A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as “phenotypic noise.” In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alon

Aspect-Controlled Neural Argument Generation

We rely on arguments in our daily lives to deliver our opinions and base them on evidence, making them more convincing in turn. However, finding and formulating arguments can be challenging. In this work, we train a language model for argument generation that can be controlled on a fine-grained level to generate sentence-level arguments for a given topic, stance, and aspect. We define argument aspect detection as a necessary method to allow this fine-granular control and crowdsource a dataset with 5,032 arguments annotated with aspects. Our evaluation shows that our generation model is able to generate high-quality, aspect-specific arguments. Moreover, these arguments can be used to improve the performance of stance detection models via data augmentation and to generate counter-arguments. We publish all datasets and code to fine-tune the language model

Intrinsic Gating Properties of a Cloned G Protein-activated Inward Rectifier K^+ Channel

The voltage-, time-, and K^+-dependent properties of a G protein-activated inwardly rectifying K^+ channel (GIRK1/KGA/Kir3.1) cloned from rat atrium were studied in Xenopus oocytes under two-electrode voltage clamp. During maintained G protein activation and in the presence of high external K^+ (V_K = 0 mV), voltage jumps from V_K to negative membrane potentials activated inward GIRK1 K^+ currents with three distinct time-resolved current components. GIRK1 current activation consisted of an instantaneous component that was followed by two components with time constants T_f~50 ms and T_s~400 ms. These activation time constants were weakly voltage dependent, increasing approximately twofold with maximal hyperpolarization from V_K. Voltage-dependent GIRK1 availability, revealed by tail currents at -80 mV after long prepulses, was greatest at potentials negative to V_K and declined to a plateau of approximately half the maximal level at positive voltages. Voltage-dependent GIRK1 availability shifted with V_K and was half maximal at V_K -20 mV; the equivalent gating charge was ~1.6 e^-. The voltage-dependent gating parameters of GIRK1 did not significantly differ for G protein activation by three heterologously expressed signaling pathways: m2 muscarinic receptors, serotonin 1A receptors, or G protein β1y2 subunits. Voltage dependence was also unaffected by agonist concentration. These results indicate that the voltage-dependent gating properties of GIRK1 are not due to extrinsic factors such as agonist-receptor interactions and G protein-channel coupling, but instead are analogous to the intrinsic gating behaviors of other inwardly rectifying K^+ channels

Transhumanism and the Anthropocene in Becky Chambers’A Closed and Common Orbit

Transhumanism has been rising in both popularity and influence on western societies and philosophical thought. Dreams of mind transfer, immortality, or cloning as well as the fear of sentient and intelligent artificial intelligence (AI) can be traced in some of Netflix’s most popular series such as Altered Carbon(2018), from the novel by Richard K. Morgan, or Orphan Black(2013), to mention just a few. Similarly, transhumanism may be spotted in Becky Chambers’ fiction. The novel analysed in this paper, AClosed and Common Orbit(2016), a sequel in the author’s Wayfarers series, explores the possibility of cloning human bodies, the production of sentient AI, and the subsequent ethical implications of both science fiction tropes. Far from showing transhumanism as a miracle solution to limitations in human bodies and capacity to avoid climate change, the text presents the suspicions and fears transhumanism may raise in the USA. This article provides evidence of how the Anthropocene and transhumanism operate in Becky Chambers’ novel, theethical effects concerning intrinsic and extrinsic values andtheirpossible subversion through a posthumanist alliance under the Anthropocene.El transhumanismo ha ganado popularidad e influencia en las sociedades occidentales, así como en su pensamiento filosófico. Ciertas fantasías transhumanistas como la transmisión de la consciencia, la inmortalidad o la clonación, así como IAs conscientes pueden rastrearse en algunas series de Netflix, comoAltered Carbon (2018) uOrphan Black(2013). Igualmente, el transhumanismo ha impregnado la ficción estadounidense, como puede verse en la novela de Becky Chamber,A Closed and Common Orbit(2016). En ella se explora la clonación de cuerpos humanos, la existencia de una IA consciente y sus consecuencias éticas. Lejos de mostrar el transhumanismo como una solución milagrosa a las limitaciones del cuerpo humano y la capacidad de evitar el cambio climático, el texto explora ansiedad es que el transhumanismo despierta en Estados Unidos. El artículo muestra evidencia de cómo la Antropoceno y el transhumanismo operan en la novela de Becky Chambers, sus efectos éticos en relación a los valores extrínsecos e intrínsecos, así como su posible subversión a través de una alianza posthumanista bajo el Antropoceno

CD28 between tolerance and autoimmunity: The side effects of animal models [version 1; referees: 2 approved]

Regulation of immune responses is critical for ensuring pathogen clearance and for preventing reaction against self-antigens. Failure or breakdown of immunological tolerance results in autoimmunity. CD28 is an important co-stimulatory receptor expressed on T cells that, upon specific ligand binding, delivers signals essential for full T-cell activation and for the development and homeostasis of suppressive regulatory T cells. Many in vivo mouse models have been used for understanding the role of CD28 in the maintenance of immune homeostasis, thus leading to the development of CD28 signaling modulators that have been approved for the treatment of some autoimmune diseases. Despite all of this progress, a deeper understanding of the differences between the mouse and human receptor is required to allow a safe translation of pre-clinical studies in efficient therapies. In this review, we discuss the role of CD28 in tolerance and autoimmunity and the clinical efficacy of drugs that block or enhance CD28 signaling, by highlighting the success and failure of pre-clinical studies, when translated to humans

Excess resistivity in graphene superlattices caused by umklapp electron-electron scattering

Umklapp processes play a fundamental role as the only intrinsic mechanism that allows electrons to transfer momentum to the crystal lattice and, therefore, provide a finite electrical resistance in pure metals. However, umklapp scattering has proven to be elusive in experiment as it is easily obscured by other dissipation mechanisms. Here we show that electron-electron umklapp scattering dominates the transport properties of graphene-on-boron-nitride superlattices over a wide range of temperatures and carrier densities. The umklapp processes cause giant excess resistivity that rapidly increases with increasing the superlattice period and are responsible for deterioration of the room-temperature mobility by more than an order of magnitude as compared to standard, non-superlattice graphene devices. The umklapp scattering exhibits a quadratic temperature dependence accompanied by a pronounced electron-hole asymmetry with the effect being much stronger for holes rather than electrons. Aside from fundamental interest, our results have direct implications for design of possible electronic devices based on heterostructures featuring superlattices

A computationally engineered RAS rheostat reveals RAS-ERK signaling dynamics.

Synthetic protein switches controlled with user-defined inputs are powerful tools for studying and controlling dynamic cellular processes. To date, these approaches have relied primarily on intermolecular regulation. Here we report a computationally guided framework for engineering intramolecular regulation of protein function. We utilize this framework to develop chemically inducible activator of RAS (CIAR), a single-component RAS rheostat that directly activates endogenous RAS in response to a small molecule. Using CIAR, we show that direct RAS activation elicits markedly different RAS-ERK signaling dynamics from growth factor stimulation, and that these dynamics differ among cell types. We also found that the clinically approved RAF inhibitor vemurafenib potently primes cells to respond to direct wild-type RAS activation. These results demonstrate the utility of CIAR for quantitatively interrogating RAS signaling. Finally, we demonstrate the general utility of our approach in design of intramolecularly regulated protein tools by applying it to the Rho family of guanine nucleotide exchange factors

Stochastic Gene Expression in a Lentiviral Positive Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity

Stochastic gene expression has been implicated in a variety of cellular processes, including cell differentiation and disease. In this issue of Cell, Weinberger et al. (2005) take an integrated computational-experimental approach to study the Tat transactivation feedback loop in HIV-1 and show that fluctuations in a key regulator, Tat, can result in a phenotypic bifurcation. This phenomenon is observed in an isogenic population where individual cells display two distinct expression states corresponding to latent and productive infection by HIV-1. These findings demonstrate the importance of stochastic gene expression in molecular "decision-making."Comment: Supplemental data available as q-bio.MN/060800

Intrinsic and Extrinsic Connections of Tet3 Dioxygenase with CXXC Zinc Finger Modules.

Tet proteins are emerging as major epigenetic modulators of cell fate and plasticity. However, little is known about how Tet proteins are targeted to selected genomic loci in distinct biological contexts. Previously, a CXXC-type zinc finger domain in Tet1 was shown to bind CpG-rich DNA sequences. Interestingly, in human and mouse the Tet2 and Tet3 genes are adjacent to Cxxc4 and Cxxc10-1, respectively. The CXXC domains encoded by these loci, together with those in Tet1 and Cxxc5, identify a distinct homology group within the CXXC domain family. Here we provide evidence for alternative mouse Tet3 transcripts including the Cxxc10-1 sequence (Tet3(CXXC)) and for an interaction between Tet3 and Cxxc4. In vitro Cxxc4 and the isolated CXXC domains of Tet1 and Tet3(CXXC) bind DNA substrates with similar preference towards the modification state of cytosine at a single CpG site. In vivo Tet1 and Tet3 isoforms with and without CXXC domain hydroxylate genomic 5-methylcytosine with similar activity. Relative transcript levels suggest that distinct ratios of Tet3(CXXC) isoforms and Tet3-Cxxc4 complex may be present in adult tissues. Our data suggest that variable association with CXXC modules may contribute to context specific functions of Tet proteins

Mammalian gene expression variability is explained by underlying cell state.

Gene expression variability in mammalian systems plays an important role in physiological and pathophysiological conditions. This variability can come from differential regulation related to cell state (extrinsic) and allele-specific transcriptional bursting (intrinsic). Yet, the relative contribution of these two distinct sources is unknown. Here, we exploit the qualitative difference in the patterns of covariance between these two sources to quantify their relative contributions to expression variance in mammalian cells. Using multiplexed error robust RNA fluorescent in situ hybridization (MERFISH), we measured the multivariate gene expression distribution of 150 genes related to Ca2+ signaling coupled with the dynamic Ca2+ response of live cells to ATP. We show that after controlling for cellular phenotypic states such as size, cell cycle stage, and Ca2+ response to ATP, the remaining variability is effectively at the Poisson limit for most genes. These findings demonstrate that the majority of expression variability results from cell state differences and that the contribution of transcriptional bursting is relatively minimal