IMPROVED SYNTHESIS OF 3-ARYL-ISOXAZOLES AS INTERMEDIATES FOR NOVEL G-QUADRUPLEX BINDING ANTI-TUMOR AGENTS

As a promising new target for chemotherapy G-quadruplexes (G4) have drawn great interest from the scientific community. Current chemotherapeutic agents exhibit broad toxicity to patients; G4 has the potential to be selectively targeted by novel chemotherapeutic agents that exhibit toxicity specific towards cancer cells. Anthracenyl isoxazolyl amides (AIMs) have shown potent anti-tumor activity and have evidence to support them as G4 binding molecules. Studies of the AIMs’ unique mechanism of action require an efficient synthesis of target molecules. For our system, methods traditionally used to synthesize isoxazoles were inefficient and gave poor yields. A critical comparison of methods to prepare sterically hindered 3-aryl isoxazoles containing fused aromatic rings using the nitrile oxide cycloaddition (NOC) revealed that modification of the method of Bode, Hachisu, Matsuura and Suzuki (BHMS), was far superior to that of the enamine method. Utilization of either triethyl amine as a base or sodium enolates of diketone, ketoester and ketoamide dipolarophiles gave much higher yields as well as fewer by-products from the NOC. Here-in is reported the improved synthesis of 3-aryl-isoxazoles via an adaption of the BHMS method. Included in this report is the crystallographic data for Ethyl 3-(10\u27-bromo-9\u27-anthracenyl)-5-methyl-4-isoxazolcarboxylate. As seen in the crystal structure of the chapter 2 title compound the isoxazole plane is nearly orthogonal to the plane of the anthracene; which is thought to be a necessity for the AIMs to interact with G4. This conformation is ideal for both pi-stacking with the guanine decks and polar interactions with the phosphate backbone of quadruplex DNA

Anthracenyl isoxazole amides (AIMs) stabilize quadruplex DNA structures in telomeric and c-MYC promotor sequences

Approximately 23,000 people are affected by malignant brain and CNS tumors in the United States each year and those afflicted have a median survival rate of only 12–15 months due to the limited treatment options available. The anthracenyl isoxazole amides (AIMs) are a novel class of compounds that have been shown to possess significant anti tumor activity in the NCI 60 cell line panel and to inhibit growth of SNB-19 glioblastoma cells at low micromolar and nanomolar concentrations. The goal of our current research is to characterize the mechanism underlying the anti tumor activity of the AIMs. We hypothesize the mechanism of growth inhibition to involve binding and stabilization of a DNA tertiary structure known as a guanine quadruplex. Various regulatory regions of DNA, such the c-MYC oncogene promoter sequence and repeating sequences formed at the end of telomeres, adopt the quadruplex conformation. Stabilization of quadruplex structures by small-molecule binding ligands has been reported to modulate the expression of genes and inhibit telomerase activity. Down-regulation of certain oncogenes or the inhibition of telomerase can cause tumor cells to undergo apoptosis or become unable to efficiently replicate. To establish whether interactions between the AIMs and quadruplex-forming sequences act to stabilize the quadruplex tertiary structure, circular dichroism spectroscopy (CD) was employed. CD is a method that utilizes the differential absorbance of left and right circularly polarized light to examine the chiral structure of molecules. CD thermal melting studies were conducted to determine whether the AIMs would increase the melting temperature of quadruplex forming sequences as an indication of increased stability. Our results demonstrated the AIMs, at two equivalents, increase the melting temperature (Tm) of both the c-MYC promoter and telomeric sequences by approximately 2–3 °C with strong statistical significance and reproducibility. Utilizing CD allows the use of low micromolar concentrations of DNA and this method will be used in the future to rapidly develop additional structure-activity relationships between novel AIMs and quadruplex forming sequences. Our laboratory has also shown chemical shifts in the imino region upon treatment with the AIMs for both the c-MYC promotor and telomeric sequence by NMR, providing additional evidence of the AIMs interaction with quadruplex structures. Interestingly, fluorescence microscopy of SNB-19 cells treated with AIMs show their localization is primarily in the mitochondria, and mitochondrial DNA contains several other important quadruplex forming sequences. Mitochondrial-dependent apoptosis has been suggested for other quadruplex binding ligands and therefore our future work will examine the potential stabilization of mitochondrial quadruplexes by these and other novel AIMs

Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses

<p>Abstract</p> <p>Background</p> <p>Pneumonia and myocarditis are the most commonly reported diseases due to <it>Histophilus somni</it>, an opportunistic pathogen of the reproductive and respiratory tracts of cattle. Thus far only a few genes involved in metabolic and virulence functions have been identified and characterized in <it>H. somni </it>using traditional methods. Analyses of the genome sequences of several <it>Pasteurellaceae </it>species have provided insights into their biology and evolution. In view of the economic and ecological importance of <it>H. somni</it>, the genome sequence of pneumonia strain 2336 has been determined and compared to that of commensal strain 129Pt and other members of the <it>Pasteurellaceae</it>.</p> <p>Results</p> <p>The chromosome of strain 2336 (2,263,857 bp) contained 1,980 protein coding genes, whereas the chromosome of strain 129Pt (2,007,700 bp) contained only 1,792 protein coding genes. Although the chromosomes of the two strains differ in size, their average GC content, gene density (total number of genes predicted on the chromosome), and percentage of sequence (number of genes) that encodes proteins were similar. The chromosomes of these strains also contained a number of discrete prophage regions and genomic islands. One of the genomic islands in strain 2336 contained genes putatively involved in copper, zinc, and tetracycline resistance. Using the genome sequence data and comparative analyses with other members of the <it>Pasteurellaceae</it>, several <it>H. somni </it>genes that may encode proteins involved in virulence (<it>e.g</it>., filamentous haemaggutinins, adhesins, and polysaccharide biosynthesis/modification enzymes) were identified. The two strains contained a total of 17 ORFs that encode putative glycosyltransferases and some of these ORFs had characteristic simple sequence repeats within them. Most of the genes/loci common to both the strains were located in different regions of the two chromosomes and occurred in opposite orientations, indicating genome rearrangement since their divergence from a common ancestor.</p> <p>Conclusions</p> <p>Since the genome of strain 129Pt was ~256,000 bp smaller than that of strain 2336, these genomes provide yet another paradigm for studying evolutionary gene loss and/or gain in regard to virulence repertoire and pathogenic ability. Analyses of the complete genome sequences revealed that bacteriophage- and transposon-mediated horizontal gene transfer had occurred at several loci in the chromosomes of strains 2336 and 129Pt. It appears that these mobile genetic elements have played a major role in creating genomic diversity and phenotypic variability among the two <it>H. somni </it>strains.</p

The 16th Data Release of the Sloan Digital Sky Surveys: First Release from the APOGEE-2 Southern Survey and Full Release of eBOSS Spectra

This paper documents the 16th data release (DR16) from the Sloan Digital Sky Surveys (SDSS), the fourth and penultimate from the fourth phase (SDSS-IV). This is the first release of data from the Southern Hemisphere survey of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2); new data from APOGEE-2 North are also included. DR16 is also notable as the final data release for the main cosmological program of the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), and all raw and reduced spectra from that project are released here. DR16 also includes all the data from the Time Domain Spectroscopic Survey and new data from the SPectroscopic IDentification of ERosita Survey programs, both of which were co-observed on eBOSS plates. DR16 has no new data from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey (or the MaNGA Stellar Library "MaStar"). We also preview future SDSS-V operations (due to start in 2020), and summarize plans for the final SDSS-IV data release (DR17)

The 16th Data Release of the Sloan Digital Sky Surveys: First Release from the APOGEE-2 Southern Survey and Full Release of eBOSS Spectra

This paper documents the 16th data release (DR16) from the Sloan Digital Sky Surveys (SDSS), the fourth and penultimate from the fourth phase (SDSS-IV). This is the first release of data from the Southern Hemisphere survey of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2); new data from APOGEE-2 North are also included. DR16 is also notable as the final data release for the main cosmological program of the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), and all raw and reduced spectra from that project are released here. DR16 also includes all the data from the Time Domain Spectroscopic Survey and new data from the SPectroscopic IDentification of ERosita Survey programs, both of which were co-observed on eBOSS plates. DR16 has no new data from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey (or the MaNGA Stellar Library "MaStar"). We also preview future SDSS-V operations (due to start in 2020), and summarize plans for the final SDSS-IV data release (DR17)

The 16th Data Release of the Sloan Digital Sky Surveys : First Release from the APOGEE-2 Southern Survey and Full Release of eBOSS Spectra

This paper documents the 16th data release (DR16) from the Sloan Digital Sky Surveys (SDSS), the fourth and penultimate from the fourth phase (SDSS-IV). This is the first release of data from the Southern Hemisphere survey of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2); new data from APOGEE-2 North are also included. DR16 is also notable as the final data release for the main cosmological program of the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), and all raw and reduced spectra from that project are released here. DR16 also includes all the data from the Time Domain Spectroscopic Survey and new data from the SPectroscopic IDentification of ERosita Survey programs, both of which were co-observed on eBOSS plates. DR16 has no new data from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey (or the MaNGA Stellar Library "MaStar"). We also preview future SDSS-V operations (due to start in 2020), and summarize plans for the final SDSS-IV data release (DR17).Peer reviewe

The Seventeenth Data Release of the Sloan Digital Sky Surveys: Complete Release of MaNGA, MaStar and APOGEE-2 Data

This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library (MaStar) accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) survey which publicly releases infra-red spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the sub-survey Time Domain Spectroscopic Survey (TDSS) data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey (SPIDERS) sub-survey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated Value Added Catalogs (VACs). This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper (MWM), Local Volume Mapper (LVM) and Black Hole Mapper (BHM) surveys

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity