels has been performed, and our results…

What Is Synthetic Biology?

Synthetic biology aims at the design and construction of biological devices and systems for useful purposes. From an ideal engineering perspective synthetic biology works from rational design made through a few conceptual pillars, namely abstraction, standardization and modularity. Nevertheless, the combination of our still fragmentary biological knowledge and the messy nature of biological devices are major challenges for engineering life in a predictive manner. It is urgent to build bridges between different disciplines, from biology to engineer and back, to pursue this extraordinary goal of making life.

Standards not that standard

There is a general assent on the key role of standards in Synthetic Biology. In two consecutive letters to this journal, suggestions on the assembly methods for the Registry of standard biological parts have been described. We fully agree with those authors on the need of a more flexible building strategy and we highlight in the present work two major functional challenges standardization efforts have to deal with: the need of both universal and orthogonal behaviors. We provide experimental data that clearly indicate that such engineering requirements should not be taken for granted in Synthetic Biology. Electronic supplementary material The online version of this article (doi:10.1186/s1303…

Hormone directed sucrose transport during fruit set induced by gibberellins in Pisum sativum

A new system has been developed to study hormone-directed transport in intact plants during parthenocarpic fruit set induced by gibberellins. Gibberellic acid (GA3) and gibberellin A1 (GA1) applied to unpollinated ovaries of pea (Pisum sativum L. cv. Alaska) promoted sucrose transport from the leaf to the site of hormone application. In vivo experiments showed an early (30 min) accumulation of [14C]-sucrose in ovaries of pea stimulated by gibberellins. This activation of sucrose transport appears to be mediated by gibberellins (GA1, GA3), increasing both loading of phloem with sucrose in the leaf (source) and sucrose unloading in the ovary (sink). The ability of pea tissue segments to take …

Should the teaching of biological evolution include the origin of life?

The development of mainstream research on the origin of life as an outcome of Darwinian evolution is discussed. It is argued that prebiotic evolution and the origin of life should not be excluded from the syllabus and should be part of classes on biological evolution, and that the transition from non-living to living matter is best understood when seen as part of evolutionary biology. The wide acceptance of evolutionary approaches to the study of the emergence of life in European and Latin American countries is discussed.

Comparative Genomics of Blattabacterium cuenoti: The Frozen Legacy of an Ancient Endosymbiont Genome

Many insect species have established long-term symbiotic relationships with intracellular bacteria. Symbiosis with bacteria has provided insects with novel ecological capabilities, which have allowed them colonize previously unexplored niches. Despite its importance to the understanding of the emergence of biological complexity, the evolution of symbiotic relationships remains hitherto a mystery in evolutionary biology. In this study, we contribute to the investigation of the evolutionary leaps enabled by mutualistic symbioses by sequencing the genome of Blattabacterium cuenoti, primary endosymbiont of the omnivorous cockroach Blatta orientalis, and one of the most ancient symbiotic associa…

The rose and the name: the unresolved debate on biotechnological terms

The largest survey on the perception of synthetic biology‐related disciplines (Porcar et al., 2019,EMBO Rep 20) recently revealed that the Spanish society does not have a very positive perception of the term synthetic biology. On the other hand, the terms biotechnology and even genetic engineering received relatively higher scores. The issue of nomenclature and perception is a classical one in science perception studies. Synthetic biologists have been debating their neologism (Synthetic Biology, from now on SB) for years. Even in a 2006 blog, Rob Carlson discussed the various labels for the new field, such as intentional biology, constructive biology, natural engineering, synthetic genomics…

A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city

AbstractMicroorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the …

Wobble Hypothesis (Genetics)

Gene connectivity and enzyme evolution in the human metabolic network

[Background] Determining the factors involved in the likelihood of a gene being under adaptive selection is still a challenging goal in Evolutionary Biology. Here, we perform an evolutionary analysis of the human metabolic genes to explore the associations between network structure and the presence and strength of natural selection in the genes whose products are involved in metabolism. Purifying and positive selection are estimated at interspecific (among mammals) and intraspecific (among human populations) levels, and the connections between enzymatic reactions are differentiated between incoming (in-degree) and outgoing (out-degree) links.

On the origin of mitosing cells: A historical appraisal of Lynn Margulis endosymbiotic theory

Although for a long-time symbiosis was considered to be quite rare and with no role in evolutionary processes, Lynn Margulis demonstrated that endosymbiotic events played a key role in the origin and evolution of eukaryotic cells. Starting with her seminal assay in the Journal of Theoretical Biology in 1967 (authored as Lynn Sagan), her lifelong work on eukaryogenesis and the role of symbiosis in evolution stands as a valid and authoritative contribution to science. As was quick to acknowledge, she was not the first to discuss the significance of symbiosis to explain the origin of mitochondria and chloroplasts, but no one else had done it to her extent and depth, nor had anyone provided a v…

A reconciliation with Darwin? : Erich Wasmann and Jaime Pujiula's divergent views on evolutionism: biologists and jesuits

Unlike the case of Galileo, the Catholic Church has managed evolutionism and Charles Darwin?s work with discretion. Among Catholic scientists, some defend a variety of evolutionism which is peppered with remarkable exceptions, such as the divine origin of life and of the human species. The Jesuit entomologist Erich Wasmann came to the conclusion that the evolutionary theory could explain his observations about myrmecophiles, so he adopted a Catholicism-tinged evolutionism, which Ernst Haeckel considered false and very dangerous. The Jesuit biologist from Catalonia, Jaime Pujiula, continued Wasmann?s work but adopted stances that were more radical than the Austrian entomologist?s, like invok…

Vida fabricada

Des que la biologia es va secularitzar i inicia l’escrutini molecular de la vida, la possibilitat de la sintesi artificial de cel·lules vivents en un laboratori fou palpable. La biologia sintetica contemporania aspira a dissenyar i fabricar noves formes de vida amb la intencio d’obtenir beneficis socials i economics, tot i que no s’ha de descartar que tambe obtindrem, per la via sintetica, recompenses cientifiques en termes d’una major comprensio de la complexitat biologica a les quals no podriem accedir per la via analitica. Es clar, per tant, que biologia sintetica es un terme que desperta expectatives, pero no es menys cert que tambe provoca inquietud. El Forum Economic Mundial ha situat…

Designing a Simulation Model of a Self-Maintaining Cellular System

This paper deals with the problem of finding a suitable framework for designing computer simulations that could help us determine the minimal requirements (both material and organizational) for the origin of the first full-fledged autonomous systems. The design of a particular model that takes into account some fundamental thermodynamic requirements is offered and discussed. Behind this work, there is a belief that Artificial Life models can inform biology on several fundamental questions (such as the origin and definition of life) but only provided that they assume more realistic and grounded premises to lead us to more conclusive results.

A Strategy for Origins of Life Research

Contents 1. Introduction 1.1. A workshop and this document 1.2. Framing origins of life science 1.2.1. What do we mean by the origins of life (OoL)? 1.2.2. Defining life 1.2.3. How should we characterize approaches to OoL science? 1.2.4. One path to life or many? 2. A Strategy for Origins of Life Research 2.1. Outcomes—key questions and investigations 2.1.1. Domain 1: Theory 2.1.2. Domain 2: Practice 2.1.3. Domain 3: Process 2.1.4. Domain 4: Future studies 2.2. EON Roadmap 2.3. Relationship to NASA Astrobiology Roadmap and Strategy documents and the European AstRoMap  Appendix I  Appendix II  Supplementary Materials  References

Engineering Bacteria to Form a Biofilm and Induce Clumping in Caenorhabditis elegans

Bacteria are needed for a vast range of biotechnological processes, which they carry out either as pure cultures or in association with other bacteria and/or fungi. The potential of bacteria as biofactories is hampered, though, by their limited mobility in solid or semisolid media such as agricultural or domestic waste. This work represents an attempt toward overcoming this limitation by associating bacterial biotechnological properties with the transport ability of the nematode Caenorhabditis elegans. We report here biofilm formation on C. elegans by engineered Escherichia coli expressing a Xhenorhabdus nematophila adhesion operon and induction of nematode social feeding behavior (clumping…

¿Tras el genoma, qué? [Ressenya]

Reseña de los libros: "La conquista del genoma humano. Craig Venter, Francis Collins, James Watson y la historia del mayor descubrimiento científico de nuestra época" de Kevin Davies, Paidós, 2001 y "The Common Thread. A story of science, politics, ethics and the human genome" de John Sulston y Georgina Ferry, Bantman Press, 2002.

High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert.

One of the most diverse ecological niches for microbial bioprospecting is soil, including that of drylands. Drylands are one of the most abundant biomes on Earth, but extreme cases, such as deserts, are considered very rare in Europe. The so-called Tabernas Desert is one of the few examples of a desert area in continental Europe, and although some microbial studies have been performed on this region, a comprehensive strategy to maximize the isolation of environmental bacteria has not been conducted to date. We report here a culturomics approach to study the bacterial diversity of this dryland by using a simple strategy consisting of combining different media, using serial dilutions of the n…

Evolutionary convergence and nitrogen metabolism in Blattabacterium strain Bge, primary endosymbiont of the cockroach Blattella germanica.

Bacterial endosymbionts of insects play a central role in upgrading the diet of their hosts. In certain cases, such as aphids and tsetse flies, endosymbionts complement the metabolic capacity of hosts living on nutrient-deficient diets, while the bacteria harbored by omnivorous carpenter ants are involved in nitrogen recycling. In this study, we describe the genome sequence and inferred metabolism of Blattabacterium strain Bge, the primary Flavobacteria endosymbiont of the omnivorous German cockroach Blattella germanica. Through comparative genomics with other insect endosymbionts and free-living Flavobacteria we reveal that Blattabacterium strain Bge shares the same distribution of functio…

Influence of pathway topology and functional class on the molecular evolution of human metabolic genes

Metabolic networks comprise thousands of enzymatic reactions functioning in a controlled manner and have been shaped by natural selection. Thanks to the genome data, the footprints of adaptive (positive) selection are detectable, and the strength of purifying selection can be measured. This has made possible to know where, in the metabolic network, adaptive selection has acted and where purifying selection is more or less strong and efficient. We have carried out a comprehensive molecular evolutionary study of all the genes involved in the human metabolism. We investigated the type and strength of the selective pressures that acted on the enzyme-coding genes belonging to metabolic pathways …

Learning how to live together: genomic insights into prokaryote–animal symbioses

Our understanding of prokaryote-eukaryote symbioses as a source of evolutionary innovation has been rapidly increased by the advent of genomics, which has made possible the biological study of uncultivable endosymbionts. Genomics is allowing the dissection of the evolutionary process that starts with host invasion then progresses from facultative to obligate symbiosis and ends with replacement by, or coexistence with, new symbionts. Moreover, genomics has provided important clues on the mechanisms driving the genome-reduction process, the functions that are retained by the endosymbionts, the role of the host, and the factors that might determine whether the association will become parasitic…

Toward minimal bacterial cells: evolution vs. design.

Abstract Recent technical and conceptual advances in the biological sciences opened the possibility of the construction of newly designed cells. In this paper we review the state of the art of cell engineering in the context of genome research, paying particular attention to what we can learn on naturally reduced genomes from either symbiotic or free living bacteria. Different minimal hypothetically viable cells can be defined on the basis of several computational and experimental approaches. Projects aiming at simplifying living cells converge with efforts to make synthetic genomes for minimal cells. The panorama of this particular view of synthetic biology lead us to consider the use of d…

Crystals and the debates on the nature, recognition and origin of life

Determination of the Core of a Minimal Bacterial Gene Set

SUMMARY The availability of a large number of complete genome sequences raises the question of how many genes are essential for cellular life. Trying to reconstruct the core of the protein-coding gene set for a hypothetical minimal bacterial cell, we have performed a computational comparative analysis of eight bacterial genomes. Six of the analyzed genomes are very small due to a dramatic genome size reduction process, while the other two, corresponding to free-living relatives, are larger. The available data from several systematic experimental approaches to define all the essential genes in some completely sequenced bacterial genomes were also considered, and a reconstruction of a minima…

Embden-Meyerhof-Parnas Pathway

Calvin-Benson Cycle

A carbon dioxide fixation pathway where a molecule of CO2 condenses with a 5-C compound (ribulose 1,5-bisphosphate) to yield two molecules of a 3-C compound (3-phosphoglycerate). These 3-C molecules serve both as precursors for biosynthesis and, through a cyclic series of enzymatic reactions, to regenerate the 5-C molecule necessary for the first carboxylating step (Fig. 1). The pathway is present in several bacterial lineages (e.g., cyanobacteria), and its acquisition by eukaryotic cells (chloroplast in algae and plants) was through the endosymbiotic association with ancient cyanobacteria.

PLASMOGENY, A NEW SCIENCE OF THE ORIGIN OF LIFE

The Church has always hampered the progress of Mankind so as to retain its hold over awareness, which is the basis of secular exploitation of the people.

Controversies on the origin of life

Different viewpoints, many with deep philosophical and historical roots, have shaped the scientific study of the origin of life. Some of these argue that primeval life was based on simple anaerobic microorganisms able to use a wide inventory of abiotic organic materials (i.e. a heterotrophic origin), whereas others invoke a more sophisticated organization, one that thrived on simple inorganic molecules (i.e. an autotrophic origin). While many scientists assume that life started as a self-replicative molecule, the first gene, a primitive self-catalytic metabolic network has also been proposed as a starting point. Even the emergence of the cell itself is a contentious issue: did boundaries an…

Citric Acid Cycle

¿Hacia la fabricación de vida?

Evelyn Fox Keller

Book review: The Ethics of Protocells: Moral and Social Implications of Creating Life in the Laboratory

Microbial communities of the Mediterranean rocky shore: ecology and biotechnological potential of the sea‐land transition

Microbial communities from harsh environments hold great promise as sources of biotechnologically relevant strains and compounds. In the present work, we have characterized the microorganisms from the supralittoral and splash zone in three different rocky locations of the Western Mediterranean coast, a tough environment characterized by high levels of irradiation and large temperature and salinity fluctuations. We have retrieved a complete view of the ecology and functional aspects of these communities and assessed the biotechnological potential of the cultivable microorganisms. All three locations displayed very similar taxonomic profiles, with the genus Rubrobacter and the families Xenoco…

Nature versus design: synthetic biology or how to build a biological non-machine.

The engineering ideal of synthetic biology presupposes that organisms are composed of standard, interchangeable parts with a predictive behaviour. In one word, organisms are literally recognized as machines. Yet living objects are the result of evolutionary processes without any purposiveness, not of a design by external agents. Biological components show massive overlapping and functional degeneracy, standard-free complexity, intrinsic variation and context dependent performances. However, although organisms are not full-fledged machines, synthetic biologists may still be eager for machine-like behaviours from artificially modified biosystems.

Can life be standardized? Current challenges in biological standardization

The concept of standard strongly evokes machines, industries, electric or mechanical devices, vehicles, or furniture. Indeed, our technological civilization would not be possible – at least in the terms it is structured today – without universal, reliable components, whose acknowledged use results in competitive costs, robustness and interchangeability. For example, an Ikea screw can be used in a wide set of structurally dissimilar furniture and an app can be run on many different smartphones. The very concept of standardization is linked to the industrial revolution and mass production of goods through assembly lines. The question we will try to answer in the present paper is the extent to…

From grass to gas: microbiome dynamics of grass biomass acidification under mesophilic and thermophilic temperatures

Background Separating acidification and methanogenic steps in anaerobic digestion processes can help to optimize the process and contribute to producing valuable sub-products such as methane, hydrogen and organic acids. However, the full potential of this technology has not been fully explored yet. To assess the underlying fermentation process in more detail, a combination of high-throughput sequencing and proteomics on the acidification step of plant material (grass) at both mesophilic and thermophilic temperatures (37 and 55 °C, respectively) was applied for the first time. Results High-strength liquor from acidified grass biomass exhibited a low biodiversity, which differed greatly depen…

Yeast cultures with UCP1 uncoupling activity as a heating device

7 páginas, 5 figuras, 3 tablas -- PAGS nros. 300-306

Bioprospecting the solar panel microbiome: High-throughput screening for antioxidant bacteria in a caenorhabditis elegansModel

Microbial communities that are exposed to sunlight typically share a series of adaptations to deal with the radiation they are exposed to, including efficient DNA repair systems, pigment production and protection against oxidative stress, which makes these environments good candidates for the search of novel antioxidant microorganisms. In this research project, we isolated potential antioxidant pigmented bacteria from a dry and highly-irradiated extreme environment: solar panels. High-throughput in vivo assays using Caenorhabditis elegans as an experimental model demonstrated the high antioxidant and ultraviolet-protection properties of these bacterial isolates that proved to be rich in car…