Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium

Microbial consortia form when multiple species colocalize and communally generate a function that none is capable of alone. Consortia abound in nature, and their cooperative metabolic activities influence everything from biodiversity in the global food chain to human weight gain. Here, we present an engineered consortium in which the microbial members communicate with each other and exhibit a “consensus” gene expression response. Two colocalized populations of Escherichia coli converse bidirectionally by exchanging acyl-homoserine lactone signals. The consortium generates the gene-expression response if and only if both populations are present at sufficient cell densities. Because neither population can respond without the other's signal, this consensus function can be considered a logical AND gate in which the inputs are cell populations. The microbial consensus consortium operates in diverse growth modes, including in a biofilm, where it sustains its response for several days

Synthetic biology: new engineering rules for an emerging discipline

Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development

Trait-based analysis of the human skin microbiome

The past decade of microbiome research has concentrated on cataloging the diversity of taxa in different environments. The next decade is poised to focus on microbial traits and function. Most existing methods for doing this perform pathway analysis using reference databases. This has both benefits and drawbacks. Function can go undetected if reference databases are coarse-grained or incomplete. Likewise, detection of a pathway does not guarantee expression of the associated function. Finally, function cannot be connected to specific microbial constituents, making it difficult to ascertain the types of organisms exhibiting particular traits—something that is important for understanding microbial success in specific environments. A complementary approach to pathway analysis is to use the wealth of microbial trait information collected over years of lab-based, culture experiments.https://doi.org/10.1186/s40168-019-0698-

Geological interpretation of volcanism and segmentation of the Mariana back-arc spreading center between 12.7°N and 18.3°N

The relationships between tectonic processes, magmatism, and hydrothermal venting along ∼600 km of the slow-spreading Mariana back-arc between 12.7°N and 18.3°N reveal a number of similarities and differences compared to slow-spreading mid-ocean ridges. Analysis of the volcanic geomorphology and structure highlights the complexity of the back-arc spreading center. Here, ridge segmentation is controlled by large-scale basement structures that appear to predate back-arc rifting. These structures also control the orientation of the chains of cross-arc volcanoes that characterize this region. Segment-scale faulting is oriented perpendicular to the spreading direction, allowing precise spreading directions to be determined. Four morphologically distinct segment types are identified: dominantly magmatic segments (Type I); magmatic segments currently undergoing tectonic extension (Type II); dominantly tectonic segments (Type III); and tectonic segments currently undergoing magmatic extension (Type IV). Variations in axial morphology (including eruption styles, neovolcanic eruption volumes, and faulting) reflect magma supply, which is locally enhanced by cross-arc volcanism associated with N-S compression along the 16.5°N and 17.0°N segments. In contrast, cross-arc seismicity is associated with N-S extension and increased faulting along the 14.5°N segment, with structures that are interpreted to be oceanic core complexes—the first with high-resolution bathymetry described in an active back-arc basin. Hydrothermal venting associated with recent magmatism has been discovered along all segment types

Exploring the functional composition of the human microbiome using a hand-curated microbial trait database

Even when microbial communities vary wildly in their taxonomic composition, their functional composition is often surprisingly stable. This suggests that a functional perspective could provide much deeper insight into the principles governing microbiome assembly. Much work to date analyzing the functional composition of microbial communities, however, relies heavily on inference from genomic features. Unfortunately, output from these methods can be hard to interpret and often suffers from relatively high error rates. We built and analyzed a domain-specific microbial trait database from known microbe-trait pairs recorded in the literature to better understand the functional composition of the human microbiome. Using a combination of phylogentically conscious machine learning tools and a network science approach, we were able to link particular traits to areas of the human body, discover traits that determine the range of body areas a microbe can inhabit, and uncover drivers of metabolic breadth. Domain-specific trait databases are an effective compromise between noisy methods to infer complex traits from genomic data and exhaustive, expensive attempts at database curation from the literature that do not focus on any one subset of taxa. They provide an accurate account of microbial traits and, by limiting the number of taxa considered, are feasible to build within a reasonable time-frame. We present a database specific for the human microbiome, in the hopes that this will prove useful for research into the functional composition of human-associated microbial communities.https://doi.org/10.1186/s12859-021-04216-

Remote Denial of Service Attacks and Countermeasures

this paper shall be assumed to be 4. The Hlen field specifies the length of the header in 32-bit words. ToS, or type of service, indicates how packets 2 should be treated based on application needs (how they should be queued, etc.). Since the Length field, which specifies the length of the entire datagram in bytes, is 16 bits, the maximum length of an IP packet is 2 --1 bytes [19]. The Identifier field, the Offset field, and one of the flags are used for handling fragmentation and reassembly. Different networks have different MTU's (maximum transmission units), meaning that maximum allowable packet sizes differ from network to network. Thus, a large packet from a network with a large MTU may need to be broken into fragments as it enters a network with a smaller MTU. The end host is responsible for reassembling the fragments. Fragments that will be reassembled into a single packet are given the same identifier. The first fragment has an offset of zero, and for the following fragments, the Offset field contains the offset in bytes from the first fragment. A flag is set in a packet to indicate that more fragments will follow [19]. Time to live (TTL) provides a way to prevent packets from floating around indefinitely in transit to their destinations. At each hop, this field is typically decremented, and the packet is discarded if the TTL field reaches zero. Since several protocols such as TCP and UDP ride on top of IP, the Protocol field is used to specify the higher level protocol to which the IP packet belongs. A checksum is performed to provide a means for determining whether or not the header has been corrupted. The source address and destination address of the packet are specified following the checksum. Options, which are not frequently used, are included at the end..

R (2005) Signal-amplifying genetic circuit enables in vivo observation of weak promoter activation in the Rhl quorum sensing system. Biotechnol Bioeng 89: 709-718. doi:10.1002/bit.20371. PubMed

Abstract: Small changes in transcriptional activity often significantly affect phenotype but are not detectable in vivo by conventional means. To address this problem, we present a technique for detecting weak transcriptional responses using signal-amplifying genetic circuits. We apply this technique to reveal previously undetectable log phase responses of several Rhl quorum sensing controlled (qsc) promoters from Pseudomonas aeruginosa. Genetic circuits with Rhl promoters and transcriptional amplification components were built and tested in Escherichia coli. This enabled us to isolate the behavior of the promoters under study from Las and quinolone interactions. To amplify qsc promoter responses to acyl-homoserine lactones (AHL), the highly efficient E repressor gene was placed downstream of several Rhl promoters and coupled to a fluorescent reporter under the control of the E P (R) promoter. With amplification, up to f100-fold differences in fluorescence levels between AHL induced and noninduced cultures were observed for promoters whose responses were otherwise not detectable. In addition, the combination of using signal amplification and performing experiments in E. coli simplified the analysis of AHL signal crosstalk. For example, we discovered that while a C4HSL/ RhlR complex activates both qscrhlA and qscphzA1, a 3OC12HSL/RhlR complex activates qscphzA1 but not qscrhlA in our system. This crosstalk information is particularly important since one of the potential uses of amplification constructs is for the detection of specific quorum sensing signals in environmental and clinical isolates. Furthermore, the process of decomposing networks into basic parts, isolating these components in a well-defined background, and using amplification to characterize both crosstalk and cognate signal responses embodies an important approach to understanding complex genetic networks.