Crystallographic Aspects, Photophysical Properties, and Theoretical Survey of Tetrachlorometallates of Group 12 Metals [Zn(II), Cd(II), and Hg(II)] with a Triply Protonated 2,4,6-Tris(2-pyridyl)-1,3,5-triazine Ligand.

Zn(II) (complex 1), Cd(II) (complex 2), and Hg(II) (complex 3) complexes have been synthesized using a triply protonated tptz (H3tptz3+) ligand and characterized mainly by single-crystal X-ray analysis. The general formula of all of the complexes is (H3tptz)3+·Cl-·[MCl4]2-·nH2O (where n = 1, 1.5, and 1.5 for complexes 1, 2, and 3, respectively). The crystallographic analysis reveals that the anion···π, anion···π+, and several hydrogen bonding interactions play a fundamental role in the stabilization of the self-assembled architectures that in turn help to enhance the dimensionality of all of the complexes. In addition, Hirshfeld surfaces and fingerprint plots have been deployed here to visualize the similarities and differences in hydrogen bonding interactions in 1-3, which are very important in forming supramolecular architectures. A density functional theory (DFT) study has been used to analyze and rationalize the supramolecular interactions by using molecular electrostatic potential (MEP) surfaces and combined QTAIM/NCI plots. Then, the device parameters for the complexes (1-3) have been thoroughly investigated by fabricating a Schottky barrier diode (SBD) on an indium tin oxide (ITO) substrate. It has been observed that the device made from complex 2 is superior to those from complexes 1 and 3, which has been explained in terms of band gaps, differences in the electronegativities of the central metal atoms, and the better supramolecular interactions involved. Finally, theoretical calculations have also been performed to analyze the experimental differences in band gaps as well as electrical conductivities observed for all of the complexes. Henceforth, the present work combined supramolecular, photophysical, and theoretical studies regarding group 12 metals in a single frame.

RETRACTED: LFQC: a lossless compression algorithm for FASTQ files.

MOTIVATION: Next-generation sequencing (NGS) technologies have revolutionized genomic research by reducing the cost of whole-genome sequencing. One of the biggest challenges posed by modern sequencing technology is economic storage of NGS data. Storing raw data is infeasible because of its enormous size and high redundancy. In this article, we address the problem of storage and transmission of large Fastq files using innovative compression techniques. RESULTS: We introduce a new lossless non-reference-based fastq compression algorithm named lossless FastQ compressor. We have compared our algorithm with other state of the art big data compression algorithms namely gzip, bzip2, fastqz, fqzcomp, G-SQZ, SCALCE, Quip, DSRC, DSRC-LZ etc. This comparison reveals that our algorithm achieves better compression ratios. The improvement obtained is up to 225%. For example, on one of the datasets (SRR065390_1), the average improvement (over all the algorithms compared) is 74.62%. AVAILABILITY AND IMPLEMENTATION: The implementations are freely available for non-commercial purposes. They can be downloaded from http://engr.uconn.edu/∼rajasek/FastqPrograms.zip.

Terpyridine derivatives as "turn-on" fluorescence chemosensors for the selective and sensitive detection of Zn2+ ions in solution and in live cells.

A terpyridine based compound L1 was designed and synthesized as an "off-on" chemosensor for the detection of Zn2+. Chemosensor L1 showed excellent selectivity and sensitivity toward Zn2+ by exhibiting a large fluorescence enhancement (∼51-fold) at 370 nm whereas other competitive metal ions did not show any noticeable change in the emission spectra of chemosensor L1. The chemosensor (L1) was shown to detect Zn2+ ions down to 9.76 µM at pH 7.4. However, chemosensor L1 binds Zn2+ in a 1 : 2 ratio (receptor : metal) with an association constant of 1.85 × 104 (R2 = 0.993) and this 1 : 2 stoichiometric fashion is established on the basis of a Job plot and mass spectroscopy. DFT/TD-DFT calculations were carried out to understand the binding nature, coordination features and electronic properties of L1 and the L1-2Zn2+ complex. In addition, this "turn-on" fluorescence probe was effectively used to image intracellular Zn2+ ions in cultured MDA-MB-468 cells.

LFQC: a lossless compression algorithm for FASTQ files.

MOTIVATION: Next Generation Sequencing (NGS) technologies have revolutionized genomic research by reducing the cost of whole genome sequencing. One of the biggest challenges posed by modern sequencing technology is economic storage of NGS data. Storing raw data is infeasible because of its enormous size and high redundancy. In this article, we address the problem of storage and transmission of large FASTQ files using innovative compression techniques. RESULTS: We introduce a new lossless non-reference based FASTQ compression algorithm named Lossless FASTQ Compressor. We have compared our algorithm with other state of the art big data compression algorithms namely gzip, bzip2, fastqz (Bonfield and Mahoney, 2013), fqzcomp (Bonfield and Mahoney, 2013), Quip (Jones et al., 2012), DSRC2 (Roguski and Deorowicz, 2014). This comparison reveals that our algorithm achieves better compression ratios on LS454 and SOLiD datasets. AVAILABILITY AND IMPLEMENTATION: The implementations are freely available for non-commercial purposes. They can be downloaded from http://engr.uconn.edu/rajasek/lfqc-v1.1.zip. CONTACT: rajasek@engr.uconn.edu.

Deoxyuridine-rich cytoplasmic DNA antagonizes STING-dependent innate immune responses and sensitizes resistant tumors to anti-PD-L1 therapy.

DNA damage and cytoplasmic DNA induce type-1 interferon (IFN-1) and potentiate responses to immune checkpoint inhibitors. Our prior work found that inhibitors of the DNA damage response kinase ATR (ATRi) induce IFN-1 and deoxyuridine (dU) incorporation by DNA polymerases, akin to antimetabolites. Whether and how dU incorporation is required for ATRi-induced IFN-1 signaling is not known. Here, we show that ATRi-dependent IFN-1 responses require uracil DNA glycosylase (UNG)-initiated base excision repair and STING. Quantitative analyses of nine distinct nucleosides reveals that ATRi induce dU incorporation more rapidly in UNG wild-type than knockout cells, and that induction of IFN-1 is associated with futile cycles of repair. While ATRi induce similar numbers of micronuclei in UNG wild-type and knockout cells, dU containing micronuclei and cytoplasmic DNA are increased in knockout cells. Surprisingly, DNA fragments containing dU block STING-dependent induction of IFN-1, MHC-1, and PD-L1. Furthermore, UNG knockout sensitizes cells to IFN-γ in vitro , and potentiates responses to anti-PD-L1 in resistant tumors in vivo . These data demonstrate an unexpected and specific role for dU-rich DNA in suppressing STING-dependent IFN-1 responses, and show that UNG-deficient tumors have a heightened response to immune checkpoint inhibitors. STATEMENT OF SIGNIFICANCE: Antimetabolites disrupt nucleotide pools and increase dU incorporation by DNA polymerases. We show that unrepaired dU potentiates responses to checkpoint inhibitors in mouse models of cancer. Patients with low tumor UNG may respond to antimetabolites combined with checkpoint inhibitors, and patients with high tumor UNG may respond to UNG inhibitors combined with checkpoint inhibitors.

Efficient techniques for genotype-phenotype correlational analysis.

BACKGROUND: Single Nucleotide Polymorphisms (SNPs) are sequence variations found in individuals at some specific points in the genomic sequence. As SNPs are highly conserved throughout evolution and within a population, the map of SNPs serves as an excellent genotypic marker. Conventional SNPs analysis mechanisms suffer from large run times, inefficient memory usage, and frequent overestimation. In this paper, we propose efficient, scalable, and reliable algorithms to select a small subset of SNPs from a large set of SNPs which can together be employed to perform phenotypic classification. METHODS: Our algorithms exploit the techniques of gene selection and random projections to identify a meaningful subset of SNPs. To the best of our knowledge, these techniques have not been employed before in the context of genotype-phenotype correlations. Random projections are used to project the input data into a lower dimensional space (closely preserving distances). Gene selection is then applied on the projected data to identify a subset of the most relevant SNPs. RESULTS: We have compared the performance of our algorithms with one of the currently known best algorithms called Multifactor Dimensionality Reduction (MDR), and Principal Component Analysis (PCA) technique. Experimental results demonstrate that our algorithms are superior in terms of accuracy as well as run time. CONCLUSIONS: In our proposed techniques, random projection is used to map data from a high dimensional space to a lower dimensional space, and thus overcomes the curse of dimensionality problem. From this space of reduced dimension, we select the best subset of attributes. It is a unique mechanism in the domain of SNPs analysis, and to the best of our knowledge it is not employed before. As revealed by our experimental results, our proposed techniques offer the potential of high accuracies while keeping the run times low.

Silica sulfuric acid: a reusable solid catalyst for one pot synthesis of densely substituted pyrrole-fused isocoumarins under solvent-free conditions.

A convenient and efficient methodology for the synthesis of densely substituted pyrrole-fused isocoumarins, which employs solid-supported silica sulfuric acid (SSA) as catalyst, has been developed. When the mixture of ninhydrin adducts of acetylacetone/ethyl acetoacetate and primary amines was heated on the solid surface of SSA under solvent-free conditions, the pyrrole-fused isocoumarins were formed in good yields. This synthetic method has several advantages such as the employment of solvent-free reaction conditions without the use of any toxic reagents and metal catalysts, the ease of product isolation, the use of a recyclable catalyst, the low cost, the easy availability of the starting materials, and the excellent yields of products.

Factors in Oncogenesis: Viral Infections in Ovarian Cancer.

Ovarian cancer (OC) is one of the leading causes of cancer death in women, with high-grade serous ovarian cancer (HGSOC) being the most lethal gynecologic malignancy among women. This high fatality rate is the result of diagnosis of a high number of new cases when cancer implants have already spread. The poor prognosis is due to our inadequate understanding of the molecular mechanisms preceding ovarian malignancy. Knowledge about the site of origination has been improved recently by the discovery of tube intraepithelial cancer (TIC), but the potential risk factors are still obscure. Due to high tumoral heterogeneity in OC, the establishment of early stage biomarkers is still underway. Microbial infection may induce or result in chronic inflammatory infection and in the pathogenesis of cancers. Microbiome research has shed light on the relationships between the host and microbiota, as well as the direct roles of host pathogens in cancer development, progression, and drug efficacy. While controversial, the detection of viruses within ovarian malignancies and fallopian tube tissues suggests that these pathogens may play a role in the development of OC. Genomic and proteomic approaches have enhanced the methods for identifying candidates in early screening. This article summarizes the existing knowledge related to the molecular mechanisms that lead to tumorigenesis in the ovary, as well as the viruses detected in OC cases and how they may elevate this process.

Structures, photoresponse properties and DNA binding abilities of 4-(4-pyridinyl)-2-pyridone salts.

Three salts [perchlorate (2), chloride (3) and tetrafluoroborate (4)] were synthesized from a 1-(2-aminoethyl)-6-hydroxy-2-oxo-1,2-dihydro-[4,4'-bipyridine]-3,5-dicarbonitrile compound (1) and characterized by spectroscopic and single crystal X-ray diffraction methods. Various noncovalent interactions (e.g., anion⋯π+, π⋯π, lp⋯π) are explored in the solid state crystal structure of the salts. Optical band gaps of all the four compounds were determined from their solid-state UV-vis spectrum. Electrical properties like electrical conductivity, photosensitivity, etc. were calculated and the results revealed that they have potential to act as optoelectronic devices. The values of the electrical parameters increase several times when they are exposed to visible light rather than in dark conditions. The light sensing properties of the salts (2-4) are enhanced compared to that of the mother organic compound 1 but the magnitude of this enhancement is not same for the three salts. This observation has been rationalized by theoretical considerations. Moreover, the DNA binding ability of one of the representative salts (compound 2) was examined to check the biological importance of the synthesized salts.

Structures, Photoresponse Properties, and Biological Activity of Dicyano-Substituted 4-Aryl-2-pyridone Derivatives.

Described in this work is the synthesis of a novel dicyano-substituted N-2-aminoethyl-4-(3-pyridinyl)-2-pyridone organic compound (1) that is characterized by several spectroscopic methods. Compound (1) was utilized for the preparation of its perchlorate (2), chloride (3), and bromide (4) salts. Single-crystal X-ray structures of these three salts were determined, and noncovalent weak interactions involving the aromatic rings, anions, and water molecules in (2-4) were investigated in detail. Solid-state UV-vis spectrum of the reported compounds (1-4) was utilized to calculate their optical band gaps, which clearly indicated that they belong to the semiconductor family. Under illumination condition, the magnitudes of electrical properties of (1) and its salts (2-4) improve remarkably although the improvement differs from salt to salt and the result was analyzed theoretically. Salt (2) was tested for its DNA binding ability.

An experimental comparison of PMSprune and other algorithms for motif search.

A comparative study of the various motif search algorithms is very important for several reasons. For example, we could identify the strengths and weaknesses of each. As a result, we might be able to devise hybrids that will perform better than the individual components. In this paper, we (either directly or indirectly) compare the performance of PMSprune (an algorithm based on the (l, d)-motif model) and several other algorithms in terms of seven measures and using well-established benchmarks. We have employed several benchmark datasets including the one used by Tompa et al. It is observed that both PMSprune and DME (an algorithm based on position-specific score matrices), in general, perform better than the 13 algorithms reported in Tompa et al. Subsequently, we have compared PMSprune and DME on other benchmark datasets including ChIP-Chip, ChIP-Seq and ABS. Between PMSprune and DME, PMSprune performs better than DME on six measures. DME performs better than PMSprune on one measure (namely, specificity).