Thermodynamics of RNA Internal Loops with a Guanosine-Guanosine Pair Adjacent to Another Noncanonical Pair

Thermodynamic parameters measured by optical melting are reported for formation of RNA duplexes containing tandem noncanonical pairs with at least one guanosine-guanosine (GG) pair. For selected sequences, imino proton NMR provides evidence that the desired duplex forms and that the structure of a GG pair adjacent to a noncanonical pair depends on context. A GG pair next to a different noncanonical pair is more stable than expected from measurements of adjacent GG pairs. This is likely due to an unfavorable stacking interaction between adjacent GG pairs, where areas of high negative charge probably overlap. The results suggest a model where tandem noncanonical pairs closed by two GC pairs are assigned the following free energy increments at 37 °C:  0.8 kcal/mol for adjacent GG pairs, 1.0 kcal/mol for GG next to UU, and −0.3 kcal/mol for all others. These values are adjusted by 0.65 kcal/mol for each closing AU pair

Thermodynamics of RNA Internal Loops with a Guanosine-Guanosine Pair Adjacent to Another Noncanonical Pair

Thermodynamic parameters measured by optical melting are reported for formation of RNA duplexes containing tandem noncanonical pairs with at least one guanosine-guanosine (GG) pair. For selected sequences, imino proton NMR provides evidence that the desired duplex forms and that the structure of a GG pair adjacent to a noncanonical pair depends on context. A GG pair next to a different noncanonical pair is more stable than expected from measurements of adjacent GG pairs. This is likely due to an unfavorable stacking interaction between adjacent GG pairs, where areas of high negative charge probably overlap. The results suggest a model where tandem noncanonical pairs closed by two GC pairs are assigned the following free energy increments at 37 °C:  0.8 kcal/mol for adjacent GG pairs, 1.0 kcal/mol for GG next to UU, and −0.3 kcal/mol for all others. These values are adjusted by 0.65 kcal/mol for each closing AU pair

Centrosome amplification induces high grade features and is prognostic of worse outcomes in breast cancer

Table S1. Patient characteristics. Table S2. Hazard ratios from multivariate analysis. Table S3. Sequences of primers used for qRT-PCR. Figure S1. Distribution of average centrosome number per cell in the breast cancer patients represented in our TMA. Figure S2. Correlations between centrosome amplification and nodal status, patient age, and tumor size. Figure S3. Centrosome clustering but not structural abnormalities correlate with worse outcomes in breast cancer. Figure S4. CIN is prognostic of worse breast cancer-related survival. Figure S5. Centrosome amplification correlates with adverse clinical factors. Figure S6. CA correlates with higher ploidy and CIN. (DOCX 6223 kb

Decoding Polo-like kinase 1 signaling along the kinetochore–centromere axis

Protein kinase signaling along the kinetochore-centromere axis is crucial to assure mitotic fidelity, yet its spatial coordination is obscure. Here, we examined how pools of human Polo-like kinase 1 (Plk1) within this axis control signaling events to elicit mitotic functions. To do this, we restricted active Plk1 to discrete subcompartments within the kinetochore-centromere axis using chemical genetics and decoded functional and phosphoproteomic signatures of each. We observe distinct phosphoproteomic and functional roles, suggesting that Plk1 exists and functions in discrete pools along this axis. Deep within the centromere, Plk1 operates to assure proper chromosome alignment and segregation. Thus, Plk1 at the kinetochore is a conglomerate of an observable bulk pool coupled with additional functional pools below the threshold of microscopic detection/resolution. Although complex, this multiplicity of locales provides an opportunity to decouple functional and phosphoproteomic signatures for a comprehensive understanding of Plk1’s kinetochore functions

Combined encoding and decoupling solution to problems of decoherence and design in solid-state quantum computing

Proposals for scalable quantum computing devices suffer not only from decoherence due to the interaction with their environment, but also from severe engineering constraints. Here we introduce a practical solution to these major concerns, addressing solid state proposals in particular. Decoherence is first reduced by encoding a logical qubit into two qubits, then completely eliminated by an efficient set of decoupling pulse sequences. The same encoding removes the need for single-qubit operations, that pose a difficult design constraint. We further show how the dominant decoherence processes can be identified empirically, in order to optimize the decoupling pulses.Comment: 5 pages, Revtex4, updated, shortened version to appear in Phys. Rev. Let

Quantum Computation with Quantum Dots and Terahertz Cavity Quantum Electrodynamics

A quantum computer is proposed in which information is stored in the two lowest electronic states of doped quantum dots (QDs). Many QDs are located in a microcavity. A pair of gates controls the energy levels in each QD. A Controlled Not (CNOT) operation involving any pair of QDs can be effected by a sequence of gate-voltage pulses which tune the QD energy levels into resonance with frequencies of the cavity or a laser. The duration of a CNOT operation is estimated to be much shorter than the time for an electron to decohere by emitting an acoustic phonon.Comment: Revtex 6 pages, 3 postscript figures, minor typos correcte

Stem cell-derived porcine macrophages as a new platform for studying host-pathogen interactions

BACKGROUND: Infectious diseases of farmed and wild animals pose a recurrent threat to food security and human health. The macrophage, a key component of the innate immune system, is the first line of defence against many infectious agents and plays a major role in shaping the adaptive immune response. However, this phagocyte is a target and host for many pathogens. Understanding the molecular basis of interactions between macrophages and pathogens is therefore crucial for the development of effective strategies to combat important infectious diseases. RESULTS: We explored how porcine pluripotent stem cells (PSCs) can provide a limitless in vitro supply of genetically and experimentally tractable macrophages. Porcine PSC-derived macrophages (PSCdMs) exhibited molecular and functional characteristics of ex vivo primary macrophages and were productively infected by pig pathogens, including porcine reproductive and respiratory syndrome virus (PRRSV) and African swine fever virus (ASFV), two of the most economically important and devastating viruses in pig farming. Moreover, porcine PSCdMs were readily amenable to genetic modification by CRISPR/Cas9 gene editing applied either in parental stem cells or directly in the macrophages by lentiviral vector transduction. CONCLUSIONS: We show that porcine PSCdMs exhibit key macrophage characteristics, including infection by a range of commercially relevant pig pathogens. In addition, genetic engineering of PSCs and PSCdMs affords new opportunities for functional analysis of macrophage biology in an important livestock species. PSCs and differentiated derivatives should therefore represent a useful and ethical experimental platform to investigate the genetic and molecular basis of host-pathogen interactions in pigs, and also have wider applications in livestock. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-021-01217-8

Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma

Asthma is caused by a combination of poorly understood genetic and environmental factors(1,2). We have systematically mapped the effects of single nucleotide polymorphisms ( SNPs) on the presence of childhood onset asthma by genome-wide association. We characterized more than 317,000 SNPs in DNA from 994 patients with childhood onset asthma and 1,243 non-asthmatics, using family and case-referent panels. Here we show multiple markers on chromosome 17q21 to be strongly and reproducibly associated with childhood onset asthma in family and case-referent panels with a combined P value of P < 10(-12). In independent replication studies the 17q21 locus showed strong association with diagnosis of childhood asthma in 2,320 subjects from a cohort of German children (P=0.0003) and in 3,301 subjects from the British 1958 Birth Cohort (P=0.0005). We systematically evaluated the relationships between markers of the 17q21 locus and transcript levels of genes in Epstein - Barr virus (EBV)-transformed lymphoblastoid cell lines from children in the asthma family panel used in our association study. The SNPs associated with childhood asthma were consistently and strongly associated (P < 10(-22)) in cis with transcript levels of ORMDL3, a member of a gene family that encodes transmembrane proteins anchored in the endoplasmic reticulum(3). The results indicate that genetic variants regulating ORMDL3 expression are determinants of susceptibility to childhood asthma.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62682/1/nature06014.pd