Rapid RNA Exchange in Aqueous Two-Phase System and Coacervate Droplets

Compartmentalization in a prebiotic setting is an important aspect of early cell formation and is crucial for the development of an artificial protocell system that effectively couples genotype and phenotype. Aqueous two-phase systems (ATPSs) and complex coacervates are phase separation phenomena that lead to the selective partitioning of biomolecules and have recently been proposed as membrane-free protocell models. We show in this study through fluorescence recovery after photobleaching (FRAP) microscopy that despite the ability of such systems to effectively concentrate RNA, there is a high rate of RNA exchange between phases in dextran/polyethylene glycol ATPS and ATP/poly-L-lysine coacervate droplets. In contrast to fatty acid vesicles, these systems would not allow effective segregation and consequent evolution of RNA, thus rendering these systems ineffective as model protocells. Electronic supplementary material The online version of this article (doi:10.1007/s11084-014-9355-8) contains supplementary material, which is available to authorized users

Numerical analysis of flexural performances of composite steel-timber beams under fire conditions

Recently, a novel type of composite structure, composite steel-timber (CST) structure, has attracted much attention by combining steel and timber in an effective way to form composite structural components, which unitises the advantages of high strength and excellent ductility of steel and decent sustainability and fire resistance of timber. However, the existing research is lacking, especially in structural fire design and analysis. In this study, based on the sequentially coupled method, the commercial finite element software ABAQUS was used to numerically simulate the dynamic performances in the temperature field and the flexural behaviours in the displacement field for a typical CST beam with a steel element embedded within the Glulam and connected by adhesives and bolts under standard fire for two hours. In the numerical simulations, the temperature distributions within the CST beam were explored, and the flexural performances of the beam in the displacement field were examined. Through the comparative analysis, the temperature distributions in the embedded steel beam and the surrounding Glulam beam under one-hour standard fire verified the advantages of this type of CST beam in structural fire design. Specifically, under a 2-hour standard fire, the surrounding Glulam could still protect the embedded steel beam from sustaining too high temperatures, so as to retain most of its material properties and help maintain the bearing capacity of the whole structure and improve the refractory limit. Parametric studies on the fire resistance of the CST beam were also conducted by adjusting the bolt spacing and the protection thickness of the Glulam. The obtained results indicated that reducing the bolt spacing and the thickness of the Glulam protection layer would have an adverse effect on the temperature distributions in the embedded steel element to a large extent, and would eventually lead to its rapid heating and strength loss and the final failure of the whole CST structure

Can Small and Synthetic Benchmarks Drive Modeling Innovation? A Retrospective Study of Question Answering Modeling Approaches

Datasets are not only resources for training accurate, deployable systems, but are also benchmarks for developing new modeling approaches. While large, natural datasets are necessary for training accurate systems, are they necessary for driving modeling innovation? For example, while the popular SQuAD question answering benchmark has driven the development of new modeling approaches, could synthetic or smaller benchmarks have led to similar innovations? This counterfactual question is impossible to answer, but we can study a necessary condition: the ability for a benchmark to recapitulate findings made on SQuAD. We conduct a retrospective study of 20 SQuAD modeling approaches, investigating how well 32 existing and synthesized benchmarks concur with SQuAD -- i.e., do they rank the approaches similarly? We carefully construct small, targeted synthetic benchmarks that do not resemble natural language, yet have high concurrence with SQuAD, demonstrating that naturalness and size are not necessary for reflecting historical modeling improvements on SQuAD. Our results raise the intriguing possibility that small and carefully designed synthetic benchmarks may be useful for driving the development of new modeling approaches.Comment: 40 pages, 13 figures; preprin

Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single-Molecule Barcodes

RNA sequencing (RNA-Seq) is a powerful tool for transcriptome profiling, but is hampered by sequence-dependent bias and inaccuracy at low copy numbers intrinsic to exponential PCR amplification. We developed a simple strategy for mitigating these complications, allowing truly digital RNA-Seq. Following reverse transcription, a large set of barcode sequences is added in excess, and nearly every cDNA molecule is uniquely labeled by random attachment of barcode sequences to both ends. After PCR, we applied paired-end deep sequencing to read the two barcodes and cDNA sequences. Rather than counting the number of reads, RNA abundance is measured based on the number of unique barcode sequences observed for a given cDNA sequence. We optimized the barcodes to be unambiguously identifiable, even in the presence of multiple sequencing errors. This method allows counting with single-copy resolution despite sequence-dependent bias and PCR-amplification noise, and is analogous to digital PCR but amendable to quantifying a whole transcriptome. We demonstrated transcriptome profiling of Escherichia coli with more accurate and reproducible quantification than conventional RNA-Seq.Chemistry and Chemical Biolog

ATP-independent reversal of a membrane protein aggregate by a chloroplast SRP subunit

Membrane proteins impose enormous challenges to cellular protein homeostasis during their post-translational targeting, and they require chaperones to keep them soluble and translocation competent. Here we show that a novel targeting factor in the chloroplast signal recognition particle (cpSRP), cpSRP43, is a highly specific molecular chaperone that efficiently reverses the aggregation of its substrate proteins. In contrast to 'ATPases associated with various cellular activities' (AAA+) chaperones, cpSRP43 uses specific binding interactions with its substrate to mediate its 'disaggregase' activity. This disaggregase capability can allow targeting machineries to more effectively capture their protein substrates and emphasizes a close connection between protein folding and trafficking processes. Moreover, cpSRP43 provides the first example to our knowledge of an ATP-independent disaggregase and shows that efficient reversal of protein aggregation can be attained by specific binding interactions between a chaperone and its substrate

Pulseq: A rapid and hardwareâ independent pulse sequence prototyping framework

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/136354/1/mrm26235.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136354/2/mrm26235_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136354/3/mrm26235-sup-0001-suppinfo.pd

Enhanced Colorimetric Differentiation between Staphylococcus aureus and Pseudomonas aeruginosa Using a Shape-Encoded Sensor Hydrogel

Herein, we demonstrate a combined fluorescent probe/shape-encoded hydrogel strategy for the fast, sensitive, and selective detection of bacterial species via their characteristic enzymes. A poly(vinyl alcohol) (PVA) hydrogel loaded with the fluorescent probe N,N′-(3-oxo-3H-spiro[isobenzofuran-1,9′-xanthene]-3′,6′-diyl)bis(2,2,3,3,3-pentafluoropropanamide) (ACS-HNE) was designed for the detection of elastase, an enzyme produced by Pseudomonas aeruginosa. Likewise, a chitosan-derived hydrogel was loaded with the fluorescent probe 4-methylumbelliferyl-α-d-glucopyranoside (MUD) by entrapment for the selective detection of α-glucosidase, an enzyme produced by Staphylococcus aureus. For an observation time of 60 min, limits of detection (LODs) of ≤20 nM for elastase and ≤30 pM for α-glucosidase were obtained, which in the latter case is 3 orders of magnitude better than related chitosan systems with covalently coupled substrate. To illustrate the potential utility of these highly sensitive sensor hydrogels as a simple point-of-care test system, shaped hydrogel slabs representing the letters P and S were manufactured to detect P. aeruginosa and S. aureus, respectively. These shapes were shown to provide an additional unique color code under UV illumination corresponding to the characteristic enzyme produced by the corresponding bacteria. This study shows potential for the future development of an effective and simple point-of-care test for the rapid identification of bacterial species that can be operated by nonspecialists

Life-Detection Technologies for the Next Two Decades

Since its inception six decades ago, astrobiology has diversified immensely to encompass several scientific questions including the origin and evolution of Terran life, the organic chemical composition of extraterrestrial objects, and the concept of habitability, among others. The detection of life beyond Earth forms the main goal of astrobiology, and a significant one for space exploration in general. This goal has galvanized and connected with other critical areas of investigation such as the analysis of meteorites and early Earth geological and biological systems, materials gathered by sample-return space missions, laboratory and computer simulations of extraterrestrial and early Earth environmental chemistry, astronomical remote sensing, and in-situ space exploration missions. Lately, scattered efforts are being undertaken towards the R&D of the novel and as-yet-space-unproven life-detection technologies capable of obtaining unambiguous evidence of extraterrestrial life, even if it is significantly different from Terran life. As the suite of space-proven payloads improves in breadth and sensitivity, this is an apt time to examine the progress and future of life-detection technologies.Comment: 6 pages, the white paper was submitted to and cited by the National Academy of Sciences in support of the Astrobiology Science Strategy for the Search for Life in the Univers