Machine-guided design of synthetic cell type-specific cis-regulatory elements

Cis-regulatory elements (CREs) control gene expression, orchestrating tissue identity, developmental timing, and stimulus responses, which collectively define the thousands of unique cell types in the body. While there is great potential for strategically incorporating CREs in therapeutic or biotechnology applications that require tissue specificity, there is no guarantee that an optimal CRE for an intended purpose has arisen naturally through evolution. Here, we present a platform to engineer and validate synthetic CREs capable of driving gene expression with programmed cell type specificity. We leverage innovations in deep neural network modeling of CRE activity across three cell types, efficient in silico optimization, and massively parallel reporter assays (MPRAs) to design and empirically test thousands of CREs. Through in vitro and in vivo validation, we show that synthetic sequences outperform natural sequences from the human genome in driving cell type-specific expression. Synthetic sequences leverage unique sequence syntax to promote activity in the on-target cell type and simultaneously reduce activity in off-target cells. Together, we provide a generalizable framework to prospectively engineer CREs and demonstrate the required literacy to write regulatory code that is fit-for-purpose in vivo across vertebrates.

In silico prediction of B and T cell epitopes of infectious salmon anemia virus proteins and molecular modeling of T cell epitopes to salmon major histocompatibility complex (MHC) class I

Infectious salmon anemia (ISA) can be devastating in farmed Atlantic salmon (Salmo salar). The disease can evolve into epidemics if it is not contained and controlled. ISA epidemics were seen in Norway in the early 1990s and Chile in 2007-2009. Consequently, there is an urgent need to develop a vaccine to prevent or treat the infection. In this study, an immunoinformatic approach was employed to predict 32 lineal B-cell epitopes based on antigenicity and surface accessibility prediction for ISAV fusion (F), hemagglutinin-esterase (HE), and matrix (M) proteins. On the other hand, twelve conformational B-cell epitopes were also predicted. We further identified six antigenic cytotoxic T lymphocyte (CTL) epitopes and investigated the binding interactions with five salmon MHC-I proteins after docking the peptides to the binding groove of the MHC-I proteins. Our results showed that all the predicted epitopes could bind to salmon MHC-I with high negative ΔG values with medium to high binding affinities. Hence, the predicted epitopes have a high potential of being recognized by Atlantic salmon MHC-I to elicit a CD8⁺ T cell response in salmon. The predicted and analyzed B and T cell antigenic epitopes in this work might present an initial set of peptides for future vaccine development against ISAV. The ability to model and predict these interactions will ultimately lead to the ability to predict potential binding for MHCs and epitopes that were not studied previously. As current knowledge of salmon MHC specificity is limited, studying and modeling interactions in the peptide/MHC complex is a key to resolving unknown epitope specificity.

O–H and (CO)N–H bond weakening by coordination to Fe(ii)

Coordination of hydroxyl/amide groups to Fe(ii) diminishes BDFEs of O–H and (CO)N–H bonds down to 76.0 and 80.5 kcal mol⁻¹ respectively.

Versatile synthesis and enlargement of functionalized distorted heptagon-containing nanographenes

Highly distorted polycyclic aromatic hydrocarbons (PAHs) are predicted to be attractive goals in nanoscience owing to the new properties they can exhibit. We have shown that a variety of functionalized distorted heptagon-containing nanographenes can be easily prepared from simple building blocks by a sequence of Co-catalyzed cyclotrimerization and cyclodehydrogenation reactions. The versatility of this strategy allows easy subsequent enlargement of these nanostructures by Ni-catalyzed cross-coupling and final cyclodehydrogenation reactions. Soluble extended distorted nanographenes 1 and 2 containing heptagon and an edge-shared pentagon-heptagon combination have been synthesized. High distortion of the polycyclic backbone of 2 caused by non-hexagonal rings and a helicene moiety was confirmed by X-ray crystallography. Experimental data reveal promising optical and electronic properties for distorted PAHs with long fluorescence lifetimes (up to 14.5 ns) and low band gaps (down to 2.27 eV). This straightforward and versatile synthetic strategy, the observed long fluorescence lifetimes and the small optical and electrochemical band gaps for the presented compounds may promote the future implementation of distorted graphene molecules in electronic devices.

Two-dimensional carbon-based conductive materials with dynamically controlled asymmetric Dirac cones

The design of two dimensional graphene-type materials with an anisotropic electron flow direction in the X- and Y-axes opens the door for the development of novel electronic materials with multiple functions in nanoelectronics. In the present work, we have studied the electronic transport properties of a new family of 2D graphene-graphyne hybrids presenting conformationally free phenylethylene subunits. This system ensures two different conductive pathways that are perpendicular to each other: an acene nanoribbon subunit, in the X-axis, with graphene-type conduction, and a free to rotate phenylethylene subunit, in the Y-axis, in which the magnitude of the conduction depends dynamically on the corresponding torsion angle. Our calculations have confirmed that this system presents two different conduction pathways, which are related to the presence of asymmetric Dirac-type cones. Moreover, the Dirac cones can be dynamically modified in the presence of an external gate electrode, which is unprecedented in the literature.

Merkel cell carcinoma and Merkel cell polyomavirus: a systematic review and meta-analysis

Several observational studies have assessed the correlation between Merkel cell carcinoma and Merkel cell polyomavirus with variable results. The objective of this systematic review was to determine whether there is a correlation between Merkel cell carcinoma and Merkel cell polyomavirus. Studies assessing the relationship between Merkel cell carcinoma and Merkel cell polyomavirus from January 2008 to August 2014 were pooled from Medline, Embase, PubMed, Cochrane Database of Systemic Reviews and Google Scholar. From each study we collected the first author's last name, publication year, country of origin, type of study design, characteristics of participants, possible variables incorporated into the multivariable analyses and the risk ratio (RR) for Merkel cell carcinoma associated with Merkel cell polyomavirus combined with the corresponding 95% confidence interval (CI). Methodological assessment of the study was evaluated using the Newcastle-Ottawa scale. Crude RR was calculated from the data provided in each article. Meta-analyses for the global RR and for the proportion of positives in both case and control samples were performed. In addition, in order to explore the sources of heterogeneity among the studies, meta-regression and sensitivity analyses are also provided. A total of 22 studies were identified for the analysis. The pooled RR from random-effects analysis was determined to be 6.32 (95% CI, 4.02-9.93). Global proportions of positive samples were 0.79 (95% CI, 0.72-0.84) and 0.12 (95% CI, 0.08-0.19) in the case and control groups, respectively. The findings support the association between Merkel cell carcinoma and Merkel cell polyomavirus. However, a non-negligible percentage of positive results have been identified in controls. Some caution must be taken in the interpretation of these results because heterogeneity between studies was found.

Stereoselective synthesis of highly functionalized indanes and dibenzocycloheptadienes through complex radical cascade reactions

Two highly stereoselective radical-mediated syntheses of densely functionalized indanes and dibenzocycloheptadienes from ortho-vinyl- and ortho-vinylaryl-substituted N-(arylsulfonyl)-acrylamides, respectively, are presented here. The chemoselective addition of in situ generated radicals (X(·)) onto the styrene moieties triggers an unprecedented reaction cascade, resulting in the formation of one new C-X bond and two new C-C bonds, a formal 1,4-aryl migration, and the extrusion of SO2 to generate an amidyl radical intermediate. This intermediate, upon H abstraction, leads to the observed 5- and 7-membered ring carbocyclic products, respectively, in a highly efficient manner.

A heterotrimetallic Ir(iii), Au(iii) and Pt(ii) complex incorporating cyclometallating bi- and tridentate ligands: simultaneous emission from different luminescent metal centres leads to broad-band light emission

Di- and tri-nuclear metal complexes incorporating Au(iii), Ir(iii) and Pt(ii) units linked via a 1,3,5-triethynylbenzene core.

Organic-based molecular switches for molecular electronics

In a general sense, molecular electronics (ME) is the branch of nanotechnology which studies the application of molecular building blocks for the fabrication of electronic components. Among the different types of molecules, organic compounds have been revealed as promising candidates for ME, due to the easy access, great structural diversity and suitable electronic and mechanical properties. Thanks to these useful capabilities, organic molecules have been used to emulate electronic devices at the nanoscopic scale. In this feature article, we present the diverse strategies used to develop organic switches towards ME with special attention to non-volatile systems.

Sodium Tetramethoxyborate: An Efficient Catalyst for Michael Additions of Stabilized Carbon Nucleophiles

Sodium tetramethoxyborate, easily prepared by reaction of inexpensive sodium borohydride with methanol, possesses a suitable combination of a Lewis base and a Lewis acid to catalyze Michael reactions at room temperature under practically neutral conditions. This reaction provides good to excellent yields of Michael addition products from a broad scope of Michael donor and Michael acceptor reagents.

Unprecedented Hydrogen Transfer from Water to Alkenes and Alkynes Mediated by TiIII and Late Transition Metals

We describe how alkenes and alkynes can be hydrogenated under mild conditions by hydrogen transfer from water mediated by titanocene(III) and a substoichiometric quantity of one of the late transition metals usually employed as hydrogenation catalysts. This process proceeds presumably by H-atom transfer from TiIII-coordinated water to the late transition metal partner (depicted in the drawing above), a mechanism in support of which we provide theoretical and experimental evidence.

Isolation and characterization of biologically active murine interleukin-6 produced in Escherichia coli

Interleukin-6 (IL-6) is a multi-functional cytokine produced and secreted by several different cell types, including those of the immune system. A cDNA coding for the mature murine IL-6 (mIL-6), which extends from amino acid (aa) 25 through 211, was cloned into a prokaryotic vector and then expressed in Escherichia coli. The recombinant mIL-6 (remIL-6) was isolated from bacterial inclusion bodies by solubilization in 4 M guanidine hydrochloride followed by gel-filtration chromatography. The protein was refolded to an active conformation by dialysis against 25 mM Na. acetate pH 5.5. A final step of purification and concentration on a cation exchange resin yielded pure and biologically active remIL-6. The purified preparation had the expected aa composition, as confirmed by aa analysis and pI of 7.0-7.1. The biological activity of the recombinant protein was measured in two systems; a proliferation assay employing 7TD1 cells, and a fibrinogen biosynthesis assay employing primary rat hepatocytes. Both assay systems demonstrated that the remIL-6 was active in the range of 10(8) units/mg, which is similar to that estimated for native cytokine. Antibodies raised in rabbits against remIL-6 neutralized the biological activity of both recombinant and native IL-6.

Sulfatide role in the sodium pump

Sodium efflux was studied in 22Na-loaded red blood cells in the presence of arylsulfatase, an enzyme that specifically hydrolyzes sulfatide. Sodium efflux was inhibited in proportion to the amount of arylsulfatase present. Maximum inhibition was almost as high as the efflux obtained in medium with K+ absent. At maximum inhibition 83.2% of the sulfatide content of the fragmented red blood cell membranes was hydrolyzed and ouabain-sensitive (Na+ + K+)-ATPase activity was inhibited by 100%. Sodium efflux, sulfatide content, and (Na+ + K+)-ATPase activity were unaffected with arylsulfatase in the presence of a high concentration of sulfatide. These results indicate that sulfatide plays a specific role in sodium and potassium ion transport. They also suggest that most sulfatide is localized externally in the red blood cell membrane.