Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules

Using total intrnal reflection fluorescence microscopy, we directly visualize in real-time, the 1D Brownian motion and transcription elongation of T7 RNA polymerase along aligned DNA molecules bound to substrates by molecular combing. We fluorescently label T7 RNA polymerase with antibodies and use flow to convect them orthogonally to the DNA alignment direction, permitting observation and estimation of the protein diffusivity along the DNA at the single-molecule level. Our observations suggest that the 1D diffusion coefficient varies from molecule to molecule over the range 6.1 × 10−11 cm2/s to 4.3 × 10−9 cm2/s. We also observe binding and transcription by T7 RNA polymerases on single combed T7 DNA molecules with an apparent association rate of 1.6 μM−1s−1. From the measured dependence of the rate of transcription on concentration of nucleotide triphosphate, we infer that the combed DNA molecules capable of interacting with proteins are under an average tension of 25 pN

Integrating comprehensive two-dimensional gas chromatography and downhole fluid analysis to validate a spill-fill sequence of reservoirs with variations of biodegradation, water washing and thermal maturity

Author Posting. © The Author(s), 2016. This is the author's version of the work. It is posted here for personal use, not for redistribution. The definitive version was published in Fuel 191 (2017): 538-554, doi:10.1016/j.fuel.2016.11.081.Optimization of crude oil production depends heavily on crude oil composition and its variation within individual reservoirs and across multiple reservoirs. In particular, asphaltene content has an enormous impact on crude oil viscosity and even the economic value of the fluids in the reservoir. Thus, it is highly desirable to understand the primary controls on crude oil composition and asphaltene distributions in reservoirs. Here, a complex oilfield in the North Sea containing six separate reservoirs is addressed. The crude oil is believed to have spilled out of deeper reservoirs into shallower reservoirs during the overall reservoir charging process. Asphaltene content is measured in-situ through downhole fluid analysis and is generally consistent with a spill-fill sequence in reservoir charging. Detailed compositional analysis of crude oil samples by comprehensive two-dimensional gas chromatography (GC×GC) is used to determine the extent and variation among the reservoirs of water washing, biodegradation and thermal maturity. Increased biodegradation and water washing in the shallower reservoirs is consistent with a spill-fill sequence. The water washing is evidently assisted by biodegradation. Moreover, analyses of four thermal maturity biomarkers show that shallower reservoirs contain less mature oil, again consistent with a spill-fill sequence. The combination of DFA for bulk compositional analysis and GC×GC for detailed compositional analysis with geochemical interpretation is an effective tool for unraveling complex oilfield scenarios

Bruton's Tyrosine Kinase Inhibition Attenuates the Cardiac Dysfunction Caused by Cecal Ligation and Puncture in Mice

Sepsis is one of the most prevalent diseases in the world. The development of cardiac dysfunction in sepsis results in an increase of mortality. It is known that Bruton's tyrosine kinase (BTK) plays a role in toll-like receptor signaling and NLRP3 inflammasome activation, two key components in the pathophysiology of sepsis and sepsis-associated cardiac dysfunction. In this study we investigated whether pharmacological inhibition of BTK (ibrutinib 30 mg/kg and acalabrutinib 3 mg/kg) attenuates sepsis associated cardiac dysfunction in mice. 10-week old male C57BL/6 mice underwent CLP or sham surgery. One hour after surgery mice received either vehicle (5% DMSO + 30% cyclodextrin i.v.), ibrutinib (30 mg/kg i.v.), or acalabrutinib (3 mg/kg i.v.). Mice also received antibiotics and an analgesic at 6 and 18 h. After 24 h, cardiac function was assessed by echocardiography in vivo. Cardiac tissue underwent western blot analysis to determine the activation of BTK, NLRP3 inflammasome and NF-\u3baB pathway. Serum analysis of 33 cytokines was conducted by a multiplex assay. When compared to sham-operated animals, mice subjected to CLP demonstrated a significant reduction in ejection fraction (EF), fractional shortening (FS), and fractional area change (FAC). The cardiac tissue from CLP mice showed significant increases of BTK, NF-\u3baB, and NLRP3 inflammasome activation. CLP animals resulted in a significant increase of serum cytokines and chemokines (TNF-\u3b1, IL-6, IFN-\u3b3, KC, eotaxin-1, eotaxin-2, IL-10, IL-4, CXCL10, and CXCL11). Delayed administration of ibrutinib and acalabrutinib attenuated the decline of EF, FS, and FAC caused by CLP and also reduced the activation of BTK, NF-\u3baB, and NLRP3 inflammasome. Both ibrutinib and acalabrutinib significantly suppressed the release of cytokines and chemokines. Our study revealed that delayed intravenous administration of ibrutinib or acalabrutinib attenuated the cardiac dysfunction associated with sepsis by inhibiting BTK, reducing NF-\u3baB activation and the activation of the inflammasome. Cytokines associated with sepsis were significantly reduced by both BTK inhibitors. Acalabrutinib is found to be more potent than ibrutinib and could potentially prove to be a novel therapeutic in sepsis. Thus, the FDA-approved BTK inhibitors ibrutinib and acalabrutinib may be repurposed for the use in sepsis

Functionally heterogeneous human satellite cells identified by single cell RNA sequencing.

Although heterogeneity is recognized within the murine satellite cell pool, a comprehensive understanding of distinct subpopulations and their functional relevance in human satellite cells is lacking. We used a combination of single cell RNA sequencing and flow cytometry to identify, distinguish, and physically separate novel subpopulations of human PAX7+ satellite cells (Hu-MuSCs) from normal muscles. We found that, although relatively homogeneous compared to activated satellite cells and committed progenitors, the Hu-MuSC pool contains clusters of transcriptionally distinct cells with consistency across human individuals. New surface marker combinations were enriched in transcriptional subclusters, including a subpopulation of Hu-MuSCs marked by CXCR4/CD29/CD56/CAV1 (CAV1+). In vitro, CAV1+ Hu-MuSCs are morphologically distinct, and characterized by resistance to activation compared to CAV1- Hu-MuSCs. In vivo, CAV1+ Hu-MuSCs demonstrated increased engraftment after transplantation. Our findings provide a comprehensive transcriptional view of normal Hu-MuSCs and describe new heterogeneity, enabling separation of functionally distinct human satellite cell subpopulations

A social relations analysis of young children's trust in their peers across the early years of school

Two hundred and five (103 female and 102 male) children enrolled in school years 1 and 2 in the United Kingdom (mean age 6 years 1 month at Time 1) were tested twice over a 1-year period. The children reported the promise keeping and secret keeping behaviours of classmates (all peers and same-gender peers) and provided friendship nominations (Time 2 only). Round robin social relations analyses for all peers and same-gender peers revealed: (a) perceiver variance, demonstrating consistent individual differences in trust beliefs in peers; (b) target variance, demonstrating consistent individual differences in eliciting trust from peers; and, (c) dyadic reciprocity, demonstrating reciprocal trust between individuals. Replicability across measures, stability, and cross-measure stability of these effects were found for all peers only. As hypothesised, the perceiver and target effects of trust were associated with the number of friendships. The findings support the concl usion that young children demonstrate multiple components of trust in dyadic relationships, which are associated with their social relationships

Weaving the internet together: Imagined communities in newspaper comment threads

Online newspapers (and other spaces) are increasingly seeking to utilise user-generated content alongside professionally developed material. However, this might leave websites increasingly vulnerable to trolls, who work to disrupt online communications in online spaces. Such behaviour can have serious consequences both in peoples online and offline lives, and for the development of coherent online communities. One means of controlling is through the manipulation of the online space to create social norms of polite behaviour through the founding of ‘imagined communities’ online. Approaching the issue from a discursive psychological perspective, this paper draws upon comments published in two online British newspaper comment sections responding to the publication of an academic article on trolling. Imagined communities are shown to arise irrespective of the presence of the virtual infrastructure to support the development of these imagined communities. Key features of imagined communities identified here are: individuation (as opposed to deindividuation); mutual influence between posters; shared history for both the users and the online space; the use of humour to cement social bonds. Analysis also revealed tensions in posters understanding of online and offline behaviours. This research holds implications for understanding online spaces, and the interactions between users within these spaces.N/

A novel genomic alteration of LSAMP associates with aggressive prostate cancer in African American men

Evaluation of cancer genomes in global context is of great interest in light of changing ethnic distribution of the world population. We focused our study on men of African ancestry because of their disproportionately higher rate of prostate cancer (CaP) incidence and mortality. We present a systematic whole genome analyses, revealing alterations that differentiate African American (AA) and Caucasian American (CA) CaP genomes. We discovered a recurrent deletion on chromosome 3q13.31 centering on the LSAMP locus that was prevalent in tumors from AA men (cumulative analyses of 435 patients: whole genome sequence, 14; FISH evaluations, 101; and SNP array, 320 patients). Notably, carriers of this deletion experienced more rapid disease progression. In contrast, PTEN and ERG common driver alterations in CaP were significantly lower in AA prostate tumors compared to prostate tumors from CA. Moreover, the frequency of inter-chromosomal rearrangements was significantly higher in AA than CA tumors. These findings reveal differentially distributed somaticmutations in CaP across ancestral groups, which have implications for precision medicine strategies. (C) 2015 The Authors. Published by Elsevier B.V

Selection, characterization and application of new RNA HIV gp 120 aptamers for facile delivery of Dicer substrate siRNAs into HIV infected cells

The envelope glycoprotein of human immunodeficiency virus (HIV) consists of an exterior glycoprotein (gp120) and a trans-membrane domain (gp41) and has an important role in viral entry into cells. HIV-1 entry has been validated as a clinically relevant anti-viral strategy for drug discovery. In the present work, several 2′-F substituted RNA aptamers that bind to the HIV-1BaL gp120 protein with nanomole affinity were isolated from a RNA library by the SELEX (Systematic Evolution of Ligands by EXponential enrichment) procedure. From two of these aptamers we created a series of new dual inhibitory function anti-gp120 aptamer–siRNA chimeras. The aptamers and aptamer–siRNA chimeras specifically bind to and are internalized into cells expressing HIV gp160. The Dicer-substrate siRNA delivered by the aptamers is functionally processed by Dicer, resulting in specific inhibition of HIV-1 replication and infectivity in cultured CEM T-cells and primary blood mononuclear cells (PBMCs). Moreover, we have introduced a ‘sticky’ sequence onto a chemically synthesized aptamer which facilitates attachment of the Dicer substrate siRNAs for potential multiplexing. Our results provide a set of novel inhibitory agents for blocking HIV replication and further validate the use of aptamers for delivery of Dicer substrate siRNAs

Long-range chemical sensitivity in the sulfur K-edge X-ray absorption spectra of substituted thiophenes

© 2014 American Chemical Society. Thiophenes are the simplest aromatic sulfur-containing compounds and are stable and widespread in fossil fuels. Regulation of sulfur levels in fuels and emissions has become and continues to be ever more stringent as part of governments' efforts to address negative environmental impacts of sulfur dioxide. In turn, more effective removal methods are continually being sought. In a chemical sense, thiophenes are somewhat obdurate and hence their removal from fossil fuels poses problems for the industrial chemist. Sulfur K-edge X-ray absorption spectroscopy provides key information on thiophenic components in fuels. Here we present a systematic study of the spectroscopic sensitivity to chemical modifications of the thiophene system. We conclude that while the utility of sulfur K-edge X-ray absorption spectra in understanding the chemical composition of sulfur-containing fossil fuels has already been demonstrated, care must be exercised in interpreting these spectra because the assumption of an invariant spectrum for thiophenic forms may not always be valid