Boronic Acid-Catalyzed Regio- and Stereoselective N-Glycosylations of Purines and Other Azole Heterocycles: Access to Nucleoside Analogues.

In the presence of an arylboronic acid catalyst, azole-type heterocycles, including purines, tetrazoles, triazoles, indazoles, and benzo-fused congeners, undergo regio- and stereoselective N-glycosylations with furanosyl and pyranosyl trichloroacetimidate donors. The protocol, which does not require stoichiometric activators, specialized leaving groups, or drying agents, provides access to nucleoside analogues and enables late-stage N-glycosylation of azole-containing pharmaceutical agents. A mechanism involving simultaneous activation of the glycosyl donor and acceptor by the organoboron catalyst has been proposed, supported by kinetic analysis and computational modeling.

On the mechanism of carboxylate elimination from carbohydrate monoester-derived radicals.

A computational study of the mechanism of hydrogen atom transfer-induced carboxylate elimination from monoacylated 1,2-diol groups in pyranosides is presented. A comprehensive analysis of the 1,2-migration, elimination and fragmentation pathways reveals that concerted elimination via a 7-membered, hydrogen-bonded transition state is favored. Relative rates of elimination inferred from an intramolecular competition experiment are consistent with the trends obtained from the calculations.

Understanding the Origins of Site Selectivity in Hydrogen Atom Transfer Reactions from Carbohydrates to the Quinuclidinium Radical Cation: A Computational Study.

The use of quinuclidine as a hydrogen atom transfer (HAT) mediator, along with a light-absorbing photoredox catalyst, has proved to be a powerful and general approach for achieving site-selective radical formation from carbohydrate substrates. Despite numerous literature reports documenting the scope and limitations of such processes, a general rationale for the origins of site selectivity in the key HAT step has not been advanced. In this study, density functional theory calculations (M06-2X/def2-TZVP/PCM(acetonitrile)) were used to model transition states for HAT to the quinuclidinium radical cation from pyranosides and furanosides having various configurations and substitution patterns. The data set (>120 transition state geometries and energies) has allowed for a detailed examination of the factors that influence the relative rates, augmented by additional analysis using the atoms in molecules (AIM) and distortion/interaction-activation strain frameworks. The trends that have emerged regarding the effects of configuration, conformation, substitution, and noncovalent interactions are consistent with experimental observations and reveal a key role for C-H···O hydrogen bonds in stabilizing transition states for HAT to the quinuclidinium radical cation.

Chimeric GFP-uracil based molecular rotor fluorophores.

Uracil has been modified at the 5-position to derive a small library of nucleobase-chromophores which were inspired by green fluorescent protein (GFP). The key steps in the syntheses were Erlenmeyer azlactone synthesis followed by amination by use of hexamethyl disilazane (HMDS) to produce the imidazolinone derivatives. The uracil analogues displayed emission in the green region of visible spectrum and exhibited microenvironmental sensitivity exemplified by polarity-based solvatochromism and viscosity-dependent emission enhancement. Solid-state quantum yields of approximately 0.2 and solvent dependent emission wavelengths beyond 500 nm were observed. Select analogues were incorporated into peptide nucleic acid (PNA) strands which upon duplex formation with DNA showed good response ranging from a turn-off of fluorescence in presence of an opposing mismatched residue to a greater than 3-fold turn-on of fluorescence upon binding to fully complementary DNA strand.

Gastroesophageal reflux disease and asthma exacerbation: A systematic review and meta-analysis.

BACKGROUND: Gastroesophageal reflux disease (GORD) is highly prevalent and often coexists with asthma exacerbation. Divergent findings about the association between the two diseases were reported. We conducted a systematic review and meta-analysis to determine whether there exists an association between GORD and asthma. METHODS: We searched MEDLINE, EMBASE, and other databases and then performed a manual search, to identify eligible studies. Pooled odds ratios (ORs) and their 95% confidence intervals (CIs) were calculated using fixed- and random-effect models. We evaluated the quality of included studies, explored heterogeneity between studies, undertook subgroup analyses, assessed publication bias, and performed sensitivity analyses. RESULTS: We identified 32 eligible studies, conducted in 14 countries and including a total of 1,612,361 patients of all ages. Overall, GORD shows a weak association with asthma exacerbation (OR = 1.27; 95% CI 1.18-1.35). This association was observed in cohort, case-control, and cross-sectional designs and in European as well as non-European populations. Subgroup analyses show that GORD is associated with frequent asthma exacerbations (≥3 exacerbations, OR = 1.59; 95% CI 1.13-2.24) and with exacerbations needing oral corticosteroid therapy (OR = 1.24; 95% CI 1.09-1.41). GORD pediatric patients are at higher odds of asthma exacerbation than adults. We did not detect any evidence of publication bias and the association between GORD and asthma exacerbation held in all undertaken sensitivity analyses. CONCLUSIONS: Gastroesophageal reflux disease and asthma exacerbation are weakly associated.

Effects of Configuration and Substitution on C-H Bond Dissociation Enthalpies in Carbohydrate Derivatives: A Systematic Computational Study.

Density functional theory was used to calculate C-H bond dissociation enthalpies (BDEs) at each position of a diverse collection of pyranosides and furanosides differing in relative configuration and substitution patterns. A detailed analysis of the resulting data set (186 BDEs, calculated at the M06-2X/def2-TZVP level of theory) highlights the ways in which stereoelectronic effects, conformational properties, and noncovalent interactions can influence the strengths of C-H bonds in carbohydrates. The results point toward opportunities to alter the radical reactivity of carbohydrate derivatives by variation of their stereochemical configuration or the positions and types of protective groups.

Community-Academic Partnerships: Addressing Health Inequities Through Community-Engaged Service Learning.

In Chicago, Black men who have sex with men (MSM) and transgender and gender nonconforming (TGNC) individuals experience higher rates of HIV diagnoses. The Southside of Chicago has a thriving house ball culture powered by MSM and TGNC individuals who are disproportionately impacted by HIV. While this community has a history of facilitating health promotion at their events, gaps exist in community-empowered education specific to this community. Through partnership between nursing students from University of Illinois Chicago (UIC) and leaders from the Southside Health Advocacy Resource Partnership (SHARP) and the University of Chicago Center for HIV Elimination (CCHE), we aimed to reduce health disparities experienced by the Black MSM/TGNC community in Chicago. We promoted COVID-19 vaccinations and obtained funding for a community-led project to reduce HIV-related stigma. Our team consisted of two community leaders, seven students, and two professors. We met weekly during the development stages and detailed notes were maintained by students and updated with next steps. Four months of collaboration demonstrated how nursing coursework can facilitate community-academic partnership and yielded a COVID-19 viral vaccination promotion video, community administration of vaccines, and SHARP's procurement of funding to implement a project to reduce HIV-related stigma. Students learned the importance of community leaders' presence when bringing health care to communities. Community leaders learned to communicate population needs and best utilize students as a resource. Enriching nursing curriculum using an integrated service-learning format offers the opportunity for student development while simultaneously serving the community.

Dengue Virus Evolution under a Host-Targeted Antiviral.

UNLABELLED: The host-targeted antiviral drug UV-4B reduces viral replication and promotes survival in a mouse model of experimental dengue virus (DENV) infection. UV-4B is an iminosugar that inhibits the α-glucosidase family of enzymes and subsequently the folding of glycosylated proteins, both viral and host. Here, we utilized next-generation sequencing to investigate evolution of a flavivirus under selective pressure by a host-targeted antiviral in vivo. In viral populations recovered from UV-4B-treated mice, there was a significant increase in the number of single-nucleotide polymorphisms (SNPs) and the ratio of nonsynonymous to synonymous SNPs compared to findings in viral populations from vehicle-treated mice. The strongest evidence of positive selection was in the glycosylated membrane protein, thereby providing in vivo validation of the mechanism of action of an iminosugar. In addition, mutations in glycosylated proteins were present only in drug-treated mice after a single passage. However, the bulk of the other mutations were present in both populations, indicating nonspecific selective pressure. Together with the continued control of viremia by UV-4B, these findings are consistent with the previously predicted high genetic barrier to escape mutations in host-targeted antivirals. IMPORTANCE: Although hundreds of millions of people are infected with DENV every year, there is currently no approved vaccine or antiviral therapy. UV-4B has demonstrated antiviral activity against DENV and is expected to enter clinical trials soon. Therefore, it is important to understand the mechanisms of DENV resistance to UV-4B. Host-targeted antivirals are thought to have a higher genetic barrier to escape mutants than directly acting antivirals, yet there are very few published studies of viral evolution under host-targeted antivirals. No study to date has described flavivirus evolution in vivo under selective pressure by a host-based antiviral drug. We present the first in vivo study of the sequential progression of viral evolution under selective pressure by a host-targeted antiviral compound. This study bolsters support for the clinical development of UV-4B as an antiviral drug against DENV, and it provides a framework to compare how treatment with other host-targeted antiflaviviral drugs in humans and different animal models influence viral genetic diversity.

Pet peeves and happiness: how do happy people complain?

The present study was designed to investigate the relationships among mindfulness, happiness, and the expression of pet peeves. Previous research has established a positive correlation between happiness and mindfulness, but, to date, no research has examined how each of these variables is related to complaining in the form of pet peeves. Four hundred ten male and female college students listed the pet peeves they had with a current or former relationship partner. They also completed measures of happiness, positive and negative affect, depression, mindfulness, relationship satisfaction, and satisfaction with life. Pet peeves were negatively correlated with relationship satisfaction, well-being, and mindfulness. Consistent with hypotheses, support was found for the mediating role of mindfulness in the relationship between happiness and pet peeves.

Synthesis of Borylated (Aminomethyl)cyclopropanes Using C1-Bisnucleophiles.

Lithiated 1,1-diborylalkanes have been used as nucleophilic coupling partners with a range of oxygen-based electrophiles, including esters, carbonyls, and epoxides. However, their reactivity with nitrogen-based electrophiles, such as aziridines, has remained relatively understudied. Herein, we show that lithiated 1,1-diborylalkanes react with α-halo and α-tosyl aziridines to yield borylated (aminomethyl)cyclopropanes-a privileged scaffold within medicinal chemistry. The reaction displays high levels of diastereoselectivity, enabling careful control of up to three stereocenters within a single transformation. DFT studies provide insight into the reaction mechanism, which diverges from that observed with analogous epihalohydrin starting materials. Derivatization studies were also performed on the products to demonstrate the utility of the boron and amine handles.

Transformations of carbohydrate derivatives enabled by photocatalysis and visible light photochemistry.

This review article highlights the diverse ways in which recent developments in the areas of photocatalysis and visible light photochemistry are impacting synthetic carbohydrate chemistry. The major topics covered are photocatalytic glycosylations, generation of radicals at the anomeric position, transformations involving radical formation at non-anomeric positions, additions to glycals, processes initiated by photocatalytic hydrogen atom transfer from sugars, and functional group interconversions at OH and SH groups. Factors influencing stereo- and site-selectivity in these processes, along with mechanistic aspects, are discussed.

Catalyst-Controlled, Site-Selective Sulfamoylation of Carbohydrate Derivatives.

Methods for site-selective sulfamoylation of secondary hydroxyl groups in pyranosides are described. Using a boronic acid catalyst, selective installation of a Boc-protected sulfamoyl group at the equatorial position of cis-diols in manno- and galacto-configured substrates has been achieved. Activation of trans-diol groups in gluco- and galacto-configured substrates is also possible by employing an organotin catalyst.

Cytosine methylation profiling of cancer cell lines.

DNA-methylation changes in human cancer are complex and vary between the different types of cancer. Capturing this epigenetic variability in an atlas of DNA-methylation changes will be beneficial for basic research as well as translational medicine. Hypothesis-free approaches that interrogate methylation patterns genome-wide have already generated promising results. However, these methods are still limited by their quantitative accuracy and the number of CpG sites that can be assessed individually. Here, we use a unique approach to measure quantitative methylation patterns in a set of >400 candidate genes. In this high-resolution study, we employed a cell-line model consisting of 59 cancer cell lines provided by the National Cancer Institute and six healthy control tissues for discovery of methylation differences in cancer-related genes. To assess the effect of cell culturing, we validated the results from colon cancer cell lines by using clinical colon cancer specimens. Our results show that a large proportion of genes (78 of 400 genes) are epigenetically altered in cancer. Although most genes show methylation changes in only one tumor type (35 genes), we also found a set of genes that changed in many different forms of cancer (seven genes). This dataset can easily be expanded to develop a more comprehensive and ultimately complete map of quantitative methylation changes. Our methylation data also provide an ideal starting point for further translational research where the results can be combined with existing large-scale datasets to develop an approach that integrates epigenetic, transcriptional, and mutational findings.

Site- and Stereoselective C-H Alkylations of Carbohydrates Enabled by Cooperative Photoredox, Hydrogen Atom Transfer, and Organotin Catalysis.

Diorganotin dihalides act as cocatalysts for site-selective and stereoselective couplings of diol-containing carbohydrates with electron-deficient alkenes in the presence of an Ir(III) photoredox catalyst and quinuclidine, a hydrogen atom transfer mediator. Quantum-chemical calculations support a proposed mechanism involving the formation of a cyclic stannylene acetal intermediate that shows enhanced reactivity toward hydrogen atom abstraction by the quinuclidinium radical cation. Addition of the carbon-centered radical to the alkene partner results in C-alkylation of the carbohydrate substrate.

Using a Self-Administered Electronic Adherence Questionnaire to Identify Poor Adherence Amongst Adolescents and Young Adults on First-Line Antiretroviral Therapy in Johannesburg, South Africa.

INTRODUCTION: The best method to measure adherence to antiretroviral therapy (ART) in resource-limited settings has not yet been established, particularly among adolescents and young adults (AYAs). The use of mobile technology may address the need for standardized tools in measuring adherence in this often marginalized population. METHODS: We conducted a cross-sectional validation study among AYAs (18-35 years) attending a South African HIV clinic between 07/2015-09/2017. We determine the diagnostic accuracy of two modes of delivering an adherence questionnaire (self-administered electronic vs interviewer-administered paper-adherence questionnaire) comprising two self-reported adherence tools (South African National Department of Health (NDoH) adherence questionnaire and the Simplified Medication Adherence Questionnaire (SMAQ)) to identify poor adherence compared to; 1) a detectable viral load (≥1000 copies/mL) and 2) a sub-optimal concentration of efavirenz (EFV) (EFV ≤1.00 µg/mL) measured by therapeutic drug monitoring (TDM). RESULTS: Of 278 included participants, 7.1% and 7.3% completing the electronic- and paper-questionnaires had a detectable viral load, while 14.7% and 16.5% had a sub-optimal concentration of EFV, respectively. According to viral load monitoring, the electronic-adherence questionnaire had a higher sensitivity (Se) in detecting poor adherence than the paper-based version across the NDoH adherence questionnaire (Se: 63.6% vs 33.3%) and SMAQ (Se: 90.9% vs 66.7%). In contrast, when using blood drug concentration (EFV ≤1.00 µg/mL), the paper-adherence questionnaire produced a higher sensitivity across both adherence tools; namely the NDoH adherence questionnaire (Se: 50.0% vs 38.1%) and SMAQ (Se: 75.0% vs 57.1%). CONCLUSION: When using more accurate real-time measures of poor adherence such as TDM in this young adult population, we observe a higher sensitivity of an interviewer-administered paper-adherence questionnaire than an identical set of self-administered adherence questions on an electronic tablet. An interviewer-administered questionnaire may elicit more accurate responses from participants through a sense of increased accountability when engaging with health care workers.

Modeling Controlled Cortical Impact Injury in 3D Brain-Like Tissue Cultures.

Traumatic brain injury (TBI) survivors suffer long term from mental illness, neurodegeneration, and neuroinflammation. Studies of 3D tissue models have provided new insights into the pathobiology of many brain diseases. Here, a 3D in vitro contusion model is developed consisting of mouse cortical neurons grown on a silk scaffold embedded in collagen and used outcomes from an in vivo model for benchmarking. Molecular, cellular, and network events are characterized in response to controlled cortical impact (CCI). In this model, CCI induces degradation of neural network structure and function and release of glutamate, which are associated with the expression of programmed necrosis marker phosphorylated Mixed Lineage Kinase Domain Like Pseudokinase (pMLKL). Neurodegeneration is observed first in the directly impacted area and it subsequently spreads over time in 3D space. CCI reduces phosphorylated protein kinase B (pAKT) and Glycogen synthase kinase 3 beta (GSK3ß) in neurons in vitro and in vivo, but discordant responses are observed in phosphprylated ribosomal S6 kinase (pS6) and phosphorylated Tau (pTau) expression. In summary, the 3D brain-like culture system mimicked many aspects of in vivo responses to CCI, providing evidence that the model can be used to study the molecular, cellular, and functional sequelae of TBI, opening up new possibilities for discovery of therapeutics.

Parallelization and optimization of genetic analyses in isolation by distance web service.

BACKGROUND: The Isolation by Distance Web Service (IBDWS) is a user-friendly web interface for analyzing patterns of isolation by distance in population genetic data. IBDWS enables researchers to perform a variety of statistical tests such as Mantel tests and reduced major axis regression (RMA), and returns vector based graphs. The more than 60 citations since 2005 confirm the popularity and utility of this website. Despite its usefulness, the data sets with over 65 populations can take hours or days to complete due to the computational intensity of the statistical tests. This is especially troublesome for web-based software analysis, since users tend to expect real-time results on the order of seconds, or at most, minutes. Moreover, as genetic data continue to increase and diversify, so does the demand for more processing power. In order to increase the speed and efficiency of IBDWS, we first determined which aspects of the code were most time consuming and whether they might be amenable to improvements by parallelization or algorithmic optimization. RESULTS: Runtime tests uncovered two areas of IBDWS that consumed significant amounts of time: randomizations within the Mantel test and the RMA calculations. We found that these sections of code could be restructured and parallelized to improve efficiency. The code was first optimized by combining two similar randomization routines, implementing a Fisher-Yates shuffling algorithm, and then parallelizing those routines. Tests of the parallelization and Fisher-Yates algorithmic improvements were performed on a variety of data sets ranging from 10 to 150 populations. All tested algorithms showed runtime reductions and a very close fit to the predicted speedups based on time-complexity calculations. In the case of 150 populations with 10,000 randomizations, data were analyzed 23 times faster. CONCLUSION: Since the implementation of the new algorithms in late 2007, datasets have continued to increase substantially in size and many exceed the largest population sizes we used in our test sets. The fact that the website has continued to work well in "real-world" tests, and receives a considerable number of new citations provides the strongest testimony to the effectiveness of our improvements. However, we soon expect the need to upgrade the number of nodes in our cluster significantly as dataset sizes continue to expand. The parallel implementation can be found at http://ibdws.sdsu.edu/.

Clinical variability of autosomal dominant cataract, microcornea and corneal opacity and novel mutation in the alpha A crystallin gene (CRYAA).

We studied 28 individuals from a four-generation Chilean family (ADC54) including 13 affected individuals with cataracts, microcornea and/or corneal opacity. All individuals underwent a complete ophthalmologic exam. We screened with a panel of polymorphic DNA markers for known loci that cause autosomal dominant cataracts, if mutated, and refined the locus using the ABI Prism Linkage Mapping Set Version 2.5, and calculated two-point lod scores. Novel PCR primers were designed for the three coding exons, including intron-exon borders, of the candidate gene alpha A crystallin (CRYAA). Clinically, affected individuals had diverse and novel cataracts with variable morphology (anterior polar, cortical, embryonal, fan-shaped, anterior subcapsular). Microcornea and corneal opacity was evident in some. Marker D21S171 gave a lod score of 4.89 (theta(m) = theta(f) = 0). CRYAA had a G414A transition that segregated with the disease and resulted in an amino acid alteration (R116H). The phenotypic variability within this family was significant with novel features of the cataracts and a corneal opacity. With the exception of iris coloboma, the clinical features in all six previously reported families with mutations in the CRYAA gene were found in this family. We identified a novel G414A transition in exon 3 of CRYAA that co-segregated with an autosomal dominant phenotype. The resulting amino acid change R116H is in a highly conserved region and represents a change in charge. The genotype-phenotype correlation of this previously unreported mutation provides evidence that other factors, genetic and/or environmental, may influence the development of cataract as a result of this alteration.

Wikidata as a semantic framework for the Gene Wiki initiative.

Open biological data are distributed over many resources making them challenging to integrate, to update and to disseminate quickly. Wikidata is a growing, open community database which can serve this purpose and also provides tight integration with Wikipedia. In order to improve the state of biological data, facilitate data management and dissemination, we imported all human and mouse genes, and all human and mouse proteins into Wikidata. In total, 59,721 human genes and 73,355 mouse genes have been imported from NCBI and 27,306 human proteins and 16,728 mouse proteins have been imported from the Swissprot subset of UniProt. As Wikidata is open and can be edited by anybody, our corpus of imported data serves as the starting point for integration of further data by scientists, the Wikidata community and citizen scientists alike. The first use case for these data is to populate Wikipedia Gene Wiki infoboxes directly from Wikidata with the data integrated above. This enables immediate updates of the Gene Wiki infoboxes as soon as the data in Wikidata are modified. Although Gene Wiki pages are currently only on the English language version of Wikipedia, the multilingual nature of Wikidata allows for usage of the data we imported in all 280 different language Wikipedias. Apart from the Gene Wiki infobox use case, a SPARQL endpoint and exporting functionality to several standard formats (e.g. JSON, XML) enable use of the data by scientists. In summary, we created a fully open and extensible data resource for human and mouse molecular biology and biochemistry data. This resource enriches all the Wikipedias with structured information and serves as a new linking hub for the biological semantic web. Database URL: https://www.wikidata.org/.