Control of bacterial population density with population feedback and molecular sequestration

Genetic engineering technology has become sophisticated enough to allow precise manipulation of bacterial genetic material. Engineering efforts with these technologies have created modified bacteria for various medical, industrial, and environmental purposes, but organisms designed for specific functions require improvements in stability, longevity, or efficiency of function. Most bacteria live in multispecies communities, whose composition may be closely linked to the effect the community has on the environment. Bacterial engineering efforts will benefit from building communities with regulated compositions, which will enable more stable and powerful community functions. We present a design of a synthetic two member bacterial community capable of maintaining its composition at a defined ratio of [cell type 1] : [cell type 2]. We have constructed the genetic motif that will act in each cell in the two member community, containing an AHL-based negative feedback loop that activates ccdB toxin, which caps population density with increasing feedback strength. It also contains one of two ccdB sequestration modules, either the ccdA protein antitoxin, or an RNA device which prevents transcription and translation of ccdB mRNA, that rescues capped population density with induction. We compare absorbance and colony counting methods of estimating bacterial population density, finding that absorbance-based methods overestimate viable population density when ccdB toxin is used to control population density. Prior modeling results show that two cell types containing this genetic circuit motif that reciprocally activate the other's ccdB sequestration device will establish a steady state ratio of cell types. Experimental testing and tuning the full two member community will help us improve our modeling of multi-member bacterial communities, learn more about the strengths and weaknesses of our design for community composition control, and identify general principles of design of compositionally-regulated microbial communities

Engineering Logical Inflammation Sensing Circuit for Modulating Gut Conditions

The mammalian gut contains trillions of microbes that interact with host cells and monitor changes in the environment. Opportunistic pathogens exploit environmental conditions to stimulate their growth and virulence, leading to a resurgence of chronic disorders such as inflammatory bowel disease (IBD). Current therapies are effective in less than 30% of patients due to the lack of adherence to prescription schedules and overall, off-target effects. Smart microbial therapeutics can be engineered to colonize the gut, providing in situ surveillance and conditional disease modulation. However, many current engineered microbes can only respond to single gut environmental factors, limiting their effectiveness. In this work, we implement the previously characterized split activator AND logic gate in the probiotic E. coli strain Nissle 1917. Our system can respond to two input signals: the inflammatory biomarker tetrathionate and a second input signal, IPTG. We report 4-6 fold induction with minimal leak when both signals are present. We model the dynamics of the AND gate using chemical reaction networks, and by tuning parameters in silico, we identified perturbations that affect our circuit's selectivity. We anticipate that our results will prove useful for designing living therapeutics for spatial targeting and signal processing in complex environments

Selenoprotein gene nomenclature

The human genome contains 25 genes coding for selenocysteine-containing proteins (selenoproteins). These proteins are involved in a variety of functions, most notably redox homeostasis. Selenoprotein enzymes with known functions are designated according to these functions: TXNRD1, TXNRD2, and TXNRD3 (thioredoxin reductases), GPX1, GPX2, GPX3, GPX4 and GPX6 (glutathione peroxidases), DIO1, DIO2, and DIO3 (iodothyronine deiodinases), MSRB1 (methionine-R-sulfoxide reductase 1) and SEPHS2 (selenophosphate synthetase 2). Selenoproteins without known functions have traditionally been denoted by SEL or SEP symbols. However, these symbols are sometimes ambiguous and conflict with the approved nomenclature for several other genes. Therefore, there is a need to implement a rational and coherent nomenclature system for selenoprotein-encoding genes. Our solution is to use the root symbol SELENO followed by a letter. This nomenclature applies to SELENOF (selenoprotein F, the 15 kDa selenoprotein, SEP15), SELENOH (selenoprotein H, SELH, C11orf31), SELENOI (selenoprotein I, SELI, EPT1), SELENOK (selenoprotein K, SELK), SELENOM (selenoprotein M, SELM), SELENON (selenoprotein N, SEPN1, SELN), SELENOO (selenoprotein O, SELO), SELENOP (selenoprotein P, SeP, SEPP1, SELP), SELENOS (selenoprotein S, SELS, SEPS1, VIMP), SELENOT (selenoprotein T, SELT), SELENOV (selenoprotein V, SELV) and SELENOW (selenoprotein W, SELW, SEPW1). This system, approved by the HUGO Gene Nomenclature Committee, also resolves conflicting, missing and ambiguous designations for selenoprotein genes and is applicable to selenoproteins across vertebrates

Abrupt climate change as an important agent of ecological change in the Northeast U.S. throughout the past 15,000 years

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Quaternary Science Reviews 28 (2009): 1693-1709, doi:10.1016/j.quascirev.2009.04.005.We use a series of tests to evaluate two competing hypotheses about the association of climate and vegetation trends in the northeastern United States over the past 15 kyrs. First, that abrupt climate changes on the scale of centuries had little influence on long-term vegetation trends, and second, that abrupt climate changes interacted with slower climate trends to determine the regional sequence of vegetation phases. Our results support the second. Large dissimilarity between temporally-close fossil pollen samples indicates large vegetation changes within 500 years across >4° of latitude at ca. 13.25-12.75, 12.0-11.5, 10.5, 8.25, and 5.25 ka. The evidence of vegetation change coincides with independent isotopic and sedimentary indicators of rapid shifts in temperature and moisture balance. In several cases, abrupt changes reversed long-term vegetation trends, such as when spruce (Picea) and pine (Pinus) pollen percentages rapidly declined to the north and increased to the south at ca. 13.25-12.75 and 8.25 ka respectively. Abrupt events accelerated other long‐term trends, such as a regional increase in beech (Fagus) pollen percentages at 8.5-8.0 ka. The regional hemlock (Tsuga) decline at ca. 5.25 ka is unique among the abrupt events, and may have been induced by high climatic variability (i.e., repeated severe droughts from 5.7-2.0 ka); autoregressive ecological and evolutionary processes could have maintained low hemlock abundance until ca. 2.0 ka. Delayed increases in chestnut (Castanea) pollen abundance after 5.8 and 2.5 ka also illustrate the potential for multi-century climate variability to influence species’ recruitment as well as mortality. Future climate changes will probably also rapidly initiate persistent vegetation change, particularly by acting as broad, regional-scale disturbances.This work was supported by NSF grants to B. Shuman (EAR‐0602408; DEB‐0816731) and J. Donnelly (EAR‐0602380)

High-Throughput Chemical Screen Identifies a Novel Potent Modulator of Cellular Circadian Rhythms and Reveals CKIα as a Clock Regulatory Kinase

A novel compound “longdaysin” was found to dramatically slow down the speed of the circadian clock through simultaneous inhibition of protein kinases CKIδ, CKIα, and ERK2

The ATLAS fast tracKer system

The ATLAS Fast TracKer (FTK) was designed to provide full tracking for the ATLAS high-level trigger by using pattern recognition based on Associative Memory (AM) chips and fitting in high-speed field programmable gate arrays. The tracks found by the FTK are based on inputs from all modules of the pixel and silicon microstrip trackers. The as-built FTK system and components are described, as is the online software used to control them while running in the ATLAS data acquisition system. Also described is the simulation of the FTK hardware and the optimization of the AM pattern banks. An optimization for long-lived particles with large impact parameter values is included. A test of the FTK system with the data playback facility that allowed the FTK to be commissioned during the shutdown between Run 2 and Run 3 of the LHC is reported. The resulting tracks from part of the FTK system covering a limited η-ϕ region of the detector are compared with the output from the FTK simulation. It is shown that FTK performance is in good agreement with the simulation. © The ATLAS collaboratio

Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes.

OBJECTIVE: Proinsulin is a precursor of mature insulin and C-peptide. Higher circulating proinsulin levels are associated with impaired β-cell function, raised glucose levels, insulin resistance, and type 2 diabetes (T2D). Studies of the insulin processing pathway could provide new insights about T2D pathophysiology. RESEARCH DESIGN AND METHODS: We have conducted a meta-analysis of genome-wide association tests of ∼2.5 million genotyped or imputed single nucleotide polymorphisms (SNPs) and fasting proinsulin levels in 10,701 nondiabetic adults of European ancestry, with follow-up of 23 loci in up to 16,378 individuals, using additive genetic models adjusted for age, sex, fasting insulin, and study-specific covariates. RESULTS: Nine SNPs at eight loci were associated with proinsulin levels (P < 5 × 10(-8)). Two loci (LARP6 and SGSM2) have not been previously related to metabolic traits, one (MADD) has been associated with fasting glucose, one (PCSK1) has been implicated in obesity, and four (TCF7L2, SLC30A8, VPS13C/C2CD4A/B, and ARAP1, formerly CENTD2) increase T2D risk. The proinsulin-raising allele of ARAP1 was associated with a lower fasting glucose (P = 1.7 × 10(-4)), improved β-cell function (P = 1.1 × 10(-5)), and lower risk of T2D (odds ratio 0.88; P = 7.8 × 10(-6)). Notably, PCSK1 encodes the protein prohormone convertase 1/3, the first enzyme in the insulin processing pathway. A genotype score composed of the nine proinsulin-raising alleles was not associated with coronary disease in two large case-control datasets. CONCLUSIONS: We have identified nine genetic variants associated with fasting proinsulin. Our findings illuminate the biology underlying glucose homeostasis and T2D development in humans and argue against a direct role of proinsulin in coronary artery disease pathogenesis

Tracing data journeys through medical case reports: Conceptualizing case reports not as 'anecdotes' but productive epistemic constructs, or why zebras can be useful

Medical case reports provide an important example of data journeying: they are used to collect data and make them available for re-use to others in the field including clinicians, biomedical researchers, and health policymakers. In this paper, I explore how data journey in case reports, with particular focus on the earliest stages of the process, namely from creation and publication of case reports to the initial re-uses of them and data within them. I investigate key themes relating to case reporting and re-use, including factors which seem to smooth the path along which the data captured by a case report journey via broader citation patterns and detailed qualitative analysis of highly re-used case reports. This analysis reveals some of the key factors associated with the case reports whose data have greater amounts of journeying including publication in a general medical journal; that the data have broader implications and evidential value for topical or even urgent issues for instance in public health; and use in the case report of multiple research methods or concepts from diverse subfields. These findings along with standardization of case reporting are shown to have epistemological implications, particularly for how we understand the journeying of data.Rachel A. Anken