Bloom Syndrome Complicated by Low-Grade Lymphoma and Non-small Cell Lung Cancer: A Case Report.

Bloom syndrome (BS) is a rare autosomal recessive genetic disorder characterized by photosensitivity, rashes on the nose and cheeks, short stature, and a predisposition to develop cancers. In this report, we discuss the diagnosis and management of a 34-year-old Canadian male BS patient, originally from Honduras, who developed B-cell lymphoma and a subsequent non-small cell lung carcinoma (NSCLC). Given the radiosensitivity of the patient due to his BS diagnosis and the early stage of the low-grade B-cell lymphoma, we relied on surveillance as the clinical approach to his management. The treatment for NSCLC was initiated in stage III of the disease and was palliative in intent. Chemotherapy (12 rounds of paclitaxel, with the dosage gradually increasing from 48 mg to 58 mg and finally to 72 mg) was employed to shrink the left upper lobe (LUL) lung mass. Subsequently, radiotherapy (3000 cGY in 20 fractions) was administered to improve symptoms further. The radiotherapy dose schedule was modified given the patient's BS diagnosis to avoid excessive toxicity. The palliative treatment course was well tolerated by the patient and resulted in symptom relief. However, his cancer progressed over the course of the treatment, ultimately resulting in his death 18 months after the initial diagnosis of NSCLC; no autopsy was performed. We believe this report will spur clinicians to engage in fruitful discussions about tailoring chemotherapy and radiation therapy regimens for treating cancer in BS patients.

Effects of charge separation, effective concentration, and aggregate formation on the phase transfer catalyzed alkylation of phenol.

The factors that influence the rate of alkylation of phenol under phase transfer catalysis (PTC) have been investigated in detail. Six linear, symmetrical tetraalkylammonium cations, Me(4)N(+), Et(4)N(+), (n-Pr)(4)N(+), (n-Bu)(4)N(+), (n-Hex)(4)N(+), and (n-Oct)(4)N(+), were examined to compare the effects of cationic radius and lipophilicity on the rate of alkylation. Tetraalkylammonium phenoxide·phenol salts were prepared, and their intrinsic reactivity was determined from initial alkylation rates with n-butyl bromide in homogeneous solution. The catalytic activity of the same tetraalkylammonium phenoxides was determined under PTC conditions (under an extraction mechanism) employing quaternary ammonium bromide catalysts. In homogeneous solution the range in reactivity was small (6.8-fold) for Me(4)N(+) to (n-Oct)(4)N(+). In contrast, under PTC conditions a larger range in reactivity was observed (663-fold). The effective concentration of the tetraalkylammonium phenoxides in the organic phase was identified as the primary factor influencing catalyst activity. Additionally, titration of active phenoxide in the organic phase confirmed the presence of both phenol and potassium phenoxide aggregates with (n-Bu)(4)N(+), (n-Hex)(4)N(+), and (n-Oct)(4)N(+), each with a unique aggregate stoichiometry. The aggregate stoichiometry did not affect the PTC initial alkylation rates.

A systematic investigation of quaternary ammonium ions as asymmetric phase-transfer catalysts. Synthesis of catalyst libraries and evaluation of catalyst activity.

Despite over three decades of research into asymmetric phase-transfer catalysis (APTC), a fundamental understanding of the factors that affect the rate and stereoselectivity of this important process are still obscure. This paper describes the initial stages of a long-term program aimed at elucidating the physical organic foundations of APTC employing a chemoinformatic analysis of the alkylation of a protected glycine imine with libraries of enantiomerically enriched quaternary ammonium ions. The synthesis of the quaternary ammonium ions follows a diversity-oriented approach wherein the tandem inter[4 + 2]/intra[3 + 2] cycloaddition of nitroalkenes serves as the key transformation. A two-part synthetic strategy comprised of (1) preparation of enantioenriched scaffolds and (2) development of parallel synthesis procedures is described. The strategy allows for the facile introduction of four variable groups in the vicinity of a stereogenic quaternary ammonium ion. The quaternary ammonium ions exhibited a wide range of activity and to a lesser degree enantioselectivity. Catalyst activity and selectivity are rationalized in a qualitative way on the basis of the effective positive potential of the ammonium ion.

A systematic investigation of quaternary ammonium ions as asymmetric phase-transfer catalysts. Application of quantitative structure activity/selectivity relationships.

Although the synthetic utility of asymmetric phase-transfer catalysis continues to expand, the number of proven catalyst types and design criteria remains limited. At the origin of this scarcity is a lack in understanding of how catalyst structural features affect the rate and enantioselectivity of phase transfer catalyzed reactions. Described in this paper is the development of quantitative structure-activity relationships (QSAR) and -selectivity relationships (QSSR) for the alkylation of a protected glycine imine with libraries of quaternary ammonium ion catalysts. Catalyst descriptors including ammonium ion accessibility, interfacial adsorption affinity, and partition coefficient were found to correlate meaningfully with catalyst activity. The physical nature of the descriptors was rationalized through differing contributions of the interfacial and extraction mechanisms to the reaction under study. The variation in the observed enantioselectivity was rationalized employing a comparative molecular field analysis (CoMFA) using both the steric and electrostatic fields of the catalysts. A qualitative analysis of the developed model reveals preferred regions for catalyst binding to afford both configurations of the alkylated product.

Codon Context Optimization in Synthetic Gene Design.

Advances in de novo synthesis of DNA and computational gene design methods make possible the customization of genes by direct manipulation of features such as codon bias and mRNA secondary structure. Codon context is another feature significantly affecting mRNA translational efficiency, but existing methods and tools for evaluating and designing novel optimized protein coding sequences utilize untested heuristics and do not provide quantifiable guarantees on design quality. In this study we examine statistical properties of codon context measures in an effort to better understand the phenomenon. We analyze the computational complexity of codon context optimization and design exact and efficient heuristic gene recoding algorithms under reasonable constraint models. We also present a web-based tool for evaluating codon context bias in the appropriate context.

Computational tools and algorithms for designing customized synthetic genes.

Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits, and genomes of bacterial scale. Freedom in de novo design of synthetic constructs provides significant power in studying the impact of mutations in sequence features, and verifying hypotheses on the functional information that is encoded in nucleic and amino acids. To aid this goal, a large number of software tools of variable sophistication have been implemented, enabling the design of synthetic genes for sequence optimization based on rationally defined properties. The first generation of tools dealt predominantly with singular objectives such as codon usage optimization and unique restriction site incorporation. Recent years have seen the emergence of sequence design tools that aim to evolve sequences toward combinations of objectives. The design of optimal protein-coding sequences adhering to multiple objectives is computationally hard, and most tools rely on heuristics to sample the vast sequence design space. In this review, we study some of the algorithmic issues behind gene optimization and the approaches that different tools have adopted to redesign genes and optimize desired coding features. We utilize test cases to demonstrate the efficiency of each approach, as well as identify their strengths and limitations.

Renovating animal facilities to withstand disasters.

In the aftermath of Superstorm Sandy, new attention has been drawn to planning for and mitigating the effects of disasters on laboratory animal facilities. A number of design approaches and solutions can be easily incorporated into a new vivarium, enhancing its ability to withstand and recover from a disaster. Renovating a vivarium poses special challenges, however. Existing conditions in the project area may dictate which approaches or solutions are feasible, and retrofitting is often more complex and expensive than incorporating the same features into new construction. The authors explain how project design teams can evaluate the types of disasters that a renovated facility will need to address and develop a design strategy that responds to these disasters in the most effective way.

Combined Lewis acid and Brønsted acid-mediated reactivity of glycosyl trichloroacetimidate donors.

Biomimetic conditions for a synthetic glycosylation reaction, inspired by the highly conserved functionality of carbohydrate active enzymes, were explored. At the outset, we sought to generate proof of principle for this approach to developing catalytic systems for glycosylation. However, control reactions and subsequent kinetic studies showed that a stoichiometric, irreversible reaction of the catalyst and glycosyl donor was occurring, with a remarkable rate variance depending upon the structure of the carboxylic acid. It was subsequently found that a combination of Brønsted acid (carboxylic acid) and Lewis acid (MgBr2) was unique in catalyzing the desired glycosylation reaction. Thus, it was concluded that the two acids act synergistically to catalyze the desired transformation. The role of the catalytic components was tested with a number of control reactions and based on these studies a mechanism is proposed herein.

Cytosporone E: racemic synthesis and preliminary antibacterial testing.

The antibiotic cytosporone E (isolated from the broth of the endophytic fungi CR 200 (Cytospora sp.) and CR 146 (Diaporthe sp.)) was synthesized as a racemic mixture. The key step in the synthesis is the Meyers ortho-alkylation of a chiral aromatic oxazoline. Preliminary antibiotic activity shows antibiosis against Gram-positive bacteria but not Gram-negative bacteria as previously reported.