Silica sources for arsenic mitigation in rice: machine learning-based predictive modeling and risk assessment.

Arsenic (As) is a well-known human carcinogen, and the consumption of rice is the main pathway for the South Asian people. The study evaluated the impact of the amendments involving CaSiO3, SiO2 nanoparticles, silica solubilizing bacteria (SSB), and rice straw compost (RSC) on mitigation of As toxicity in rice. The translocation of As from soil to cooked rice was tracked, and the results showed that RSC and its combination with SSB were the most effective in reducing As loading in rice grain by 53.2%. To determine the risk of dietary exposure to As, the average daily intake (ADI), hazard quotient (HQ), and incremental lifetime cancer risk (ILCR) were computed. The study observed that the ADI was reduced to one-third (0.24 µg kg-1bw) under RSC+SSB treatments compared to the control. An effective prediction model was established using random forest model and described the accumulation of As by rice grains depend on bioavailable As, P, and Fe which explained 48.5, 5.07%, and 2.6% of the variation in the grain As, respectively. The model anticipates that to produce As benign rice grain, soil should have P and Fe concentration more than 30 mg kg-1 and 12 mg kg-1, respectively if soil As surpasses 2.5 mg kg-1.

G4 Sensing Pyridyl-Thiazole Polyamide Represses c-KIT Expression in Leukemia Cells.

Specific sensing and functional tuning of nucleic acid secondary structures remain less explored to date. Herein, we report a thiazole polyamide TPW that binds specifically to c-KIT1 G-quadruplex (G4) with sub-micromolar affinity and ∼1 : 1 stoichiometry and represses c-KIT proto-oncogene expression. TPW shows up to 10-fold increase in fluorescence upon binding with c-KIT1 G4, but shows weak or no quantifiable binding to other G4s and ds26 DNA. TPW can increase the number of G4-specific antibody (BG4) foci and mark G4 structures in cancer cells. Cell-based assays reveal that TPW can efficiently repress c-KIT expression in leukemia cells via a G4-dependent process. Thus, the polyamide can serve as a promising probe for G-quadruplex recognition with the ability to specifically alter c-KIT oncogene expression.

Ionophore constructed from non-covalent assembly of a G-quadruplex and liponucleoside transports K+-ion across biological membranes.

The selective transport of ions across cell membranes, controlled by membrane proteins, is critical for a living organism. DNA-based systems have emerged as promising artificial ion transporters. However, the development of stable and selective artificial ion transporters remains a formidable task. We herein delineate the construction of an artificial ionophore using a telomeric DNA G-quadruplex (h-TELO) and a lipophilic guanosine (MG). MG stabilizes h-TELO by non-covalent interactions and, along with the lipophilic side chain, promotes the insertion of h-TELO within the hydrophobic lipid membrane. Fluorescence assays, electrophysiology measurements and molecular dynamics simulations reveal that MG/h-TELO preferentially transports K+-ions in a stimuli-responsive manner. The preferential K+-ion transport is presumably due to conformational changes of the ionophore in response to different ions. Moreover, the ionophore transports K+-ions across CHO and K-562 cell membranes. This study may serve as a design principle to generate selective DNA-based artificial transporters for therapeutic applications.

G-Quadruplex-Binding Small Molecule Induces Synthetic Lethality in Breast Cancer Cells by Inhibiting c-MYC and BCL2 Expression.

Herein, a prolinamide-derived peptidomimetic that preferentially binds to c-MYC and BCL2 G-quadruplexes present in the promoter regions of apoptosis-related genes (c-MYC and BCL2) over other DNA quadruplexes are described. Biological assays, such as real-time quantitative reverse transcription, western blot, dual luciferase, and small interfering RNA knockdown assays, indicate that the ligand triggers a synthetic lethal interaction by simultaneously inhibiting the expression of c-MYC and BCL2 genes through their promoter G-quadruplexes. The ligand shows antiproliferative activity in MCF-7 cells that overexpress both MYC and BCL2 genes, in comparison to cells that overexpress either of the two. Moreover, the ligand induces S-phase cell-cycle arrest, DNA damage, and apoptosis in MCF-7 cells.

The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from north-east India and its comparison with related Dendrobium species.

The medicinal orchid genus Dendrobium belonging to the Orchidaceae family is a huge genus comprising about 800-1,500 species. To better illustrate the species status in the genus Dendrobium, a comparative analysis of 33 available chloroplast genomes retrieved from NCBI RefSeq database was compared with that of the first complete chloroplast genome of D. nobile from north-east India based on next-generation sequencing methods (Illumina HiSeq 2500-PE150). Our results provide comparative chloroplast genomic information for taxonomical identification, alignment-free phylogenomic inference and other statistical features of Dendrobium plastomes, which can also provide valuable information on their mutational events and sequence divergence.

Water vapor flux in tropical lowland rice.

A field experiment was conducted at Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India in the dry seasons of 2015 and 2016 to assess the water vapor flux (FH2O) and its relationship with other climatic variables. The FH2O and climatic variables were measured by an eddy covariance system and a micrometeorological observatory. Daily mean FH2O during the dry seasons of 2015 and 2016 were 0.009-0.092 g m-2 s-1 and 0.014-0.101 g m-2 s-1, respectively. Seasonal average FH2O was 14.6% higher in 2016 than that in 2015. Diurnal variation for FH2O showed a bell-shaped curve with its peak at 13:30-14:00 Indian Standard Time (IST) in both the years. Carbon dioxide flux was found higher with rise in FH2O. This relationship was stronger at higher vapor pressure deficit (VPD) (20 ≤ VPD ≤ 40 and VPD > 40 hPa). The FH2O showed significant positive correlation with latent heat flux, net radiation flux, photosynthatically active radiation, air, water and soil temperatures, shortwave down and upwell radiations, maximum and minimum temperatures, evaporation, and relative humidity in both the years. Principal component analysis showed that FH2O was very close to latent heat flux in both the years (Pearson correlation coefficient close to 1). The two-dimensional observation map of the principal component F1 and F2 showed the observations taken during the vegetative stage and panicle initiation stage, and flowering stage and maturity stage were closer to each other. It can be concluded that the most important climatic variables controlling the FH2O were latent heat of vaporization, net radiation, air temperature, soil temperatures, and water temperature.

Chemical Regulation of DNA i-Motifs for Nanobiotechnology and Therapeutics.

DNA sequences rich in cytosine have the propensity, under acidic pH, to fold into four-stranded intercalated DNA structures called i-motifs. Recent studies have provided significant breakthroughs that demonstrate how chemists can manipulate these structures for nanobiotechnology and therapeutics. The first section of this Minireview discusses the development of advanced functional nanostructures by synthetic conjugation of i-motifs with organic scaffolds and metal nanoparticles and their role in therapeutics. The second section highlights the therapeutic targeting of i-motifs with chemical scaffolds and their significance in biology. For this, first we shed light on the long-lasting debate regarding the stability of i-motifs under physiological conditions. Next, we present a comparative analysis of recently reported small molecules for specifically targeting i-motifs over other abundant DNA structures and modulating their function in cellular systems. These advances provide new insights into i-motif-targeted regulation of gene expression, telomere maintenance, and therapeutic applications.

Induction of apoptosis, anti-proliferation, tumor-angiogenic suppression and down-regulation of Dalton's Ascitic Lymphoma (DAL) induced tumorigenesis by poly-l-lysine: A mechanistic study.

PURPOSE: The present study, attempts to validate the molecular mechanism(s) of Poly-l-lysine (PLL) induced apoptosis, anti-proliferative and anti-tumorigenic properties in in-vitro HUVECs cells and Dalton's Ascitic Lymphoma (DAL) and in in-vivo DAL cell bearing BALB/c mice model. MATERIALS AND METHODS: The cell proliferation assay and morphological assay was carried out using the MTT assay and Giemsa staining method. The antitumor activity of PLL was evaluated in BALB/c mice at 20 and 40 mg/kg/b.w doses for 21 days for DAL solid tumor model. Several tumor evaluation endpoints, hematological and biochemical parameters were estimated. Additionally, the tumor apoptosis, anti-proliferative and anti-tumor angiogenesis effects were assessed using western blots and immunohistochemistry. RESULTS: PLL significantly decreased cell proliferation in in-vitro HUVECs and DAL cells without significant effects on normal cell growth. PLL also induced alteration in cellular morphology in DAL cells. Therafter, in the BALB/c mouse model, PLL had noticeable inhibition in DAL-induced tumorigenesis. This inhibition was evident through reduced solid tumor volume and weight versus the control group. However, PLL promoted tumor apoptosis and suppressed cell-proliferation and tumor-angiogenesis. PLL also increased hematological markers significantly compared to 5-flurouracil (5-FU). The amount of TdT in the nuclei of DAL cells in mice treated with PLL was significantly increased while in contrast decreases of anti-apoptotic protein Bcl-2 expression were observed. PLL also significantly upregulated the pro-apoptotic protein Bax and activated caspase-3. Measurable decreases of cyclin-D1 were observed through PLL treatments, an indicator of cell-cycle arrest. These studies also indicate PLL's induction and anti-proliferative effects through suppression of the c-Myc and Ki-67 proliferation-indices. Additionally, PLL inhibited tumor-angiogenesis through suppression of VEGF and CD34 protein expression levels and reduction ofmicrovesseldensityversus similar parameters in tumors from control mice. CONCLUSION: The present study offers opportunities and hopes for possible anti-tumortherapies with PLL in the near future and warrants further formulation developments.

Cell penetrating thiazole peptides inhibit c-MYC expression via site-specific targeting of c-MYC G-quadruplex.

The structural differences among different G-quadruplexes provide an opportunity for site-specific targeting of a particular G-quadruplex structure. However, majority of G-quadruplex ligands described thus far show little selectivity among different G-quadruplexes. In this work, we delineate the design and synthesis of a crescent-shaped thiazole peptide that preferentially stabilizes c-MYC quadruplex over other promoter G-quadruplexes and inhibits c-MYC oncogene expression. Biophysical analysis such as Förster resonance energy transfer (FRET) melting and fluorescence spectroscopy show that the thiazole peptide TH3 can selectively interact with the c-MYC G-quadruplex over other investigated G-quadruplexes and duplex DNA. NMR spectroscopy reveals that peptide TH3 binds to the terminal G-quartets and capping regions present in the 5'- and 3'-ends of c-MYC G-quadruplex with a 2:1 stoichiometry; whereas structurally related distamycin A is reported to interact with quadruplex structures via groove binding and end stacking modes with 4:1 stoichiometry. Importantly, qRT-PCR, western blot and dual luciferase reporter assay show that TH3 downregulates c-MYC expression by stabilizing the c-MYC G-quadruplex in cancer cells. Moreover, TH3 localizes within the nucleus of cancer cells and exhibits antiproliferative activities by inducing S phase cell cycle arrest and apoptosis.

Enzyme-Regulated DNA-Based Logic Device.

Herein, we report a carbazole (Cz) ligand that displays distinct turn-on fluorescence signals upon interaction with human telomeric G-quadruplex ( h-TELO) and nuclease enzymes. Interestingly, Cz selectively binds and stabilizes the mixed hybrid topology of h-TELO G-quadruplex that withstands digestion by exonucleases and nuclease S1. The distinct fluorescence signatures of Cz-stabilized h-TELO with nucleases are used to design conceptually novel DNA devices for selectively detecting the enzymatic activity of DNase I as well as performing logic operations. An INHIBIT logic gate is constructed using h-TELO and DNase I as the inputs while the inputs of h-TELO and nuclease S1 form a YES logic gate. Furthermore, a two-input two-output reusable logic device with "multireset" function is developed by using h-TELO and DNase I as inputs. On the basis of this platform, combinatorial logic systems (INHIBIT-INHIBIT and NOR-OR) have been successfully installed using different combinations of nucleases as inputs. Moreover, this new strategy of using a synthetic dual emissive probe and enzyme/DNA inputs for constructing reusable logic device may find important applications in biological computing and information processing.

Preferential targeting of i-motifs and G-quadruplexes by small molecules.

i-Motifs and G-quadruplexes are dynamic nucleic acid secondary structures, which are believed to play key roles in gene expression. We herein report two peptidomimetic ligands (PBP1 and PBP2) that selectively target i-motifs and G-quadruplexes over double-stranded DNA. These peptidomimetics, regioisomeric with respect to the position of triazole/prolinamide motifs, have been synthesized using a modular method involving Cu(i)-catalyzed azide and alkyne cycloaddition. The para-isomer, PBP1 exhibits high selectivity for i-motifs while the meta-isomer PBP2 binds selectively to G-quadruplex structures. Interestingly, these ligands have the ability to induce G-quadruplex or i-motif structures from the unstructured single-stranded DNA conformations, as observed using single molecule Förster resonance energy transfer (smFRET) studies. The quantitative real-time polymerase chain reaction (qRT-PCR), western blot, and dual-luciferase assays indicate that PBP1 upregulates and PBP2 downregulates BCL-2 gene expression in cancer cells.

Poly-L-Lysine Inhibits Tumor Angiogenesis and Induces Apoptosis in Ehrlich Ascites Carcinoma and in Sarcoma S-180 Tumor

Background: This study focuses on the role of Poly-L-lysine (PLL), an essential amino acid, on molecular changes of tumor angiogenesis suppression, pro-apoptotic and anti-apoptotic gene expression after treatment on Ehrlich ascites carcinoma (EAC) and solid sarcoma-180 tumor cells bearing mice. Materials and Methods: The cell viability was carried out using MTT assay. The antitumor activity was evaluated by treatment with PLL at 20 and 40mg/kg/b.w doses for 14 days in EAC ascites tumor and 21 days for Sarcoma-180 solid tumor model. Several tumor evaluation studies, haematological and biochemical parameters were estimated. Importantly, the tumor cell apoptosis was assessed using microscopic observations, DNA fragmentation assay, Flow cytometric analysis, cell-cycle and electron-microscopic study, following which, the expression of several signal proteins related to pro-apoptosis, anti-apoptosis and tumor angiogenesis were quantified using western blotting and immunohistochemistry study. Results: Precisely, PLL had cytotoxic effect on K562; A549; U937 and B16F10 cancer cells. Significant decreases in liquid and solid tumors and increased life span of treated mice were observed (P<0.05). Typical morphological changes, apoptosis bleb phenomenon and sub-G1 cell cycle arrests revealed that PLL promoted apoptotic cell death. Western blot and immunohistochemistry confirms, PLL activated apoptotic signalling cascades through down regulation of Bcl-2 and CD31 protein and upregulation of Bax and p53 proteins. The anti-angiogenic effects were also accompanied with decreased VEGF expression and reduced peritoneal-angiogenesis and microvessel density. Conclusions: The antitumor and antitumor-angiogenic activity of PLL was confirmed from all the results via up and down regulation of relevant signal proteins reported in this publication.

Chloroplast Genome Sequence Annotation of Dendrobium nobile (Asparagales: Orchidaceae), an Endangered Medicinal Orchid from Northeast India.

Orchidaceae constitutes one of the largest families of angiosperms. Owing to the significance of orchids in plant biology, market needs and current sustainable technology levels, basic research on the biology of orchids and their applications in the orchid industry is increasing. Although chloroplast (cp) genomes continue to be evolutionarily informative, there is very limited information available on orchid chloroplast genomes in public repositories. Here, we report the complete cp genome sequence of Dendrobium nobile from Northeast India (Orchidaceae, Asparagales), bearing the GenBank accession number KX377961, which will provide valuable information for future research on orchid genomics and evolution, as well as the medicinal value of orchids. Phylogenetic analyses using Bayesian methods recovered a monophyletic grouping of all Dendrobium species (D. nobile, D. huoshanense, D. officinale, D. pendulum, D. strongylanthum and D. chrysotoxum). The relationships recovered among the representative orchid species from the four subfamilies, i.e., Cypripedioideae, Epidendroideae, Orchidoideae and Vanilloideae, were consistent within the family Orchidaceae.

Age estimation for the genus Cymbidium (Orchidaceae: Epidendroideae) with implementation of fossil data calibration using molecular markers (ITS2 & matK) and phylogeographic inference from ancestral area reconstruction.

Intercontinental dislocations between tropical regions harboring two-thirds of the flowering plants have always drawn attention from taxonomists and biogeographers. One such family belonging to angiosperms is Orchidaceae with an herbaceous habit and high species diversity in the tropics. Here, we investigate the evolutionary and biogeographical history of the genus Cymbidium, which represents a monophyletic subfamily (Epidendroideae) of the orchids and comprises 50 odd species that are distinctly distributed in tropical to temperate regions. Much is not known about correlations among the level of CAM activity (one of the photosynthetic pathways often regarded as an adaptation to water stress in land plants), habitat, life forms, and phylogenetic relationships of orchids from an evolutionary perspective. A relatively well-resolved and highly supported phylogeny for Cymbidium orchids is reconstructed based on sequence analysis of ITS2 and matK regions from the chloroplast DNA available in public repositories viz. GenBank at NCBI. This study examines a genus level analysis by integrating different molecular matrices to existing fossil data on orchids in a molecular Bayesian relaxed clock employed in BEAST and assessed divergence times for the genus Cymbidium with a focus on evolutionary history of photosynthetic characters. Our study has enabled age estimations (45Ma) as well as ancestral area reconstruction for the genus Cymbidium using BEAST by addition of previously analyzed two internal calibration points.

Complete Chloroplast Genome Sequence of Dendrobium nobile from Northeastern India.

The orchid species Dendrobium nobile belonging to the family Orchidaceae and genus Dendrobium (a vast genus that encompasses nearly 1,200 species) has an herbal medicinal history of about 2000 years in east and south Asian countries. Here, we report the complete chloroplast genome sequence of D. nobile from northeastern India for the first time.

Synthesis of Fluorescent Binaphthyl Amines That Bind c-MYC G-Quadruplex DNA and Repress c-MYC Expression.

Two novel binaphthyl amines have been designed and synthesized using Buchwald amination and oxidative homocoupling as key steps. The binaphthyl amine containing two triazole rings shows higher affinity for c-MYC G-quadruplex, exhibits fluorescence "turn-on" response with c-MYC, and stains the nucleus in cells. The triazolyl binaphthyl amine shows cytotoxicity for cancer cells by inducing G2/M phase cell cycle arrest and apoptosis. Moreover, both ligands can downregulate c-MYC expression at transcriptional and translational levels.

Northeast India Helminth Parasite Information Database (NEIHPID): Knowledge Base for Helminth Parasites.

Most metazoan parasites that invade vertebrate hosts belong to three phyla: Platyhelminthes, Nematoda and Acanthocephala. Many of the parasitic members of these phyla are collectively known as helminths and are causative agents of many debilitating, deforming and lethal diseases of humans and animals. The North-East India Helminth Parasite Information Database (NEIHPID) project aimed to document and characterise the spectrum of helminth parasites in the north-eastern region of India, providing host, geographical distribution, diagnostic characters and image data. The morphology-based taxonomic data are supplemented with information on DNA sequences of nuclear, ribosomal and mitochondrial gene marker regions that aid in parasite identification. In addition, the database contains raw next generation sequencing (NGS) data for 3 foodborne trematode parasites, with more to follow. The database will also provide study material for students interested in parasite biology. Users can search the database at various taxonomic levels (phylum, class, order, superfamily, family, genus, and species), or by host, habitat and geographical location. Specimen collection locations are noted as co-ordinates in a MySQL database and can be viewed on Google maps, using Google Maps JavaScript API v3. The NEIHPID database has been made freely available at http://nepiac.nehu.ac.in/index.php.

Selective recognition of c-MYC G-quadruplex DNA using prolinamide derivatives.

Herein we report the design, synthesis, biophysical and biological evaluation of triazole containing prolinamide derivatives as selective c-MYC G-quadruplex binding ligands. A modular synthetic route has been devised for prolinamide derivatives using a copper(i) catalyzed azide-alkyne cycloaddition (CuAAC). The Förster resonance energy transfer (FRET) melting assay indicates that prolinamide trimers can significantly stabilize G-quadruplex structures over duplex DNA compared to prolinamide dimers. The fluorescent intercalator displacement (FID) assay shows that a trimer with prolinamide side chains at the para-position of the benzene ring can discriminate between different quadruplex structures and exhibits the highest binding affinity towards the c-MYC G-quadruplex structure. Molecular modeling studies reveal that the prolinamide trimer stacks upon the terminal G-quartet of the c-MYC G-quadruplex. Atomic force microscopy (AFM) analysis reveals that the tris-prolinamide ligand can be used to regulate the assembly of novel supramolecular nanoarchitectures. Further, in vitro cellular studies with human hepatocellular carcinoma (HepG2) cells indicate that the tris-prolinamide derivatives can inhibit cell proliferation and reduce c-MYC expression in cancer cells.

Small molecule regulated dynamic structural changes of human G-quadruplexes.

The changes in structure and dynamics of oncogenic (c-MYC) and telomeric (h-TELO) G-rich DNA sequences due to the binding of a novel carbazole derivative (BTC) are elucidated using single-molecule Förster resonance energy transfer (sm-FRET), fluorescence correlation spectroscopy (FCS) and NMR spectroscopy. In contrast to the previous reports on the binding of ligands to pre-folded G-quadruplexes, this work illustrates how ligand binding changes the conformational equilibria of both unstructured G-rich DNA sequences and K+-folded G-quadruplexes. The results demonstrate that K+ free c-MYC and h-TELO exist as unfolded and partially folded conformations. The binding of BTC shifts the equilibria of both investigated DNA sequences towards the folded G-quadruplex structure, increases the diffusion coefficients and induces faster end-to-end contact formation. BTC recognizes a minor conformation of the c-MYC quadruplex and the two-tetrad basket conformations of the h-TELO quadruplex.

Complete mitochondrial genome annotation of the giant intestinal fluke, Fasciolopsis buski (Indian isolate) as revealed by ion torrent and illuminanext-generation sequencing.

The complete mitogenome sequences of the intestinal fluke Fasciolopsis buski are presented for the first time in this study. It is 14,119 bp long and is thus the shortest trematode mitochondrial genome sequenced to date. The F. buski mtDNA genome has a close resemblance with F. hepatica and has a similar gene order tallying with that of other trematodes. The overall base composition of F. buski mitogenome is 17.89% for A, 9.16% for C, 27.59% for G and 45.36% for T, and has a GC content of 36.75%. The assembled mitogenome (GenBank accession number KX449331) consists of 12 protein-coding genes (PCGs), 22 transfer RNAs and two ribosomal RNA genes. The mtDNA for the intestinal fluke reported herein would help investigate Fasciolidae taxonomy and systematics with the aid of mtDNA NGS data.