scholarly journals Magnitude and mechanism of siderophore-mediated competition in bacterial interactions

2016 ◽  
Author(s):  
Konstanze T. Schiessl ◽  
Elisabeth M.-L. Janssen ◽  
Stephan M. Kraemer ◽  
Kristopher McNeill ◽  
Martin Ackermann
Keyword(s):  
Competitive Inhibition ◽  
Experimental System ◽  
Genetically Engineered ◽  
Microbial Interactions ◽  
Natural Environments ◽  
Genomic Information ◽  
Cooperative Interactions ◽  
Functional Investigation ◽  
Insight Into ◽  
Induce Growth Inhibition

Whether microbial interactions are predominantly cooperative or competitive is a central question in microbial ecology, and determines the composition and stability of microbial communities. The secretion of iron chelators called siderophores is a model system for cooperative interactions, even though these chelators can also mediate competition by depriving competitors of iron. Using a genetically engineered experimental system based on thePseudomonas aeruginosasiderophore pyochelin, we found that secreting siderophores to inhibit a competitor can lead to higher benefits than secreting siderophores to make iron available. Based on thermodynamic modeling, we propose that competitive inhibition by siderophores is efficient in kinetically controlled saturated systems, where dissolution of precipitated iron phases is slow. Under these conditions, met in many natural environments, secreted siderophores temporarily reduce the concentration of available iron and can thus induce growth inhibition in a competing strain, even at high iron concentrations. These findings give insight into the function of siderophores: In addition to its cooperative nature, siderophore secretion could also be a widespread mechanism for mediating competitive interactions. Our functional investigation reveals a complexity in microbial interaction networks that would remain hidden when focusing on genomic information alone.

scholarly journals Chi-Dependent Intramolecular Recombination in Escherichia coli

Genetics ◽  
1998 ◽  
Vol 148 (2) ◽  
pp. 545-557
Author(s):  
Rachel Friedman-Ohana ◽  
Iris Karunker ◽  
Amikam Cohen
Keyword(s):  
Escherichia Coli ◽  
Homologous Recombination ◽  
Experimental System ◽  
Cis Acting ◽  
Enzymes Activity ◽  
Intramolecular Recombination ◽  
Insight Into

Abstract Homologous recombination in Escherichia coli is enhanced by a cis-acting octamer sequence named Chi (5′-GCTGGTGG-3′) that interacts with RecBCD. To gain insight into the mechanism of Chi-enhanced recombination, we recruited an experimental system that permits physical monitoring of intramolecular recombination by linear substrates released by in vivo restriction from infecting chimera phage. Recombination of the released substrates depended on recA, recBCD and cis-acting Chi octamers. Recombination proficiency was lowered by a xonA mutation and by mutations that inactivated the RuvABC and RecG resolution enzymes. Activity of Chi sites was influenced by their locations and by the number of Chi octamers at each site. A single Chi site stimulated recombination, but a combination of Chi sites on the two homologs was synergistic. These data suggest a role for Chi at both ends of the linear substrate. Chi was lost in all recombinational exchanges stimulated by a single Chi site. Exchanges in substrates with Chi sites on both homologs occurred in the interval between the sites as well as in the flanking interval. These observations suggest that the generation of circular products by intramolecular recombination involves Chi-dependent processing of one end by RecBCD and pairing of the processed end with its duplex homolog.

scholarly journals The Use of Non-Canonical Amino Acids as a Novel Biocontainment Strategy

2018 ◽  
Vol 5 (1) ◽  
Author(s):  
Jourdan Witt
Keyword(s):  
Oral Delivery ◽  
Genetically Modified Organisms ◽  
Vaccine Development ◽  
Open Systems ◽  
Genetically Modified ◽  
Environmental Safety ◽  
Genetically Engineered ◽  
Natural Environments ◽  
Delivery Vector ◽  
The Impact

Advancements in synthetic biology have led to the use of genetically modified organisms in research and industrial fields. Bacteria were one of the first organisms to be genetically engineered due to their fast growth and simple genetics, and have emerged as a major scientific and commercial interest. For instance, modified commensal bacteria can be used as an oral delivery vector of therapeutics, or as probiotics to target specific pathogens in the gastrointestinal tract. The impact of the release of pathogens used in research or vaccine development could be catastrophic to the environment and public health. In addition, there is growing concern about using genetically modified organisms in open systems, as there is a possibility for unintentional proliferation into natural environments. Therefore, is imperative that the environmental safety of genetically modified organisms are addressed, and that adequate biocontainment mechanisms are developed.

Slow and Fast (Gamma) Neuronal Oscillations in the Perirhinal Cortex and Lateral Amygdala

2001 ◽  
Vol 85 (4) ◽  
pp. 1661-1672 ◽  
Author(s):  
Dawn R. Collins ◽  
J. Guillaume Pelletier ◽  
Denis Paré
Keyword(s):  
Spontaneous Activity ◽  
Perirhinal Cortex ◽  
Field Potentials ◽  
Lateral Amygdala ◽  
Cooperative Interactions ◽  
Close Relationship ◽  
Lesion Studies ◽  
Highly Correlated ◽  
Fast Oscillations ◽  
Insight Into

Most lesion studies emphasize the distinct contributions of the amygdala and perirhinal cortex to memory. Yet, the presence of strong reciprocal excitatory projections between these two structures suggests that they are functionally coupled. To gain some insight into this issue, the present study examined whether the close anatomical ties existing between perirhinal and lateral amygdala (LA) neurons are expressed in their spontaneous activity. To this end, multiple simultaneous recordings of single unit discharges and local field potentials were performed in the LA and perirhinal cortex in ketamine-xylazine anesthetized cats. The perirhinal cortex and LA exhibited a similar pattern of spontaneous activity. Recordings at both sites were dominated by a slow focal oscillation at 1 Hz onto which was superimposed a faster rhythm (≈30 Hz) whose amplitude fluctuated cyclically. Computing crosscorrelograms between focal waves recorded simultaneously in the perirhinal cortex and LA revealed a close relationship between their spontaneous activity. Even when recording sites were separated by as much as 8 mm, the slow focal oscillation remained highly correlated ( r ≥ 0.7). In contrast, the correlation between fast oscillations was usually lower ( r ≈ 0.3). Perievent histograms of neuronal discharges revealed that the firing probability of most LA and perirhinal neurons increased during the depth-negative component of the slow oscillation. In addition, respectively, 47 and 64% of LA and perirhinal neurons exhibited a significant modulation of firing probability in relation to the fast oscillations. Finally, crosscorrelating unit discharges simultaneously recorded in the LA and perirhinal cortex confirmed the presence of phase-related oscillatory events in both structures. In summary, our results suggest that the interconnections existing between the perirhinal cortex and LA can support the genesis of coherent neuronal activities at various frequencies. These results imply that cooperative interactions must be taking place between these structures.

Experimental Study on Single-Phase Gas Flow in Microtubes

2011 ◽  
Vol 133 (11) ◽  
Author(s):  
T. T. Zhang ◽  
L. Jia ◽  
C. W. Li ◽  
L. X. Yang ◽  
Y. Jaluria
Keyword(s):  
Heat Transfer ◽  
Gas Flow ◽  
Single Phase ◽  
Slip Flow ◽  
Experimental System ◽  
Flow Region ◽  
Flow And Heat Transfer ◽  
Wide Range ◽  
Physical Insight ◽  
Insight Into

An experimental system for single-phase gas flow in microtubes has been developed. The effects of viscous heating and compressibility on the flow and temperature field were studied for a wide range of governing parameters. Also, an analytical/numerical model of the flow was developed. Numerical results for the flow and heat transfer in the slip flow region were found to agree quite well with the experimental data, lending support to the model. The study provides greater physical insight into and understanding the effects of viscous dissipation and compressibility in microtube flow and the associated heat transfer. In addition, the combined experimental and numerical simulation approaches of the process can be used for control and optimization of systems based on microtube heat transfer.

Mechanistic Insight into H2S Adsorption and Dissociation on MoP(010): A Density Functional Investigation

2017 ◽  
Vol 1142 ◽  
pp. 300-305
Author(s):  
Gui Xia Li ◽  
Hou Yu Zhu ◽  
Lian Ming Zhao ◽  
Wen Yue Guo ◽  
Xiao Qing Lu ◽  
...  
Keyword(s):  
Density Functional ◽  
Co Adsorption ◽  
Adsorbed Species ◽  
Functional Theory ◽  
Mechanistic Insight ◽  
Structure Sensitive ◽  
Bond Scission ◽  
Functional Investigation ◽  
Adsorption And Dissociation ◽  
Insight Into

H2S adsorption and dissociation on MoP(010) were investigated using density functional theory (DFT) together with periodic slab models. Several different possibilities for H2S, SH, S and H adsorption were considered. Our results show that the H2S, SH and H prefer to adsorb at bridge site, while S adsorbs preferentially at hcp and bridge sites. Additionally, the optimum co-adsorption configurations for SH/H and S/H were determined. The results indicate that the co-adsorbed species repel each other slightly on MoP(010) surface. Finally, the potential energy profile of H2S dissociation on MoP(010) surface was given out. The dissociation energy barriers of the S–H bond scission exhibit that H2S prefers to dissociate on MoP(010) surface. When compared with MoP(001) surface, the obvious differences in H2S decomposition arise demonstrate that the MoP-based catalysts are structure-sensitive.

scholarly journals System Identification of a MEMS Gyroscope

1999 ◽  
Vol 123 (2) ◽  
pp. 201-210 ◽  
Author(s):  
Robert T. M’Closkey ◽  
Steve Gibson ◽  
Jason Hui
Keyword(s):  
System Identification ◽  
Angular Rate ◽  
Experimental System ◽  
Primary Objective ◽  
Input Output ◽  
Output Data ◽  
Mems Gyroscope ◽  
Principal Axes ◽  
Frequency Split ◽  
Insight Into

This paper reports the experimental system identification of the Jet Propulsion Laboratory MEMS vibratory rate gyroscope. A primary objective is to estimate the orientation of the stiffness matrix principal axes for important sensor dynamic modes with respect to the electrode pick-offs in the sensor. An adaptive lattice filter is initially used to identify a high-order two-input/two-output transfer function describing the input/output dynamics of the sensor. A three-mode model is then developed from the identified input/output model to determine the axes’ orientation. The identified model, which is extracted from only two seconds of input/output data, also yields the frequency split between the sensor’s modes that are exploited in detecting the rotation rate. The principal axes’ orientation and frequency split give direct insight into the source of quadrature measurement error that corrupts detection of the sensor’s angular rate.

scholarly journals System Biology Modeling with Compositional Microbiome Data Reveals Personalized Gut Microbial Dynamics and Keystone Species

2018 ◽  
Author(s):  
Chenhao Li ◽  
Lisa Tucker-Kellogg ◽  
Niranjan Nagarajan
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Keystone Species ◽  
Microbial Interactions ◽  
Natural Environments ◽  
Sequencing Data ◽  
Predator Prey ◽  
Public Datasets ◽  
Microbiome Data

AbstractA growing body of literature points to the important roles that different microbial communities play in diverse natural environments and the human body. The dynamics of these communities is driven by a range of microbial interactions from symbiosis to predator-prey relationships, the majority of which are poorly understood, making it hard to predict the response of the community to different perturbations. With the increasing availability of high-throughput sequencing based community composition data, it is now conceivable to directly learn models that explicitly define microbial interactions and explain community dynamics. The applicability of these approaches is however affected by several experimental limitations, particularly the compositional nature of sequencing data. We present a new computational approach (BEEM) that addresses this key limitation in the inference of generalised Lotka-Volterra models (gLVMs) by coupling biomass estimation and model inference in an expectation maximization like algorithm (BEEM). Surprisingly, BEEM outperforms state-of-the-art methods for inferring gLVMs, while simultaneously eliminating the need for additional experimental biomass data as input. BEEM’s application to previously inaccessible public datasets (due to the lack of biomass data) allowed us for the first time to analyse microbial communities in the human gut on a per individual basis, revealing personalised dynamics and keystone species.

scholarly journals Using causality and correlation analysis to decipher microbial interactions in activated sludge

2021 ◽  
Author(s):  
Weiwei Cai ◽  
Xiangyu Han ◽  
Hong Yao
Keyword(s):  
Time Series ◽  
Activated Sludge ◽  
Network Theory ◽  
Time Series Data ◽  
Microbial Interactions ◽  
Series Data ◽  
Natural Environments ◽  
Cell Aggregate ◽  
Causality Analysis ◽  
Mutualistic Relationship

Network theory is widely used to understand microbial interactions in activated sludge and numerous other artificial and natural environments. However, when using correlation-based methods, it is not possible to identify the directionality of interactions within microbiota. Based on the classic Granger test of sequencing-based time-series data, a new Microbial Causal Correlation Network (MCCN) was constructed with distributed ecological interaction on the directed, associated links. As a result of applying MCCN to a time series of activated sludge data, we found that the hub species OTU56, classified as belonging the genus Nitrospira, was responsible for completing nitrification in activated sludge, and mainly interacted with Proteobacteria and Bacteroidetes in the form of amensal and commensal relationships, respectively. Phylogenetic tree suggested a mutualistic relationship between Nitrospira and denitrifiers. Zoogloea displayed the highest ncf value within the classified OTUs of the MCCN, indicating that it could be a foundation for activated sludge through forming the characteristic cell aggregate matrices into which other organisms embed during floc formation. Overall, the introduction of causality analysis greatly expands the ability of a network to shed a light on understanding the interactions between members of a microbial community.

scholarly journals A Review of Nervonic Acid Production in Plants: Prospects for the Genetic Engineering of High Nervonic Acid Cultivars Plants

2021 ◽  
Vol 12 ◽  
Author(s):  
Fang Liu ◽  
Pandi Wang ◽  
Xiaojuan Xiong ◽  
Xinhua Zeng ◽  
Xiaobo Zhang ◽  
...  
Keyword(s):  
Genetic Engineering ◽  
Genetically Engineered ◽  
Commercial Application ◽  
Nervonic Acid ◽  
Plant Oil ◽  
Plant Seed ◽  
Oil Crops ◽  
Transgenic Technologies ◽  
Production Mechanisms ◽  
Insight Into

Nervonic acid (NA) is a very-long-chain monounsaturated fatty acid that plays crucial roles in brain development and has attracted widespread research interest. The markets encouraged the development of a refined, NA-enriched plant oil as feedstocks for the needed further studies of NA biological functions to the end commercial application. Plant seed oils offer a renewable and environmentally friendly source of NA, but their industrial production is presently hindered by various factors. This review focuses on the NA biosynthesis and assembly, NA resources from plants, and the genetic engineering of NA biosynthesis in oil crops, discusses the factors that affect NA production in genetically engineered oil crops, and provides prospects for the application of NA and prospective trends in the engineering of NA. This review emphasizes the progress made toward various NA-related topics and explores the limitations and trends, thereby providing integrated and comprehensive insight into the nature of NA production mechanisms during genetic engineering. Furthermore, this report supports further work involving the manipulation of NA production through transgenic technologies and molecular breeding for the enhancement of crop nutritional quality or creation of plant biochemical factories to produce NA for use in nutraceutical, pharmaceutical, and chemical industries.

scholarly journals The Cardamine enshiensis genome reveals whole genome duplication and insight into selenium hyperaccumulation and tolerance

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Chuying Huang ◽  
Hongqin Ying ◽  
Xibiao Yang ◽  
Yuan Gao ◽  
Tuo Li ◽  
...  
Keyword(s):  
Genome Duplication ◽  
Cellular Responses ◽  
Flavonoid Biosynthesis ◽  
Chromatin Interaction ◽  
Strong Interactions ◽  
Interaction Patterns ◽  
Genomic Information ◽  
Hyperaccumulating Plant ◽  
Insight Into ◽  
Chromosome Level

AbstractCardamine enshiensis is a well-known selenium (Se)-hyperaccumulating plant. Se is an essential trace element associated with many health benefits. Despite its critical importance, genomic information of this species is limited. Here, we report a chromosome-level genome assembly of C. enshiensis, which consists of 443.4 Mb in 16 chromosomes with a scaffold N50 of 24 Mb. To elucidate the mechanism of Se tolerance and hyperaccumulation in C. enshiensis, we generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes. The results reveal that flavonoid, glutathione, and lignin biosynthetic pathways may play important roles in protecting C. enshiensis from stress induced by Se. Hi-C analysis of chromatin interaction patterns showed that the chromatin of C. enshiensis is partitioned into A and B compartments, and strong interactions between the two telomeres of each chromosome were correlated with histone modifications, epigenetic markers, DNA methylation, and RNA abundance. Se supplementation could affect the 3D chromatin architecture of C. enshiensis at the compartment level. Genes with compartment changes after Se treatment were involved in selenocompound metabolism, and genes in regions with topologically associated domain insulation participated in cellular responses to Se, Se binding, and flavonoid biosynthesis. This multiomics research provides molecular insight into the mechanism underlying Se tolerance and hyperaccumulation in C. enshiensis.

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