Implementing re-configurable biological computation with distributed multicellular consortia

The use of synthetic biological circuits to deal with numerous biological challenges has been proposed in several studies, but its implementation is still remote. A major problem encountered is the complexity of the cellular engineering needed to achieve complex biological circuits and the lack of general-purpose biological systems. The generation of re-programmable circuits can increase circuit flexibility and the scalability of complex cell-based computing devices. Here we present a new architecture to produce reprogrammable biological circuits that allow the development of a variety of different functions with minimal cell engineering. We demonstrate the feasibility of creating several circuits using only a small set of engineered cells, which can be externally reprogrammed to implement simple logics in response to specific inputs. In this regard, depending on the computation needs, a device composed of a number of defined cells can generate a variety of circuits without the need of further cell engineering or rearrangements. In addition, the inclusion of a memory module in the circuits strongly improved the digital response of the devices. The reprogrammability of biological circuits is an intrinsic capacity that is not provided in electronics and it may be used as a tool to solve complex biological problems.

Development and evaluation of culture media based on extracts of the cyanobacterium Arthrospira platensis

Continuous advances in the fields of industrial biotechnology and pharmacy require the development of new formulations of culture media based on new nutrient sources. These new sources must be sustainable, high yielding, and non-animal-based, with minimal environmental impact. Thus, culture media prepared from cyanobacterial extracts can be an interesting alternative to the current formulations. In this study, we prepared various minimal formulations of culture media using the extracts of Arthrospira platensis, and analyzed the efficiency of these formulations, based on their effect on the production of biomass and molecules of industrial interest, using different types of bacteria. All media formulations prepared in this study showed better performance than conventional media, including those based on animal ingredients. Thus, based on their versatility and high-yielding capacity, we conclude that culture media prepared from cyanobacterial extracts are a good alternative to conventional media for meeting the current demands of the cosmetic and pharmaceutical industries.

Two-Component Biosensors: Unveiling the Mechanisms of Predictable Tunability

Many studies have been devoted to the engineering of cellular biosensors by exploiting intrinsic natural sensors. However, biosensors rely not only on input detection but also on an adequate response range. It is therefore often necessary to tune natural systems to meet the demands of specific applications in a predictable manner. In this study, we explored the customizability of two-component bacterial biosensors by modulating the main biosensor component, i.e., the receptor protein. We developed a mathematical model that describes the functional relationship between receptor abundance and activation threshold, sensitivity, dynamic range, and operating range. The defined mathematical framework allows the design of the genetic architecture of a two-component biosensor that can perform as required with minimal genetic engineering. To experimentally validate the model and its predictions, a library of biosensors was constructed. The good agreement between theoretical designs and experimental results indicates that modulation of receptor protein abundance allows optimization of biosensor designs with minimal genetic engineering.

Plug-and-Play Multicellular Circuits with Time-Dependent Dynamic Responses

Synthetic biology studies aim to develop cellular devices for biomedical applications. These devices, based on living instead of electronic or electromechanic technology, might provide alternative treatments for a wide range of diseases. However, the feasibility of these devices depends, in many cases, on complex genetic circuits that must fulfill physiological requirements. In this work, we explored the potential of multicellular architectures to act as an alternative to complex circuits for implementation of new devices. As a proof of concept, we developed specific circuits for insulin or glucagon production in response to different glucose levels. Here, we show that fundamental features, such as circuit's affinity or sensitivity, are dependent on the specific configuration of the multicellular consortia, providing a method for tuning these properties without genetic engineering. As an example, we have designed and built circuits with an incoherent feed-forward loop architecture (FFL) that can be easily adjusted to generate single pulse responses. Our results might serve as a blueprint for future development of cellular devices for glycemia regulation in diabetic patients.

Synthetic associative learning in engineered multicellular consortia

Associative learning (AL) is one of the key mechanisms displayed by living organisms in order to adapt to their changing environments. It was recognized early as a general trait of complex multicellular organisms but is also found in 'simpler' ones. It has also been explored within synthetic biology using molecular circuits that are directly inspired in neural network models of conditioning. These designs involve complex wiring diagrams to be implemented within one single cell, and the presence of diverse molecular wires become a challenge that might be very difficult to overcome. Here we present three alternative circuit designs based on two-cell microbial consortia able to properly display AL responses to two classes of stimuli and displaying long- and short-term memory (i.e. the association can be lost with time). These designs might be a helpful approach for engineering the human gut microbiome or even synthetic organoids, defining a new class of decision-making biological circuits capable of memory and adaptation to changing conditions. The potential implications and extensions are outlined.

A Synthetic Multicellular Memory Device

Changing environments pose a challenge to living organisms. Cells need to gather and process incoming information, adapting to changes in predictable ways. This requires in particular the presence of memory, which allows different internal states to be stored. Biological memory can be stored by switches that retain information on past and present events. Synthetic biologists have implemented a number of memory devices for biological applications, mostly in single cells. It has been shown that the use of multicellular consortia provides interesting advantages to implement biological circuits. Here we show how to build a synthetic biological memory switch using an eukaryotic consortium. We engineered yeast cells that can communicate and retain memory of changes in the extracellular environment. These cells were able to produce and secrete a pheromone and sense a different pheromone following NOT logic. When the two strains were cocultured, they behaved as a double-negative-feedback motif with memory. In addition, we showed that memory can be effectively changed by the use of external inputs. Further optimization of these modules and addition of other cells could lead to new multicellular circuits that exhibit memory over a broad range of biological inputs.

Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia

Engineered synthetic biological devices have been designed to perform a variety of functions from sensing molecules and bioremediation to energy production and biomedicine. Notwithstanding, a major limitation of in vivo circuit implementation is the constraint associated to the use of standard methodologies for circuit design. Thus, future success of these devices depends on obtaining circuits with scalable complexity and reusable parts. Here we show how to build complex computational devices using multicellular consortia and space as key computational elements. This spatial modular design grants scalability since its general architecture is independent of the circuit’s complexity, minimizes wiring requirements and allows component reusability with minimal genetic engineering. The potential use of this approach is demonstrated by implementation of complex logical functions with up to six inputs, thus demonstrating the scalability and flexibility of this method. The potential implications of our results are outlined.

Synthetic biological circuits have been built for different purposes. Nevertheless, the way these devices have been designed so far present several limitations: complex genetic engineering is required to implement complex circuits, and once the parts are built, they are not reusable. We proposed to distribute the computation in several cellular consortia that are physically separated, thus ensuring implementation of circuits independently of their complexity and using reusable components with minimal genetic engineering. This approach allows an easy implementation of multicellular computing devices for secretable inputs or biosensing purposes.

Computational implementation of a tunable multicellular memory circuit for engineered eukaryotic consortia

Cells are complex machines capable of processing information by means of an entangled network of molecular interactions. A crucial component of these decision-making systems is the presence of memory and this is also a specially relevant target of engineered synthetic systems. A classic example of memory devices is a 1-bit memory element known as the flip-flop. Such system can be in principle designed using a single-cell implementation, but a direct mapping between standard circuit design and a living circuit can be cumbersome. Here we present a novel computational implementation of a 1-bit memory device using a reliable multicellular design able to behave as a set-reset flip-flop that could be implemented in yeast cells. The dynamics of the proposed synthetic circuit is investigated with a mathematical model using biologically-meaningful parameters. The circuit is shown to behave as a flip-flop in a wide range of parameter values. The repression strength for the NOT logics is shown to be crucial to obtain a good flip-flop signal. Our model also shows that the circuit can be externally tuned to achieve different memory states and dynamics, such as persistent and transient memory. We have characterized the parameter domains for robust memory storage and retrieval as well as the corresponding time response dynamics.

How to make a synthetic multicellular computer

Biological systems perform computations at multiple scales and they do so in a robust way. Engineering metaphors have often been used in order to provide a rationale for modeling cellular and molecular computing networks and as the basis for their synthetic design. However, a major constraint in this mapping between electronic and wet computational circuits is the wiring problem. Although wires are identical within electronic devices, they must be different when using synthetic biology designs. Moreover, in most cases the designed molecular systems cannot be reused for other functions. A new approximation allows us to simplify the problem by using synthetic cellular consortia where the output of the computation is distributed over multiple engineered cells. By evolving circuits in silico, we can obtain the minimal sets of Boolean units required to solve the given problem at the lowest cost using cellular consortia. Our analysis reveals that the basic set of logic units is typically non-standard. Among the most common units, the so called inverted IMPLIES (N-Implies) appears to be one of the most important elements along with the NOT and AND functions. Although NOR and NAND gates are widely used in electronics, evolved circuits based on combinations of these gates are rare, thus suggesting that the strategy of combining the same basic logic gates might be inappropriate in order to easily implement synthetic computational constructs. The implications for future synthetic designs, the general view of synthetic biology as a standard engineering domain, as well as potencial drawbacks are outlined.

Dynamic signaling in the Hog1 MAPK pathway relies on high basal signal transduction

Appropriate regulation of the Hog1 mitogen-activated protein kinase (MAPK) pathway is essential for cells to survive osmotic stress. Here, we show that the two sensing mechanisms upstream of Hog1 display different signaling properties. The Sho1 branch is an inducible nonbasal system, whereas the Sln1 branch shows high basal signaling that is restricted by a MAPK-mediated feedback mechanism. A two-dimensional mathematical model of the Snl1 branch, including high basal signaling and a Hog1-regulated negative feedback, shows that a system with basal signaling exhibits higher efficiency, with faster response times and higher sensitivity to variations in external signals, than would systems without basal signaling. Analysis of two other yeast MAPK pathways, the Fus3 and Kss1 signaling pathways, indicates that high intrinsic basal signaling may be a general property of MAPK pathways allowing rapid and sensitive responses to environmental changes.

Distributed robustness in cellular networks: insights from synthetic evolved circuits

Evolved natural systems are known to display some sort of distributed robustness against the loss of individual components. Such type of robustness is not just the result of redundancy. Instead, it seems to be based on degeneracy, i.e. the ability of elements that are structurally different to perform the same function or yield the same output. Here, we explore the problem of how relevant is degeneracy in a class of evolved digital systems formed by NAND gates, and what types of network structures underlie the resilience of evolved designs to the removal or loss of a given unit. It is shown that our fault tolerant circuits are obtained only if robustness arises in a distributed manner. No such reliable systems were reached just by means of redundancy, thus suggesting that reliable designs are necessarily tied to degeneracy.

Circumcision and neonatal tetanus: disclosure of risk and its reduction by topical antibiotics

BACKGROUND

Previous case-control studies have paradoxically suggested that circumcisions protect against neonatal tetanus (NNT), but these observations have not been adjusted for differences in the length of survival of cases and controls.

METHODS

Boy cases (n = 133) and their sex-matched controls (n = 399) were extracted from a population-based study of NNT undertaken in Punjab Province, Pakistan. In the resulting file, circumcisions were censored such that analysis was restricted to only those that occurred before onset in cases or before age of onset in the matched case for controls. The effect of topical antibiotics in circumcision wounds was then evaluated.

RESULTS

After adjusting for confounders, circumcision before onset posed a significant risk for NNT (matched odds ratio [OR] = 3.1, 95% CI: 1.2-8.0). The risk of NNT in those circumcised before onset and treated with topical antibiotics did not differ significantly from the referent group who had not been circumcised before onset (matched OR = 1.1, 95% CI: 0.2-6.8), whereas the lack of topical use was associated with significant risk (matched OR = 4.2, 95% CI: 1.4-12.6). This suggests that topical antibiotics are likely to be highly effective in preventing NNT from circumcision wounds. We estimated an overall risk of about 16 fatal NNT cases per 1000 live boy births with circumcision wounds that were not protected by topical antibiotics, and that circumcision and umbilical wounds each accounted for about half of this overall risk in these boys.

CONCLUSIONS

Topical antibiotics should be routinely applied to all wounds created by traditional circumcisions, to prevent NNT and sepsis from these frequently unsterile procedures.

Protective effects of topical antimicrobials against neonatal tetanus

BACKGROUND

Case-control studies previously conducted in Pakistan suggested that topical antimicrobials might provide protection against neonatal tetanus (NNT) when applied to the umbilical cord wound during the first several days of life. The present case-control study, the largest such study yet reported, was undertaken in Punjab Province, Pakistan and afforded further opportunities to evaluate such effects.

METHODS

A population-based, matched, case-control study was undertaken to assess topical antimicrobials and other factors related to NNT risk in rural parts of Punjab Province.

RESULTS

Continuous use of antimicrobial agents (antibiotics and antiseptics) at delivery and during the first few days after delivery was highly protective in univariate testing (matched odds ratio 0.2 [95% confidence interval: 0.11-0.64], P = 0.003), and remained significantly protective when other delivery and cord care practices were controlled. In contrast, applying nothing to the wound was risky compared with antimicrobial exposures. Hand washing and delivery by a trained birth attendant appeared protective. Application of animal dung or ash to the umbilical wound was hazardous. Similarly, predelivery cutaneous or intravaginal exposure of mothers to ghee (clarified butter) and delivery on a surface prepared with dried cow dung were risky, with significant interaction noted between them. Mortality and NNT were far more likely among previous births to mothers of cases.

CONCLUSIONS

Topical antimicrobials offer a new, effective and inexpensive means to prevent NNT, and could usefully complement maternal immunization with tetanus toxoid in controlling the disease. Special prevention efforts should be directed towards mothers of NNT cases.

Value of the determination of TNF-alpha in the plasma of patients with non-Hodgkins lymphoma

The present report describes the value of the plasma determination of TNF-alpha, at diagnosis, in 43 patients with non-Hodgkin's lymphoma (NHL), related to their clinical presentation and the new International Prognosis Index (IPI). We also compare the levels of TNF-alpha with those of LDH, beta-2-microglobulin (beta-2-m), and ferritin. At diagnosis, the mean values of the quotients between the marker values and the maximum value of normal (ratio:r-) are placed 7 times higher than normal for r-TNF-alpha, whereas those of r-beta-2-m and r-LDH are 2,4 and 1,4 times more respectively. We found a relationship between the value of r-TNF-alpha and the ECOG, Ann Arbor stage, the number of affected extranodal sites, and between the values of r-beta-2-m with r-LDH. The best correlation was obtained between the values of r-TNF-alpha and r-beta-2-m and IPI, however r-TNF-alpha best stratify the four risk groups in this prognosis index.