Developing and applying a microdroplet co-cultivation and omics toolbox for elucidating complex microbiomes

We have been developing, expanding, and applying a technological pipeline, based on nanoliter-scale microfluidic droplets, to co-cultivate and dissect subsets of complex microbial communities in order to elucidate molecular mechanisms underlying their structures and functions. The pipeline consists of droplet generation, cocultivation, isolation, and analysis such as metagenomic sequencing (Figure 1). We apply this technological framework to the study of a range of microbial communities closely related to human health or the environment. For instance, we demonstrate the anaerobic co-cultivation of diverse sub-communities from a human fecal sample and the de novo reconstruction of genomes from a microdroplet. We observe that many of the cultivated bacteria in these encapsulated sub-communities represent the microbial “dark matter”. In particular, we have constructed the draft genome of a novel Neisseriaceae, representing a new candidate genus with potential contributions to fatty acid utilization and biosynthesis of proatherogenic intermediates. Please click Additional Files below to see the full abstract

Improving InSAR geodesy using global atmospheric models

Spatial and temporal variations of pressure, temperature and water vapor content in the atmosphere introduce significant confounding delays in Interferometric Synthetic Aperture Radar (InSAR) observations of ground deformation and bias estimatesof regional strain rates. Producing robust estimates of tropospheric delays remains one of the key challenges in increasing the accuracy of ground deformation measurements using InSAR. Recent studies revealed the efficiency of global atmospheric reanalysis to mitigate the impact of tropospheric delays, motivating further exploration of their potential. Here, we explore the effectiveness of these models in several geographic and tectonic settings on both single interferograms and time series analysis products. Both hydrostatic and wet contributions to the phase delay are important to account for. We validate these path delay corrections by comparing with estimates of vertically integrated atmospheric water vapor content derived from the passive multi-spectral imager MERIS, onboard the ENVISAT satellite. Generally, the performance of the prediction depends on the vigor of atmospheric turbulence. We discuss (1) how separating atmospheric and orbital contributions allows one to better measure long wavelength deformation, (2) how atmospheric delays affect measurements of surface deformation following earthquakes and (3) we show that such a method allows us to reduce biases in multi-year strain rate estimates by reducing the influence of unevenly sampled seasonal oscillations of the tropospheric delay

Data Analytics Capabilities for Digital Service Development: A Case Study

Data analytics capabilities (DAC) have become important for business organizations in delivering successful digital services to their customers. The success of digital services depends on how efficiently business organizations can deploy DAC in association with other organizational capabilities. Prior information systems (IS) literature has also argued the importance of IS capabilities for digital service development. However, few studies have examined how DAC and IS capabilities will work together for digital service development. To address the research gap, we conducted a case study in a forest machine manufacturing organization. The research findings revealed that IS capabilities such as IS skills, IS infrastructure, and IS-enabled intangibles facilitated DAC’s technical, managerial, and organizational dimension for digital service development. This study contributes to the DAC literature by investigating the role of DAC and IS capabilities in developing digital services in business organizations

A Programmable Escherichia coli Consortium via Tunable Symbiosis

Synthetic microbial consortia that can mimic natural systems have the potential to become a powerful biotechnology for various applications. One highly desirable feature of these consortia is that they can be precisely regulated. In this work we designed a programmable, symbiotic circuit that enables continuous tuning of the growth rate and composition of a synthetic consortium. We implemented our general design through the cross-feeding of tryptophan and tyrosine by two E. coli auxotrophs. By regulating the expression of genes related to the export or production of these amino acids, we were able to tune the metabolite exchanges and achieve a wide range of growth rates and strain ratios. In addition, by inverting the relationship of growth/ratio vs. inducer concentrations, we were able to “program” the co-culture for pre-specified attributes with the proper addition of inducing chemicals. This programmable proof-of-concept circuit or its variants can be applied to more complex systems where precise tuning of the consortium would facilitate the optimization of specific objectives, such as increasing the overall efficiency of microbial production of biofuels or pharmaceuticals

Submarine landslides along the Malacca Strait-Mergui Basin shelf margin: Insights from sequence-stratigraphic analysis

The enormously destructive tsunami of December 2004, caused by sudden motion of the Sunda megathrust beneath the Indian Ocean, raised concerns about tectonically induced tsunami worldwide. Submarine landslides may also trigger dangerous tsunami. However, the potential and repeat time for such events is in most places poorly known due to inadequate exploration of the sea floor and age constraints. The high sediment flux and tectonic subsidence rate of the Malacca Strait-Mergui Basin shelf margin NE of northernmost Sumatra provide a favorable environment to generate and preserve submarine landslides. From ten seismic reflection profiles acquired in 2006, we identify three sediment packages that exhibit sliding characteristics such as headscarps, distorted beds and debris-toe structures. We assign lowstand marine isotope stages to the paleo-shoreline indicators observed in the profiles. We then determine the ages of these submarine landslides as 20–30 ka, 342–364 ka and 435–480 ka by the paleo-shoreline indicators that bound the top and bottom of the slide bodies. This sequence-stratigraphic approach shows that these events occurred near times of sea-level lowstands, which implies that a large amount of direct sediment influx during glacial periods is an essential precondition for basin-margin submarine landsliding. Spatiotemporal variations of sediment input due to lobe switching or Asian monsoon intensity changes also control basin-margin instability. Because we are currently at a highstand stage, and sediment flux to the continental margin is relatively small, so the chance of having a repeat submarine landslide and landslide tsunami along this basin-margin is low

Temperature regulation as a tool for enabling and programming synthetic microbial communities

As target applications grow more elaborate, researchers are developing new approaches to program increasingly complex functionality into synthetic biology platforms. One emerging approach is engineering cooperative, multi-species synthetic microbial communities, which offer significant potential advantages compared to single species systems for numerous applications such as biosynthesis of target compounds through complex pathways enabled by division of labor. However, population dynamics, inter-species interactions, and differing ecological niches of resident microorganisms also introduce complexities that must be addressed to achieve effective and robust synthetic microbial communities. One fundamental challenge is regulation of community composition. At the most basic level, maintaining coexistence of resident community members is required to enable the desired community level functionality. Additionally, community composition often needs to be tuned to optimize overall functionality. For example, when a complex pathway is divided into multiple components hosted by different community members, fluxes through different enzymatic reactions can be coordinated through modulation of each sub-population size to maximize overall efficiency. This type of microbial community manipulation has not been fully utilized in synthetic biology applications, likely due in part to limited available tools. Here we develop temperature regulation as a general tool to enable coexistence and control community composition in synthetic microbial communities. We demonstrate that rationally selected constant temperature regimes can be used to enable coexistence of species from distinct thermal niches. Furthermore, cycling temperature regimes can be used to regulate relative species abundance in microbial communities. We employ mathematical modeling to design cycling temperature regimes for desired community compositions and related features. As microbial communities are increasingly used in a variety of applications, we envision that tools for modulating community composition will continue to expand and we see temperature regulation as a powerful new approach in this area

PCAIM joint inversion of InSAR and ground-based geodetic time series: Application to monitoring magmatic inflation beneath the Long Valley Caldera

This study demonstrates the interest of using a Principal Component Analysis-based Inversion Method (PCAIM) to analyze jointly InSAR and ground-based geodetic time series of crustal deformation. A major advantage of this approach is that the InSAR tropospheric biases are naturally filtered out provided they do not introduce correlated or high amplitude noise in the input times series. This approach yields source models which are well-constrained both in time and space due to the temporal resolution of the ground-based geodetic data and the spatial resolution of the InSAR data. The technique is computationally inexpensive allowing for the inversion of large datasets. To demonstrate the performance of this approach, we apply it to the 1997–98 magmatic inflation event in the Long Valley Caldera, California

Shallow Rupture of the 2011 Tarlay Earthquake (M_w 6.8), Eastern Myanmar

We use L‐band Advanced Land Observation Satellite PALSAR data to infer the distribution of subsurface fault slip during the Tarlay earthquake (M_w 6.8) in eastern Myanmar. We find the total length of surface rupture is approximately 30 km, with nearly 2 m maximum surface offset along the westernmost section of the Nam Ma fault (the Tarlay segment). Finite‐fault inversions constrained by Interferometric Synthetic Aperture Radar (InSAR) and pixel‐tracking data suggest that fault slip is concentrated within the upper 10 km of the crust. Maximum slip exceeds 4 m at a depth between 3 and 5 km. Comparison between field measurements and near‐fault deformation obtained from the InSAR range‐offset result suggests about 10%–80% of displacement occurred within a 1 km wide zone off the main surface fault trace. This off‐fault deformation may explain the shallow slip deficit that we observed during this earthquake. We estimate a recurrence interval for Tarlay‐like events to be 1600–6500 yrs at this section of the Nam Ma fault. A detailed paleoseismological study is essential to clarify the slip behavior and the earthquake recurrence interval of the Nam Ma fault