Permanent genetic memory with >1-byte capacity

Genetic memory enables the recording of information in the DNA of living cells. Memory can record a transient environmental signal or cell state that is then recalled at a later time. Permanent memory is implemented using irreversible recombinases that invert the orientation of a unit of DNA, corresponding to the [0,1] state of a bit. To expand the memory capacity, we have applied bioinformatics to identify 34 phage integrases (and their cognate attB and attP recognition sites), from which we build 11 memory switches that are perfectly orthogonal to each other and the FimE and HbiF bacterial invertases. Using these switches, a memory array is constructed in Escherichia coli that can record 1.375 bytes of information. It is demonstrated that the recombinases can be layered and used to permanently record the transient state of a transcriptional logic gate.United States. Defense Advanced Research Projects Agency (DARPA CLIO N66001-12-C-4016)United States. Defense Advanced Research Projects Agency (DARPA CLIO N66001-12-C-4018)United States. Office of Naval Research. Multidisciplinary University Research Initiative (N00014-13-1-0074)National Institutes of Health (U.S.) (GM095765)National Institute of General Medical Sciences (U.S.) (P50 GM098792)National Science Foundation (U.S.). Synthetic Biology Engineering Research Center (SynBERC EEC0540879)FA9550-11-C-0028American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowship (32 CFR 168a

Permanent genetic memory with >1-byte capacity

Genetic memory enables the recording of information in the DNA of living cells. Memory can record a transient environmental signal or cell state that is then recalled at a later time. Permanent memory is implemented using irreversible recombinases that invert the orientation of a unit of DNA, corresponding to the [0,1] state of a bit. To expand the memory capacity, we have applied bioinformatics to identify 34 phage integrases (and their cognate attB and attP recognition sites), from which we build 11 memory switches that are perfectly orthogonal to each other and the FimE and HbiF bacterial invertases. Using these switches, a memory array is constructed in Escherichia coli that can record 1.375 bytes of information. It is demonstrated that the recombinases can be layered and used to permanently record the transient state of a transcriptional logic gate.United States. Defense Advanced Research Projects Agency (DARPA CLIO N66001-12-C-4016)United States. Defense Advanced Research Projects Agency (DARPA CLIO N66001-12-C-4018)United States. Office of Naval Research. Multidisciplinary University Research Initiative (N00014-13-1-0074)National Institutes of Health (U.S.) (GM095765)National Institute of General Medical Sciences (U.S.) (P50 GM098792)National Science Foundation (U.S.). Synthetic Biology Engineering Research Center (SynBERC EEC0540879)FA9550-11-C-0028American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowship (32 CFR 168a

Evidence for a deep, distributed and dynamic code for animacy in human ventral anterior temporal cortex.

Funder: European Research Council; Grant(s): GAP: 502670428 - BRAIN2MIND_NEUROCOMPHow does the human brain encode semantic information about objects? This paper reconciles two seemingly contradictory views. The first proposes that local neural populations independently encode semantic features; the second, that semantic representations arise as a dynamic distributed code that changes radically with stimulus processing. Combining simulations with a well-known neural network model of semantic memory, multivariate pattern classification, and human electrocorticography, we find that both views are partially correct: information about the animacy of a depicted stimulus is distributed across ventral temporal cortex in a dynamic code possessing feature-like elements posteriorly but with elements that change rapidly and nonlinearly in anterior regions. This pattern is consistent with the view that anterior temporal lobes serve as a deep cross-modal 'hub' in an interactive semantic network, and more generally suggests that tertiary association cortices may adopt dynamic distributed codes difficult to detect with common brain imaging methods

Noroviruses Co-opt the Function of Host Proteins VAPA and VAPB for Replication via a Phenylalanine-Phenylalanine-Acidic-Tract-Motif Mimic in Nonstructural Viral Protein NS1/2.

The Norovirus genus contains important human pathogens, but the role of host pathways in norovirus replication is largely unknown. Murine noroviruses provide the opportunity to study norovirus replication in cell culture and in small animals. The human norovirus nonstructural protein NS1/2 interacts with the host protein VAMP-associated protein A (VAPA), but the significance of the NS1/2-VAPA interaction is unexplored. Here we report decreased murine norovirus replication in VAPA- and VAPB-deficient cells. We characterized the role of VAPA in detail. VAPA was required for the efficiency of a step(s) in the viral replication cycle after entry of viral RNA into the cytoplasm but before the synthesis of viral minus-sense RNA. The interaction of VAPA with viral NS1/2 proteins is conserved between murine and human noroviruses. Murine norovirus NS1/2 directly bound the major sperm protein (MSP) domain of VAPA through its NS1 domain. Mutations within NS1 that disrupted interaction with VAPA inhibited viral replication. Structural analysis revealed that the viral NS1 domain contains a mimic of the phenylalanine-phenylalanine-acidic-tract (FFAT) motif that enables host proteins to bind to the VAPA MSP domain. The NS1/2-FFAT mimic region interacted with the VAPA-MSP domain in a manner similar to that seen with bona fide host FFAT motifs. Amino acids in the FFAT mimic region of the NS1 domain that are important for viral replication are highly conserved across murine norovirus strains. Thus, VAPA interaction with a norovirus protein that functionally mimics host FFAT motifs is important for murine norovirus replication.IMPORTANCE Human noroviruses are a leading cause of gastroenteritis worldwide, but host factors involved in norovirus replication are incompletely understood. Murine noroviruses have been studied to define mechanisms of norovirus replication. Here we defined the importance of the interaction between the hitherto poorly studied NS1/2 norovirus protein and the VAPA host protein. The NS1/2-VAPA interaction is conserved between murine and human noroviruses and was important for early steps in murine norovirus replication. Using structure-function analysis, we found that NS1/2 contains a short sequence that molecularly mimics the FFAT motif that is found in multiple host proteins that bind VAPA. This represents to our knowledge the first example of functionally important mimicry of a host FFAT motif by a microbial protein

Fenebrutinib in H1 antihistamine-refractory chronic spontaneous urticaria: a randomized phase 2 trial

Bruton’s tyrosine kinase (BTK) is crucial for FcεRI-mediated mast cell activation and essential for autoantibody production by B cells in chronic spontaneous urticaria (CSU). Fenebrutinib, an orally administered, potent, highly selective, reversible BTK inhibitor, may be effective in CSU. This double-blind, placebo-controlled, phase 2 trial (EudraCT ID 2016-004624-35) randomized 93 adults with antihistamine-refractory CSU to 50 mg daily, 150 mg daily and 200 mg twice daily of fenebrutinib or placebo for 8 weeks. The primary end point was change from baseline in urticaria activity score over 7 d (UAS7) at week 8. Secondary end points were the change from baseline in UAS7 at week 4 and the proportion of patients well-controlled (UAS7 ≤ 6) at week 8. Fenebrutinib efficacy in patients with type IIb autoimmunity and effects on IgG-anti-FcεRI were exploratory end points. Safety was also evaluated. The primary end point was met, with dose-dependent improvements in UAS7 at week 8 occurring at 200 mg twice daily and 150 mg daily, but not at 50 mg daily of fenebrutinib versus placebo. Asymptomatic, reversible grade 2 and 3 liver transaminase elevations occurred in the fenebrutinib 150 mg daily and 200 mg twice daily groups (2 patients each). Fenebrutinib diminished disease activity in patients with antihistamine-refractory CSU, including more patients with refractory type IIb autoimmunity. These results support the potential use of BTK inhibition in antihistamine-refractory CSU

Acquisition of pneumococci specific effector and regulatory Cd4+ T cells localising within human upper respiratory-tract mucosal lymphoid tissue

The upper respiratory tract mucosa is the location for commensal Streptococcus (S.) pneumoniae colonization and therefore represents a major site of contact between host and bacteria. The CD4(+) T cell response to pneumococcus is increasingly recognised as an important mediator of immunity that protects against invasive disease, with data suggesting a critical role for Th17 cells in mucosal clearance. By assessing CD4 T cell proliferative responses we demonstrate age-related sequestration of Th1 and Th17 CD4(+) T cells reactive to pneumococcal protein antigens within mucosal lymphoid tissue. CD25(hi) T cell depletion and utilisation of pneumococcal specific MHCII tetramers revealed the presence of antigen specific Tregs that utilised CTLA-4 and PDL-1 surface molecules to suppress these responses. The balance between mucosal effector and regulatory CD4(+) T cell immunity is likely to be critical to pneumococcal commensalism and the prevention of unwanted pathology associated with carriage. However, if dysregulated, such responses may render the host more susceptible to invasive pneumococcal infection and adversely affect the successful implementation of both polysaccharide-conjugate and novel protein-based pneumococcal vaccines

Regional Similarities and NOx‐Related Increases in Biogenic Secondary Organic Aerosol in Summertime Southeastern United States

During the 2013 Southern Oxidant and Aerosol Study, Fourier transform infrared spectroscopy (FTIR) and aerosol mass spectrometer (AMS) measurements of submicron mass were collected at Look Rock (LRK), Tennessee, and Centreville (CTR), Alabama. Carbon monoxide and submicron sulfate and organic mass concentrations were 15–60% higher at CTR than at LRK, but their time series had moderate correlations (r ~ 0.5). However, NOx had no correlation (r = 0.08) between the two sites with nighttime‐to‐early‐morning peaks 3–10 times higher at CTR than at LRK. Organic mass (OM) sources identified by FTIR Positive Matrix Factorization (PMF) had three very similar factors at both sites: fossil fuel combustion‐related organic aerosols, mixed organic aerosols, and biogenic organic aerosols (BOA). The BOA spectrum from FTIR is similar (cosine similarity > 0.6) to that of lab‐generated particle mass from the photochemical oxidation of both isoprene and monoterpenes under high NOx conditions from chamber experiments. The BOA mass fraction was highest during the night at CTR but in the afternoon at LRK. AMS PMF resulted in two similar pairs of factors at both sites and a third nighttime NOx‐related factor (33% of OM) at CTR but a daytime nitrate‐related factor (28% of OM) at LRK. NOx was correlated with BOA and LO‐OOA for NOx concentrations higher than 1 ppb at both sites, producing 0.5 ± 0.1 μg/m3 for CTR‐LO‐OOA and 1.0 ± 0.3 μg/m3 for CTR‐BOA additional biogenic OM for each 1 ppb increase of NOx.Key PointsAerosol concentration and composition are largely similar at two different forested sites during summertime in the southeastern United StatesFTIR of ambient biogenic SOA factors are similar to isoprene and monoterpene chamber experiment, supporting NOx‐related oxidation pathwaysNOx increases biogenic SOA by 0.5 ± 0.1 μg/m3 for CTR‐LO‐OOA and 1.0 ± 0.3 μg/m3 for CTR‐BOA for each ppb NOx above 1 ppb at Centreville but not at Look Rock (where NOx was usually below 1 ppb)Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146465/1/jgrd54860-sup-0001-SI.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146465/2/jgrd54860.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146465/3/jgrd54860_am.pd

Monocytes regulate the mechanism of T-cell death by inducing Fas-mediated apoptosis during bacterial infection.

Monocytes and T-cells are critical to the host response to acute bacterial infection but monocytes are primarily viewed as amplifying the inflammatory signal. The mechanisms of cell death regulating T-cell numbers at sites of infection are incompletely characterized. T-cell death in cultures of peripheral blood mononuclear cells (PBMC) showed 'classic' features of apoptosis following exposure to pneumococci. Conversely, purified CD3(+) T-cells cultured with pneumococci demonstrated necrosis with membrane permeabilization. The death of purified CD3(+) T-cells was not inhibited by necrostatin, but required the bacterial toxin pneumolysin. Apoptosis of CD3(+) T-cells in PBMC cultures required 'classical' CD14(+) monocytes, which enhanced T-cell activation. CD3(+) T-cell death was enhanced in HIV-seropositive individuals. Monocyte-mediated CD3(+) T-cell apoptotic death was Fas-dependent both in vitro and in vivo. In the early stages of the T-cell dependent host response to pneumococci reduced Fas ligand mediated T-cell apoptosis was associated with decreased bacterial clearance in the lung and increased bacteremia. In summary monocytes converted pathogen-associated necrosis into Fas-dependent apoptosis and regulated levels of activated T-cells at sites of acute bacterial infection. These changes were associated with enhanced bacterial clearance in the lung and reduced levels of invasive pneumococcal disease

Two PI 3-Kinases and One PI 3-Phosphatase Together Establish the Cyclic Waves of Phagosomal PtdIns(3)P Critical for the Degradation of Apoptotic Cells

Cyclic oscillations in the level of phosphatidylinositol 3-phosphate in phagosomes, regulated by two phosphoinositide kinases and one phosphatase, are critical for phagosome maturation and degradation of apoptotic cells

Modern microwave methods in solid state inorganic materials chemistry: from fundamentals to manufacturing

No abstract available