On the Transformation Capability of Feasible Mechanisms for Programmable Matter

We study theoretical models of programmable matter systems, consisting of n spherical modules kept together by magnetic or electrostatic forces and able to perform two minimal mechanical operations (movements): rotate and/or slide. The goal is for an initial shape A to transform to some target shape B by a sequence of movements. Most of the paper focuses on transformability (feasibility) questions. When only rotation is available, we prove that deciding whether two given shapes can transform to each other, is in P. Under the additional restriction of maintaining global connectivity, we prove inclusion in PSPACE and explore minimum seeds that can make otherwise infeasible transformations feasible. Allowing both rotations and slidings yields universality: any two connected shapes of the same order can be transformed to each other without breaking connectivity, in O(n2) sequential and O(n) parallel time (both optimal). We finally provide a type of distributed transformation

On the Transformation Capability of Feasible Mechanisms for Programmable Matter

In this work, we study theoretical models of \emph{programmable matter} systems. The systems under consideration consist of spherical modules, kept together by magnetic forces and able to perform two minimal mechanical operations (or movements): \emph{rotate} around a neighbor and \emph{slide} over a line. In terms of modeling, there are $n$ nodes arranged in a 2-dimensional grid and forming some initial \emph{shape}. The goal is for the initial shape $A$ to \emph{transform} to some target shape $B$ by a sequence of movements. Most of the paper focuses on \emph{transformability} questions, meaning whether it is in principle feasible to transform a given shape to another. We first consider the case in which only rotation is available to the nodes. Our main result is that deciding whether two given shapes $A$ and $B$ can be transformed to each other, is in $\mathbf{P}$. We then insist on rotation only and impose the restriction that the nodes must maintain global connectivity throughout the transformation. We prove that the corresponding transformability question is in $\mathbf{PSPACE}$ and study the problem of determining the minimum \emph{seeds} that can make feasible, otherwise infeasible transformations. Next we allow both rotations and slidings and prove universality: any two connected shapes $A,B$ of the same order, can be transformed to each other without breaking connectivity. The worst-case number of movements of the generic strategy is $\Omega(n^2)$. We improve this to $O(n)$ parallel time, by a pipelining strategy, and prove optimality of both by matching lower bounds. In the last part of the paper, we turn our attention to distributed transformations. The nodes are now distributed processes able to perform communicate-compute-move rounds. We provide distributed algorithms for a general type of transformations

Optimization of Recombinant Membrane Protein Production in the Engineered Escherichia coli Strains SuptoxD and SuptoxR.

Membrane proteins (MPs) execute a wide variety of critical biological functions in all living organisms and constitute approximately half of current targets for drug discovery. As in the case of soluble proteins, the bacterium Escherichia coli has served as a very popular overexpression host for biochemical/structural studies of membrane proteins as well. Bacterial recombinant membrane protein production, however, is typically hampered by poor cellular accumulation and severe toxicity for the host, which leads to low levels of final biomass and minute volumetric yields. In previous work, we generated the engineered E. coli strains SuptoxD and SuptoxR, which upon coexpression of the effector genes djlA or rraA, respectively, can suppress the cytotoxicity caused by MP overexpression and produce enhanced MP yields. Here, we systematically looked for gene overexpression and culturing conditions that maximize the accumulation of membrane-integrated and well-folded recombinant MPs in these strains. We have found that, under optimal conditions, SuptoxD and SuptoxR achieve greatly enhanced recombinant production for a variety of MP, irrespective of their archaeal, eubacterial, or eukaryotic origin. Furthermore, we demonstrate that the use of these engineered strains enables the production of well-folded recombinant MPs of high quality and at high yields, which are suitable for functional and structural studies. We anticipate that SuptoxD and SuptoxR will become broadly utilized expression hosts for recombinant MP production in bacteria

Discovering novel hydrolases from hot environments

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this recordNovel hydrolases from hot and other extreme environments showing appropriate performance and/or novel functionalities and new approaches for their systematic screening are of great interest for developing new processes, for improving safety, health and environment issues. Existing processes could benefit as well from their properties. The workflow, based on the HotZyme project, describes a multitude of technologies and their integration from discovery to application, providing new tools for discovering, identifying and characterizing more novel thermostable hydrolases with desired functions from hot terrestrial and marine environments. To this end, hot springs worldwide were mined, resulting in hundreds of environmental samples and thousands of enrichment cultures growing on polymeric substrates of industrial interest. Using high-throughput sequencing and bioinformatics, 15 hot spring metagenomes, as well as several sequenced isolate genomes and transcriptomes were obtained. To facilitate the discovery of novel hydrolases, the annotation platform Anastasia and a whole-cell bioreporter-based functional screening method were developed. Sequence-based screening and functional screening together resulted in about 100 potentially new hydrolases of which more than a dozen have been characterized comprehensively from a biochemical and structural perspective. The characterized hydrolases include thermostable carboxylesterases, enol lactonases, quorum sensing lactonases, gluconolactonases, epoxide hydrolases, and cellulases. Apart from these novel thermostable hydrolases, the project generated an enormous amount of samples and data, thereby allowing the future discovery of even more novel enzymes.European CommissionEuropean Union FP

A global view on star formation: The GLOSTAR Galactic plane survey. VII. Supernova remnants in the Galactic longitude range 28∘<l<36∘28^\circ<l<36^\circ

Context. While over 1000 supernova remnants (SNRs) are estimated to exist in the Milky Way, only less than 400 have been found to date. In the context of this apparent deficiency, more than 150 SNR candidates were recently identified in the D-configuration Very Large Array (VLA-D) continuum images of the 4--8 GHz global view on star formation (GLOSTAR) survey, in the Galactic longitude range $-2^\circ<l<60^\circ$. Aims. We attempt to find evidence of nonthermal synchrotron emission from 35 SNR candidates in the region of Galactic longitude range $28^\circ<l<36^\circ$, and also to study the radio continuum emission from the previously confirmed SNRs in this region. Methods. Using the short-spacing corrected GLOSTAR VLA-D+Effelsberg images, we measure ${\sim}6$ GHz total and linearly polarized flux densities of the SNR candidates and the SNRs that were previously confirmed. We also attempt to determine the spectral indices by measuring flux densities from complementary Galactic plane surveys and from the temperature-temperature plots of the GLOSTAR-Effelsberg images. Results. We provide evidence of nonthermal emission from four candidates that have spectral indices and polarization consistent with a SNR origin, and, considering their morphology, we are confident that three of these (G28.36+0.21, G28.78-0.44, and G29.38+0.10) are indeed SNRs. However, about $25\%$ of the candidates have spectral index measurements that indicate thermal emission, and the rest of them are too faint to have a good constraint on the spectral index yet. Conclusions. Additional observations at longer wavelengths and higher sensitivities will shed more light on the nature of these candidates. A simple Monte-Carlo simulation reiterates the view that future studies must persist with the current strategy of searching for SNRs with small angular size to solve the problem of the Milky Way's missing SNRs.Comment: To be published in A&A. 21 pages, 15 figure

A global view on star formation: The GLOSTAR Galactic plane survey VIII. Formaldehyde absorption in Cygnus~X

Cygnus X is one of the closest and most active high-mass star-forming regions in our Galaxy, making it one of the best laboratories for studying massive star formation. As part of the GLOSTAR Galactic plane survey, we performed large scale simultaneous H$_{2}$CO (1$_{1,0}$-1$_{1,1}$) spectral line and radio continuum imaging observations toward Cygnus X at $\lambda\sim$6 cm with the Karl G. Jansky Very Large Array and the Effelsberg-100 m radio telescope. Our Effelsberg observations reveal widespread H$_{2}$CO (1$_{1,0}$-1$_{1,1}$) absorption with a spatial extent of $\gtrsim$50 pc in Cygnus~X for the first time. On large scales of 4.4 pc, the relative orientation between local velocity gradient and magnetic field tends to be more parallel at H$_{2}$ column densities of $\gtrsim$1.8$\times 10^{22}$~cm$^{-2}$. On the smaller scale of 0.17 pc, our VLA+Effelsberg combined data reveal H$_{2}$CO absorption only toward three bright H{\scriptsize II} regions. Our observations demonstrate that H$_{2}$CO (1$_{1,0}$-1$_{1,1}$) is commonly optically thin. Kinematic analysis supports the assertion that molecular clouds generally exhibit supersonic motions on scales of 0.17-4.4 pc. We show a non-negligible contribution of the cosmic microwave background radiation in producing extended absorption features in Cygnus X. Our observations suggest that H$_{2}$CO ($1_{1,0}-1_{1,1}$) can trace molecular gas with H$_{2}$ column densities of $\gtrsim 5 \times 10^{21}$ cm$^{-2}$. The ortho-H$_{2}$CO fractional abundance with respect to H$_{2}$ has a mean value of 7.0$\times 10^{-10}$. A comparison of velocity dispersions on different linear scales suggests that the dominant $-3$ km s$^{-1}$ velocity component in the prominent DR21 region has nearly identical velocity dispersions on scales of 0.17-4.4 pc, which deviates from the expected behavior of classic turbulence.Comment: 27 pages, 23 figures, accepted for publication in A&

A Predictive Model of Intein Insertion Site for Use in the Engineering of Molecular Switches

Inteins are intervening protein domains with self-splicing ability that can be used as molecular switches to control activity of their host protein. Successfully engineering an intein into a host protein requires identifying an insertion site that permits intein insertion and splicing while allowing for proper folding of the mature protein post-splicing. By analyzing sequence and structure based properties of native intein insertion sites we have identified four features that showed significant correlation with the location of the intein insertion sites, and therefore may be useful in predicting insertion sites in other proteins that provide native-like intein function. Three of these properties, the distance to the active site and dimer interface site, the SVM score of the splice site cassette, and the sequence conservation of the site showed statistically significant correlation and strong predictive power, with area under the curve (AUC) values of 0.79, 0.76, and 0.73 respectively, while the distance to secondary structure/loop junction showed significance but with less predictive power (AUC of 0.54). In a case study of 20 insertion sites in the XynB xylanase, two features of native insertion sites showed correlation with the splice sites and demonstrated predictive value in selecting non-native splice sites. Structural modeling of intein insertions at two sites highlighted the role that the insertion site location could play on the ability of the intein to modulate activity of the host protein. These findings can be used to enrich the selection of insertion sites capable of supporting intein splicing and hosting an intein switch

Computing with bacterial constituents, cells and populations: from bioputing to bactoputing

The relevance of biological materials and processes to computing—aliasbioputing—has been explored for decades. These materials include DNA, RNA and proteins, while the processes include transcription, translation, signal transduction and regulation. Recently, the use of bacteria themselves as living computers has been explored but this use generally falls within the classical paradigm of computing. Computer scientists, however, have a variety of problems to which they seek solutions, while microbiologists are having new insights into the problems bacteria are solving and how they are solving them. Here, we envisage that bacteria might be used for new sorts of computing. These could be based on the capacity of bacteria to grow, move and adapt to a myriad different fickle environments both as individuals and as populations of bacteria plus bacteriophage. New principles might be based on the way that bacteria explore phenotype space via hyperstructure dynamics and the fundamental nature of the cell cycle. This computing might even extend to developing a high level language appropriate to using populations of bacteria and bacteriophage. Here, we offer a speculative tour of what we term bactoputing, namely the use of the natural behaviour of bacteria for calculating

SuptoxD2.0: A second-generation engineered Escherichia coli strain achieving further enhanced levels of recombinant membrane protein production

The bacterium Escherichia coli is among the most popular hosts for recombinant protein production, including that of membrane proteins (MPs). We have recently generated the specialized MP-producing E. coli strain SuptoxD, which upon co-expression of the effector gene djlA, is capable of alleviating two major bottlenecks in bacterial recombinant MP production: it suppresses the toxicity that frequently accompanies the MP-overexpression process and it markedly increases the cellular accumulation of membrane incorporated and properly folded recombinant MP. Combined, these two positive effects result in dramatically enhanced volumetric yields for various recombinant MPs of both prokaryotic and eukaryotic origin. Based on the observation that djlA is found in the genomes of various pathogenic bacteria, the aim of the present work was to investigate (a) whether other naturally occurring DjlA variants can exert the MP toxicity-suppressing and production-promoting effects similarly to the E. coli DjlA and (b) if we can identify a DjlA variant whose efficiency surpasses that of the E. coli DjlA of SuptoxD. We report that a quite surprisingly broad variety of homologous DjlA proteins exert beneficial effects on recombinant MP when overexpressed in E. coli. Furthermore, we demonstrate that the Salmonella enterica DjlA is an even more potent enhancer of MP productivity compared with the E. coli DjlA of SuptoxD. Based on this, we constructed a second-generation SuptoxD strain, termed SuptoxD2.0, whose MP-production capabilities surpass significantly those of the original SuptoxD, and we anticipate that SuptoxD2.0 will become a broadly utilized expression host for recombinant MP production in bacteria. © 2020 Wiley Periodicals LL

Optimization of Recombinant Membrane Protein Production in the Engineered Escherichia coli Strains SuptoxD and SuptoxR

Membrane proteins (MPs) execute a wide variety of critical biological functions in all living organisms and constitute approximately half of current targets for drug discovery. As in the case of soluble proteins, the bacterium Escherichia coli has served as a very popular overexpression host for biochemical/structural studies of membrane proteins as well. Bacterial recombinant membrane protein production, however, is typically hampered by poor cellular accumulation and severe toxicity for the host, which leads to low levels of final biomass and minute volumetric yields. In previous work, we generated the engineered E. coli strains SuptoxD and SuptoxR, which upon coexpression of the effector genes djlA or rraA, respectively, can suppress the cytotoxicity caused by MP overexpression and produce enhanced MP yields. Here, we systematically looked for gene overexpression and culturing conditions that maximize the accumulation of membrane-integrated and well-folded recombinant MPs in these strains. We have found that, under optimal conditions, SuptoxD and SuptoxR achieve greatly enhanced recombinant production for a variety of MP, irrespective of their archaeal, eubacterial, or eukaryotic origin. Furthermore, we demonstrate that the use of these engineered strains enables the production of well-folded recombinant MPs of high quality and at high yields, which are suitable for functional and structural studies. We anticipate that SuptoxD and SuptoxR will become broadly utilized expression hosts for recombinant MP production in bacteria. © 2019 American Chemical Society