Modular Synthesis of Phthalaldehyde Derivatives Enabling Access to Photoacid Generator-Bound Self-Immolative Polymer Resists with Next-Generation Photolithographic Properties

The resolution, line edge roughness, and sensitivity (RLS) trade-off has fundamentally limited the lithographic performance of chemically amplified resists. Production of next-generation transistors using extreme ultraviolet (EUV) lithography depends on a solution to this problem. A resist that simultaneously increases the effective reaction radius of its photogenerated acids while limiting their diffusion radius should provide an elegant solution to the RLS barrier. Here, we describe a generalized synthetic approach to phthalaldehyde derivatives using sulfur(VI) fluoride exchange click chemistry that dramatically expands usable chemical space by enabling virtually any non-ionic photoacid generator (PAG) to be tethered to phthalaldehyde. The resulting polymers represent the first ever PAG-tethered self-immolative resists in an architecture that simultaneously displays high contrast, extraordinary sensitivity, and low roughness under EUV exposure. We believe this class of resists will ultimately enable researchers to overcome the RLS trade-off

Cationic Co–Salphen Complexes Bisligated by DMAP as Catalysts for the Copolymerization of Cyclohexene Oxide with Phthalic Anhydride or Carbon Dioxide

For the copolymerization of cyclohexene oxide (CHO) with phthalic anhydride (PA), cationic complex [Co­(III)­(dmap)₂–Salphen]­[BF₄] (<b>3</b>) showed higher activity than a combination of Co–Salphen–Cl (<b>2</b>) with 1 equiv of DMAP. The catalytic activity was further improved by using a bimetallic complex <b>5</b> in which the Co­(III)­(dmap)₂–Salphen moiety was bridged by a 1,2,5,6-substituted naphthalene linker. A similar trend of catalytic activity was detected for the copolymerization of CHO with CO₂

A Statistical Framework for Improving Genomic Annotations of Prokaryotic Essential Genes

<div><p>Large-scale systematic analysis of gene essentiality is an important step closer toward unraveling the complex relationship between genotypes and phenotypes. Such analysis cannot be accomplished without unbiased and accurate annotations of essential genes. In current genomic databases, most of the essential gene annotations are derived from whole-genome transposon mutagenesis (TM), the most frequently used experimental approach for determining essential genes in microorganisms under defined conditions. However, there are substantial systematic biases associated with TM experiments. In this study, we developed a novel Poisson model–based statistical framework to simulate the TM insertion process and subsequently correct the experimental biases. We first quantitatively assessed the effects of major factors that potentially influence the accuracy of TM and subsequently incorporated relevant factors into the framework. Through iteratively optimizing parameters, we inferred the actual insertion events occurred and described each gene’s essentiality on probability measure. Evaluated by the definite mapping of essential gene profile in <i>Escherichia coli</i>, our model significantly improved the accuracy of original TM datasets, resulting in more accurate annotations of essential genes. Our method also showed encouraging results in improving subsaturation level TM datasets. To test our model’s broad applicability to other bacteria, we applied it to <i>Pseudomonas aeruginosa PAO1</i> and <i>Francisella tularensis novicida</i> TM datasets. We validated our predictions by literature as well as allelic exchange experiments in <i>PAO1</i>. Our model was correct on six of the seven tested genes. Remarkably, among all three cases that our predictions contradicted the TM assignments, experimental validations supported our predictions. In summary, our method will be a promising tool in improving genomic annotations of essential genes and enabling large-scale explorations of gene essentiality. Our contribution is timely considering the rapidly increasing essential gene sets. A Webserver has been set up to provide convenient access to this tool. All results and source codes are available for download upon publication at <a href="http://research.cchmc.org/essentialgene/" target="_blank">http://research.cchmc.org/essentialgene/</a>.</p> </div

Three factors have strong associations with false TM assignments.

<p>(A) Gene length. The lengths of TmEs are significantly shorter than those in the PEC dataset and total genes. Many of these short genes may be false essential genes. (B) Position of insertions. Essential genes mistakenly assigned to be non-essential by TM often have insertions in the 25% extreme-ends (5% in 5′ end and 20% in 3′ end). These insertions do not completely disrupt a gene’s function. (C) Number of insertions. 75% of the essential genes mistakenly assigned to be non-essential by TM only have one insertion in them.</p

Validation using allelic exchange experiments in <i>Pseudomonas aeruginosa PAO1</i>. E – Essential; N – Non-essential.

<p>Validation using allelic exchange experiments in <i>Pseudomonas aeruginosa PAO1</i>. E – Essential; N – Non-essential.</p

Illustration of the statistical model.

<p>In a TM experiment, if a gene has no observed insertions, meaning it is TM essential or TmEs, what could it be? There are two possibilities: (1) Part A: It never had any insertion and was missed by all transposons by chance. This means we do not have useful information to infer what this gene could be, and it is completely blind for us. For any blind gene, we can only try our best guess and assume that the chance of that gene to be essential is equal to the overall essential gene rate (Pr(overall essential)), and that a gene to be non-essential is equal to  = 1-. (2) Part B: It actually had insertions, but all inserted mutations died. This means that this gene is truly essential. In this way, we can now split the TM assigned essential genes into two parts, TETmE and FETmE. Similarly, if in the TM experiment, a gene is observed to have insertions, meaning it is TM nonessential, what could it really be? There are also two possibilities: (1) Part C: All these observed insertions are ineffective, and did not interrupt the gene function. This means again we are blind about this gene. So it has a certain chance to be essential , and also has a certain chance to be nonessential . (2) Part D: There was at least one effective insertion, and it did interrupt the gene function. . This means this gene is truly non-essential.</p

Network-Based Analysis on Orthogonal Separation of Human Plasma Uncovers Distinct High Density Lipoprotein Complexes

High density lipoprotein (HDL) particles are blood-borne complexes whose plasma levels have been associated with protection from cardiovascular disease (CVD). Recent studies have demonstrated the existence of distinct HDL subspecies; however, these have been difficult to isolate and characterize biochemically. Here, we present the first report that employs a network-based approach to systematically infer HDL subspecies. Healthy human plasma was separated into 58 fractions using our previously published three orthogonal chromatography techniques. Similar local migration patterns among HDL proteins were captured with a novel similarity score, and individual comigration networks were constructed for each fraction. By employing a graph mining algorithm, we identified 183 overlapped cliques, among which 38 were further selected as candidate HDL subparticles. Each of these 38 subparticles had at least two literature supports. In addition, GO function enrichment analysis showed that they were enriched with fundamental biological and CVD protective functions. Furthermore, gene knockout experiments in mouse model supported the validity of these subparticles related to three apolipoproteins. Finally, analysis of an apoA-I deficient human patient’s plasma provided additional support for apoA-I related complexes. Further biochemical characterization of these putative subspecies may facilitate the mechanistic research of CVD and guide targeted therapeutics aimed at its mitigation