Multiplexing cell‐cell communication Sexton, John T; Tabor, Jeffrey J
Molecular systems biology,
July 2020, Letnik:
16, Številka:
7
Journal Article
Recenzirano
Odprti dostop
The engineering of advanced multicellular behaviors, such as the programmed growth of biofilms or tissues, requires cells to communicate multiple aspects of physiological information. Unfortunately, ...few cell‐cell communication systems have been developed for synthetic biology. Here, we engineer a genetically encoded channel selector device that enables a single communication system to transmit two separate intercellular conversations. Our design comprises multiplexer and demultiplexer sub‐circuits constructed from a total of 12 CRISPRi‐based transcriptional logic gates, an acyl homoserine lactone‐based communication module, and three inducible promoters that enable small molecule control over the conversations. Experimentally parameterized mathematical models of the sub‐components predict the steady state and dynamical performance of the full system. Multiplexed cell‐cell communication has applications in synthetic development, metabolic engineering, and other areas requiring the coordination of multiple pathways among a community of cells.
Synopsis
A synthetic genetic system is engineered that enables bacteria to have two separate conversations over a single chemical “wire” by separating the conversations in time.
A novel library of CRISPRi‐based transcriptional NOT and NOR gates is designed and characterized.
Multiplexer sub‐circuits are constructed and validated.
Sub‐circuits are linked to small‐molecule inducers and a cell‐cell communication system.
Engineered bacteria are co‐cultured to demonstrate the full system switching dynamically between conversations.
A synthetic genetic system is engineered that enables bacteria to have two separate conversations over a single chemical “wire” by separating the conversations in time.
Assessing the potential impacts of 21st-century climate change on species distributions and ecological processes requires climate scenarios with sufficient spatial resolution to represent the varying ...effects of climate change across heterogeneous physical, biological, and cultural landscapes. Unfortunately, the native resolutions of global climate models (usually approximately 2 ° × 2 ° or coarser) are inadéquate for modeling future changes in, e.g., biodiversity, species distributions, crop yields, and water resources. Also, 21st-century climate projections must be debiased prior to use, i.e., corrected for systematic offsets between modeled representations and observations of present climates. We have downscaled future temperature and precipitation projections from the World Climate Research Programme's (WCRP's) CMIP3 multi-model data set to 10-minute resolution and debiased these simulations using the change-factor approach and observational data from the Climatic Research Unit (CRU). These downscaled data sets are available online and include monthly mean temperatures and precipitation for 2041–2060 and 2081–2100, for 24 climate models and the A1B, A2, and B1 emission scenarios. This paper describes the downscaling method and compares the downscaled and native-resolution simulations. Sharp differences between the original and downscaled data sets are apparent at regional to continental scales, particularly for temperature in mountainous areas and in areas with substantial differences between observed and simulated 20th-century climatologies. Although these data sets in principle could be downscaled further, a key practical limitation is the density of observational networks, particularly for precipitation-related variables in tropical mountainous regions. These downscaled data sets can be used for a variety of climate-impact assessments, including assessments of 21st-century climate-change impacts on biodiversity and species distributions.
Light is a powerful tool for manipulating living cells because it can be applied with high resolution across space and over time. We previously constructed a red light-sensitive Escherichia coli ...transcription system based on a chimera between the red/far-red switchable cyanobacterial phytochrome Cph1 and the E. coli EnvZ/OmpR two-component signaling pathway. Here, we report the development of a green light-inducible transcription system in E. coli based on a recently discovered green/red photoswitchable two-component system from cyanobacteria. We demonstrate that the transcriptional output is proportional to the intensity of green light applied and that the green sensor is orthogonal to the red sensor at intensities of 532-nm light less than 0.01 W/m2. Expression of both sensors in a single cell allows two-color optical control of transcription both in batch culture and in patterns across a lawn of engineered cells. Because each sensor functions as a photoreversible switch, this system should allow the spatial and temporal control of the expression of multiple genes through different combinations of light wavelengths. This feature aids precision single-cell and population-level studies in systems and synthetic biology.
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In our earlier work we showed that either spermidine or spermine could support the growth of spe2Δ or spe3Δ polyamine-requiring mutants, but it was unclear whether the cells had a specific ...requirement for either of these amines. In the current work, we demonstrate that spermidine is specifically required for the growth of Saccharomyces cerevisiae. We were able to show this specificity by using a spe3Δ fms1Δ mutant that lacked both spermidine synthase and the FMS1-encoded amine oxidase that oxidizes spermine to spermidine. The polyamine requirement for the growth of this double mutant could only be satisfied by spermidine; i.e., spermine was not effective because it cannot be oxidized to spermidine in the absence of the FMS1 gene. We also showed that at least one of the reasons for the absolute requirement for spermidine for growth is the specificity of its function as a necessary substrate for the hypusine modification of eIF5A. Spermine itself cannot be used for the hypusine modification, unless it is oxidized to spermidine by the Fms1 amine oxidase. We have quantified the conversion of spermine in vivo and have shown that this conversion is markedly increased in a strain overexpressing the Fms1 protein. We have also shown this conversion in enzymatic studies by using the purified amine oxidase from yeast.
The timing and mechanisms of past hydroclimate change in northeast Mexico are poorly constrained, limiting our ability to evaluate climate model performance. To address this, we present a multiproxy ...speleothem record of past hydroclimate variability spanning 62.5 to 5.1 ka from Tamaulipas, Mexico. Here we show a strong influence of Atlantic and Pacific sea surface temperatures on orbital and millennial scale precipitation changes in the region. Multiple proxies show no clear response to insolation forcing, but strong evidence for dry conditions during Heinrich Stadials. While these trends are consistent with other records from across Mesoamerica and the Caribbean, the relative importance of thermodynamic and dynamic controls in driving this response is debated. An isotope-enabled climate model shows that cool Atlantic SSTs and stronger easterlies drive a strong inter-basin sea surface temperature gradient and a southward shift in moisture convergence, causing drying in this region.
Objective
Exploring associations between antenatal detection of fetal growth restriction (FGR) and adverse outcome.
Design
Retrospective, observational, register‐based study.
Setting
Zealand, ...Denmark.
Population or sample
Children born from 1 September 2012 to 31 August 2015.
Methods
Diagnoses from birth until 1 January 2018 were retrieved from The National Patient Registry. Detection was defined as estimated fetal weight less than the 2.3rd centile. Cox regression was used to associate detection status with the hazard rate of adverse outcome, adjusted for fetal weight deviation, maternal age, ethnicity, body mass index and smoking.
Main outcome measures
Adverse neonatal outcome, adverse neuropsychiatric outcome, respiratory disorders, endocrine disorders, gastrointestinal/urogenital disorders.
Results
A total of 2425 FGR children were included. An association was found for gastrointestinal/urogenital disorders (hazard ratio HR 1.68, 95% CI 1.26–2.23, P < 0.001) and respiratory disorders (HR 1.22, 95% CI 1.02–1.46, P = 0.03) in detected versus undetected infants. For adverse neuropsychiatric outcome, HR was 1.32 (95% CI 1.00–1.75, P = 0.05). There was no evidence of an association between detection and adverse neonatal outcome (HR 1.00, 95% CI 0.62–1.61, P = 0.99) and endocrine disorders (HR 1.39, 95% CI 0.88–2.19, P = 0.16). Detected infants were smaller (median −28% versus −25%, P < 0.0001), more often born preterm (odds ratio OR 4.15, 3.12–5.52, P < 0.0001) and more often born after induction or caesarean section (OR 5.19, 95% CI 4.13–6.51, P < 0.0001). Stillbirth risk was increased in undetected FGR fetuses (OR 2.63, 95% CI 1.37–5.04, P = 0.004).
Conclusions
We found an association between detection of FGR and risk of adverse childhood conditions, possibly caused by prematurity. Iatrogenic prematurity may be inevitable in stillbirth prevention, but is accompanied by a risk of long‐term childhood conditions.
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Antenatal detection of growth‐restricted fetuses is associated with adverse childhood outcomes but fewer intrauterine deaths.
Tweetable
Antenatal detection of growth‐restricted fetuses is associated with adverse childhood outcomes but fewer intrauterine deaths.
Exome sequencing (ES) and whole genome sequencing (WGS) putatively identify all adverse functional alleles of protein-coding genes. Accordingly, while ES/WGS are transformative new tools for gene ...discovery in human and medical genetics research, they also generate new manifestations of ethical issues related to the consent process, data sharing, and return of results. These manifestations have yet to be comprehensively framed, due in part to the rapidity with which new technologies for ES/WGS are being applied and because of a lack of empirical data to provide guidance. Accordingly, researchers, funding agencies, and policy makers have largely dealt with these issues intuitively. We explain how use of ES/WGS challenges: (i) models under which informed consent is typically obtained; (ii) how harms associated with data sharing are considered; and (iii) the nature of obligations surrounding unanticipated findings. We provide broad guidance about interim ways to contend with these issues and make broad recommendations for areas for novel resource and policy development.
This study investigated the role of cattle immune responses in the pathogenesis of buffalo fly (
) (BF) lesions. Brangus steers phenotyped for lesion development were divided into three groups: high ...lesion susceptibility (HL), low lesion susceptibility (LL) and no lesions (NL), based on lesion severity scores. Each steer was injected intradermally with different concentrations of BF,
(Og), and
(Md) antigens. At 1 h post-injection, wheal areas at BF injection sites were found to be significantly larger in HL than NL cattle, but there were no significant differences (
< 0.05) found between either the HL or NL cattle and LL cattle. At 24, 48, and 72 h post-injection, the skinfold thickness response to both BF and Md antigens was significantly greater in the HL group than the NL group. However, skin thickness was significantly greater for the BF antigens than the Md antigens (
< 0.05). There were no significant differences found between the LL and NL animals in response to the BF antigens at any time, and no significant differences were determined between any of the lesion groups in response to the Og antigens. Histological examination of skin sections taken from the BF antigen injection sites in HL cattle at 72 h post-injection revealed necrosis of the epidermis and superficial dermis, along with severe eosinophilic inflammation. This study suggests that differences in the hypersensitivity to BF antigens underlie differences amongst the cattle in their susceptibility to the development of BF lesions, and breeding for immune-related biomarkers may assist in selecting more BF lesion-resistant cattle.
We demonstrate the successful application of exome sequencing to discover a gene for an autosomal dominant disorder, Kabuki syndrome (OMIM%147920). We subjected the exomes of ten unrelated probands ...to massively parallel sequencing. After filtering against existing SNP databases, there was no compelling candidate gene containing previously unknown variants in all affected individuals. Less stringent filtering criteria allowed for the presence of modest genetic heterogeneity or missing data but also identified multiple candidate genes. However, genotypic and phenotypic stratification highlighted MLL2, which encodes a Trithorax-group histone methyltransferase: seven probands had newly identified nonsense or frameshift mutations in this gene. Follow-up Sanger sequencing detected MLL2 mutations in two of the three remaining individuals with Kabuki syndrome (cases) and in 26 of 43 additional cases. In families where parental DNA was available, the mutation was confirmed to be de novo (n = 12) or transmitted (n = 2) in concordance with phenotype. Our results strongly suggest that mutations in MLL2 are a major cause of Kabuki syndrome.
Radiative coupling of induced plasmonic fields in metal nanoparticles has drawn increasing attention in the recent literature due to a combination of improved experimental methods to study such ...phenomena and numerous potential applications, such as plasmonic nanoparticle rulers and plasmonic circuitry. Many groups, including ours, have used a near-exponential fit to express the size scaling of plasmonic coupling. First, we show experimental agreement between previously simulated nanorod coupling and plasmonic coupling in electron beam lithography (EBL) fabricated nanorods using the near-exponential expression. Next, we study the effect of nanoparticle orientation on plasmonic coupling using EBL and DDA simulations. We develop a mathematical relationship that is consistent with our findings and quantitatively describes plasmonic coupling between nanorods as a function of orientation, separation, induced dipole strength, and the dielectric constant of the medium. For applications utilizing plasmonic coupling to become viable with particle shapes that do not have spherical symmetry, such as nanoprisms and nanorods, comparison of the experimental and theoretical results of how particle orientation affects plasmonic coupling is essential.
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