Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

Microbial communities are complex dynamical systems harbouring many species interacting together to implement higher-level functions. Among these higher-level functions, conversion of organic matter into simpler building blocks by microbial communities underpins biogeochemical cycles and animal and plant nutrition, and is exploited in biotechnology. A prerequisite to predicting the dynamics and stability of community-mediated metabolic conversions is the development and calibration of appropriate mathematical models. Here, we present a generic, extendable thermodynamic model for community dynamics and calibrate a key parameter of this thermodynamic model, the minimum energy requirement associated with growth-supporting metabolic pathways, using experimental population dynamics data from synthetic communities composed of a sulfate reducer and two methanogens. Our findings show that accounting for thermodynamics is necessary in capturing the experimental population dynamics of these synthetic communities that feature relevant species using low energy growth pathways. Furthermore, they provide the first estimates for minimum energy requirements of methanogenesis (in the range of −30 kJ mol−1) and elaborate on previous estimates of lactate fermentation by sulfate reducers (in the range of −30 to −17 kJ mol−1 depending on the culture conditions). The open-source nature of the developed model and demonstration of its use for estimating a key thermodynamic parameter should facilitate further thermodynamic modelling of microbial communities

The Computer-Controlled Oculometer: A Prototype Interactive Eye Movement Tracking System

One kind of eye movement tracking device which has great potential is the digital computer-controlled Oculometer, an instrument which non-invasively measures point of regard of the subject, as well as pupil diameter and blink occurrence. In conjunction with a computer-generated display which can change in real time as a function of the subject's eye motions, the computer-controlled Oculometer makes possible a variety of interactive measurement and control systems. Practical applications of such schemes have had to await the development of an instrument design which does not inconvenience the subject, and which conveniently interfaces with a digital computer (see ref. 1). This report describes an Oculometer subsystem and an eye-tracking/control program designed for use with the PDP-6 computer of the MIT Project MAC Artificial Intelligence Group. The oculometer electro-optic subsystem utilizes near-infrared light reflected specularly off the front surface of the subject's cornea and diffusely off the retina, producing a bright pupil with an overriding corneal highlight. An electro-optic scanning aperture vidissector within the unit, driven by a digital eye-tracking algorithm programmed into the PDP-6 computer, detects and tracks the centers of the corneal highlight and the bright pupil to give eve movement measurements. A computer-controlled, moving mirror head motion tracker directly coupled to the vidissector tracker permits the subject reasonable freedom of movement. Various applications of this system, which are suggested by the work reported here, include; (a) using the eye as a control device, (b) recording eye fixation and exploring patterns, (c) game playing, (d) training machines, and (e) psychophysiological testing and recording

Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer

Methane producing microbial communities are of ecological and biotechnological interest. Syntrophic interactions among sulphate reducers and aceto/hydrogenotrophic and obligate hydrogenotrophic methanogens form a key component of these communities, yet, the impact of these different syntrophic routes on methane production and their stability against sulphate availability are not well understood. Here, we construct model synthetic communities using a sulphate reducer and two types of methanogens representing different methanogenesis routes. We find that tri-cultures with both routes increase methane production by almost two-fold compared to co-cultures, and are stable in the absence of sulphate. With increasing sulphate, system stability and productivity decreases, and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate. We show that this is due to a shift in these methanogens’ metabolism towards co-utilisation of hydrogen with acetate. These findings indicate the important role of hydrogen dynamics in the stability and productivity of syntrophic communities

Medium shapes the microbial community of water filters with implications for effluent quality

Little is known about the forces that determine the assembly of diverse bacterial communities inhabiting drinking water treatment filters and how this affects drinking water quality. Two contrasting ecological theories can help to understand how natural microbial communities assemble; niche theory and neutral theory, where environmental deterministic factors or stochastic factors predominate respectively. This study investigates the development of the microbial community on two common contrasting filter materials (quartz sand and granular activated carbon-GAC), to elucidate the main factors governing their assembly, through the evaluation of environmental (i.e. filter medium type) and stochastic forces (random deaths, births and immigration). Laboratory-scale filter columns were used to mimic a rapid gravity filter; the microbiome of the filter materials, and of the filter influent and effluent, was characterised using next generation 16S rRNA gene amplicon sequencing and flow-cytometry. Chemical parameters (i.e. dissolved organic carbon, trihalomethanes formation) were also monitored to assess the final effluent quality. The filter communities seemed to be strongly assembled by selection rather than neutral processes, with only 28% of those OTUs shared with the source water detected on the filter medium following predictions using a neutral community model. GAC hosted a phylogenetically more diverse community than sand. The two filter media communities seeded the effluent water, triggering differences in both water quality and community composition of the effluents. Overall, GAC proved to be better than sand in controlling microbial growth, by promoting higher bacterial decay rates and hosting less bacterial cells, and showed better performance for putative pathogen control by leaking less Legionella cells into the effluent water

Transcriptomic-wide discovery of direct and indirect HuR RNA targets in activated CD4+ T cells

Due to poor correlation between steady state mRNA levels and protein product, purely transcriptomic profiling methods may miss genes posttranscriptionally regulated by RNA binding proteins (RBPs) and microRNAs (miRNAs). RNA immunoprecipitation (RIP) methods developed to identify in vivo targets of RBPs have greatly elucidated those mRNAs which may be regulated via transcript stability and translation. The RBP HuR (ELAVL1) and family members are major stabilizers of mRNA. Many labs have identified HuR mRNA targets; however, many of these analyses have been performed in cell lines and oftentimes are not independent biological replicates. Little is known about how HuR target mRNAs behave in conditional knock-out models. In the present work, we performed HuR RIP-Seq and RNA-Seq to investigate HuR direct and indirect targets using a novel conditional knock-out model of HuR genetic ablation during CD4+ T activation and Th2 differentiation. Using independent biological replicates, we generated a high coverage RIP-Seq data set (>160 million reads) that was analyzed using bioinformatics methods specifically designed to find direct mRNA targets in RIP-Seq data. Simultaneously, another set of independent biological replicates were sequenced by RNA-Seq (>425 million reads) to identify indirect HuR targets. These direct and indirect targets were combined to determine canonical pathways in CD4+ T cell activation and differentiation for which HuR plays an important role. We show that HuR may regulate genes in multiple canonical pathways involved in T cell activation especially the CD28 family signaling pathway. These data provide insights into potential HuR-regulated genes during T cell activation and immune mechanisms

Real-time Likelihood Methods for Improved Gamma-ray Transient Detection and Localization

We present a maximum likelihood (ML) algorithm that is fast enough to detect gamma-ray transients in real time on low-performance processors often used for space applications. We validate the routine with simulations and find that, relative to algorithms based on excess counts, the ML method is nearly twice as sensitive, allowing detection of 240-280% more short gamma-ray bursts. We characterize a reference implementation of the code, estimating its computational complexity and benchmarking it on a range of processors. We exercise the reference implementation on archival data from the Fermi Gamma-ray Burst Monitor (GBM), verifying the sensitivity improvements. In particular, we show that the ML algorithm would have detected GRB 170817A even if it had been nearly four times fainter. We present an ad hoc but effective scheme for discriminating transients associated with background variations. We show that the on-board localizations generated by ML are accurate, but that refined off-line localizations require a detector response matrix with about ten times finer resolution than is current practice. Increasing the resolution of the GBM response matrix could substantially reduce the few-degree systematic uncertainty observed in the localizations of bright bursts.Comment: 18 pages, 11 figure

Repetitive posterior iliac crest autograft harvest resulting in an unstable pelvic fracture and infected non-union: case report and review of the literature

Fractures of the pelvic ring have been well studied, and the biomechanical relationship between the anterior and posterior elements is an important concept to understand these complex injuries. The vast majority of these injuries are due to trauma. However, in rare circumstances, autogenous bone graft harvesting may lead to an unstable pelvic ring. In this case report, we describe a rare complication in a 70-year old female patient who developed an unstable pelvis and an infected non-union secondary to repeated posterior iliac graft harvest. The orthopaedic surgeon should be aware of this detrimental complication associated with extensive or repeated posterior iliac crest graft harvest

Theory of apparent circular dichroism in a magnetic field

We present a microscopic theory of apparent circular dichroism in chiral thin films, cast explicitly in terms of molecular property tensors. Our theory provides a general foundation for ab initio calculations and reveals that the films should exhibit an interesting magnetochiral apparent circular dichroism and other novel effects when subjected to a static magnetic field