Toward a Rhetoric of DNA: The Advent of CRISPR

The nucleic acid DNA, which contains an organism’s genetic information, consists of a four-letter alphabet that has until recently been characterized as a read-only text. The development of a quick, inexpensive DNA targeting and manipulation technique called CRISPR, pronounced “crisper,” though, has changed DNA from this arhetorical, read-only data set, as it has been characterized in the rhetoric literature to date, to a fully rhetorical text—one that can be not only read but created, interpreted, copied, altered, and stored as well. The Book of Nature, an idea with roots in antiquity but popularized during the nineteenth century, provides proof of concept in the form of an historical and theoretical context in which DNA can be viewed in this light. Once ensconced in the Book of Nature, DNA can longer be considered a code; rather, it is a text. DNA text has structural components that are similar to those of traditional text, and now, with CRISPR, it also has purposes, audiences, and stakeholders. Given the enormous potential of DNA text for both good and ill, rhetoricians of science and medicine must participate in discussions of the complex literacy, policy, and ethics issues this new form of text brings about

How do geomorphic characteristics affect the source of tree water uptake in restored river floodplains?

Alpine rivers and their floodplains have been highly modified by human activities during the last decades. River restoration projects aim to counteract these negative impacts and to restore ecosystem services provided by riparian habitats. We studied two recently restored river sites in the Ahr/Aurino and Mareit/Mareta Rivers (Italian Alps) to investigate how geomorphic conditions, soil moisture, and groundwater level affect the source of water used by grey alder (Alnus incana (L.) Moench). We compared the isotopic composition (δ2H) of tree sap at different locations (low terraces formed during bed incision and recent floodplains formed after restoration) with that of potential water sources, that is, groundwater, soil water, and rainfall. The monthly variation in the isotopic composition of rainfall was reflected in both shallow and deeper soil water, as well as in the isotopic composition of sap. The redistribution of precipitation and groundwater in the soil differed between the post-restoration floodplain sites and the post-incision terraces, leading to a different relation between the sap water, soil water, and groundwater isotopic composition. The results show that transpiration of A. incana trees growing on recent floodplains is mostly supported by stream-fed soil water, whereas trees growing on terraces mainly use precipitation-fed soil water. These marked, morphology-related differences in the source of transpiration water of grey alder highlight how channel degradation still affects the ecohydrological processes in Alpine fluvial corridors. Nonetheless, large restoration interventions—in terms of channel widening—can enable the self-formation of new floodplain areas characterized by stream water-fed riparian ecosystems

Iterative algorithm versus analytic solutions of the parametrically driven dissipative quantum harmonic oscillator

We consider the Brownian motion of a quantum mechanical particle in a one-dimensional parabolic potential with periodically modulated curvature under the influence of a thermal heat bath. Analytic expressions for the time-dependent position and momentum variances are compared with results of an iterative algorithm, the so-called quasiadiabatic propagator path integral algorithm (QUAPI). We obtain good agreement over an extended range of parameters for this spatially continuous quantum system. These findings indicate the reliability of the algorithm also in cases for which analytic results may not be available a priori.Comment: 15 pages including 11 figures, one reference added, minor typos correcte

Human cytomegalovirus protein RL1 degrades the antiviral factor SLFN11 via recruitment of the CRL4 E3 ubiquitin ligase complex.

Human cytomegalovirus (HCMV) is an important human pathogen and a paradigm of viral immune evasion, targeting intrinsic, innate, and adaptive immunity. We have employed two orthogonal multiplexed tandem mass tag-based proteomic screens to identify host proteins down-regulated by viral factors expressed during the latest phases of viral infection. This approach revealed that the HIV-1 restriction factor Schlafen-11 (SLFN11) was degraded by the poorly characterized, late-expressed HCMV protein RL1, via recruitment of the Cullin4-RING E3 Ubiquitin Ligase (CRL4) complex. SLFN11 potently restricted HCMV infection, inhibiting the formation and spread of viral plaques. Overall, we show that a restriction factor previously thought only to inhibit RNA viruses additionally restricts HCMV. We define the mechanism of viral antagonism and also describe an important resource for revealing additional molecules of importance in antiviral innate immunity and viral immune evasion

The Grizzly, September 22, 1992

It\u27s That Time Again: 1992 Sorority Pledging Gets Under Way at Ursinus • Dean Kane: On Alcohol Policy • The Axe Falls on Underage Drinking at Ursinus • Koester Named Head of SAC • Freshman Officers Elected • Freshman Facts • Rushing Views • Author Victor Hernandez Cruz to Read and Speak at Ursinus • Ursinus Radio WVOU • Jazz Great Dazzles Ursinus • Christ on Campus • Movie Review: Sneakers • Letters to the Editor • Lady Bears Play Tough • Volleyball Team Working to Improve • Intramurals • Youthful Soccer Squad Struggles • Grizzlies Split: Defense Shines • U.C. on the Sea • X-Country Runs Awayhttps://digitalcommons.ursinus.edu/grizzlynews/1298/thumbnail.jp

Molecular determinants of binding to the Plasmodium subtilisin-like protease 1.

PfSUB1, a subtilisin-like protease of the human malaria parasite Plasmodium falciparum, is known to play important roles during the life cycle of the parasite and has emerged as a promising antimalarial drug target. In order to provide a detailed understanding of the origin of binding determinants of PfSUB1 substrates, we performed molecular dynamics simulations in combination with MM-GBSA free energy calculations using a homology model of PfSUB1 in complex with different substrate peptides. Key interactions, as well as residues that potentially make a major contribution to the binding free energy, are identified at the prime and nonprime side of the scissile bond and comprise peptide residues P4 to P2'. This finding stresses the requirement for peptide substrates to interact with both prime and nonprime side residues of the PfSUB1 binding site. Analyzing the energetic contributions of individual amino acids within the peptide-PfSUB1 complexes indicated that van der Waals interactions and the nonpolar part of solvation energy dictate the binding strength of the peptides and that the most favorable interactions are formed by peptide residues P4 and P1. Hot spot residues identified in PfSUB1 are dispersed over the entire binding site, but clustered areas of hot spots also exist and suggest that either the S4-S2 or the S1-S2' binding site should be exploited in efforts to design small molecule inhibitors. The results are discussed with respect to which binding determinants are specific to PfSUB1 and, therefore, might allow binding selectivity to be obtained

Analysis of the real EADGENE data set: Comparison of methods and guidelines for data normalisation and selection of differentially expressed genes (Open Access publication)

A large variety of methods has been proposed in the literature for microarray data analysis. The aim of this paper was to present techniques used by the EADGENE (European Animal Disease Genomics Network of Excellence) WP1.4 participants for data quality control, normalisation and statistical methods for the detection of differentially expressed genes in order to provide some more general data analysis guidelines. All the workshop participants were given a real data set obtained in an EADGENE funded microarray study looking at the gene expression changes following artificial infection with two different mastitis causing bacteria: Escherichia coli and Staphylococcus aureus. It was reassuring to see that most of the teams found the same main biological results. In fact, most of the differentially expressed genes were found for infection by E. coli between uninfected and 24 h challenged udder quarters. Very little transcriptional variation was observed for the bacteria S. aureus. Lists of differentially expressed genes found by the different research teams were, however, quite dependent on the method used, especially concerning the data quality control step. These analyses also emphasised a biological problem of cross-talk between infected and uninfected quarters which will have to be dealt with for further microarray studies