Mutual response hypothesis between surface temperature and aerosol (BC and non-BC) mass concentration observed in an urban environment

The mutual response between near surface aerosol concentration and surface temperature works in a complicated manner. A recent study has introduced a hypothesis of mutual response between surface temperature and near surface black carbon (BC) mass concentration which states that 'more fall in morning hour surface temperature (T) contribute to the enhancement of BC fumigation peak after the sunrise which positively impacts the extra rise in mid-day temperature over a region during the day time'. Morning hour surface temperature is proportionally linked with the strength of the night time near surface temperature inversion which contributes to the enhancement of the fumigation peak of BC aerosols after the sunrise and the enhanced fumigation peak can impact the degree of the mid-day surface temperature rise by influencing the instantaneous heating. However, it didn't mention the role of non-BC aerosols. Further, the hypothesis was drawn based on the co-located ground-based observations of surface temperature and BC concentration at a rural location of peninsular India. Though, it was mentioned that the hypothesis can be tested independently of locations, but was not thoroughly validated for an urban environment where the loading of both BC and non-BC aerosols are high. In this context, the first objective of the present work is to methodically test the BC -T hypothesis over an Indian metropolitan city, Kolkata, using the suite of measurements obtained from Kolkata Camp Observatory of NARL (KCON) along with other supporting data. In addition, the validity of the hypothesis for the non-BC fraction of PM_2.5 aerosols over the same location is also tested. Besides ascertaining the above-mentioned hypothesis over an urban location, it is found that the enhancement of non-BC PM_2.5 aerosols peak after the sunrise can negatively influences the mid-day temperature rise over a region during the day time.

Targeting Oncogene Promoters and Ribosomal RNA Biogenesis by G-Quadruplex Binding Ligands Translate to Anticancer Activity

G-Quadruplex (GQ) nucleic acids are promising therapeutic targets in anticancer research due to their structural robustness, polymorphism, and gene-regulatory functions. Here, we presented the structure-activity relationship of carbazole-based monocyanine ligands using region-specific functionalization with benzothiazole (TCA and TCZ), lepidine (LCA and LCZ), and quinaldine (QCA and QCZ) acceptor moieties and evaluated their binding profiles with different oncogenic GQs. Their differential turn-on fluorescence emission upon GQ binding confirmed the GQ-to-duplex selectivity of all carbazole ligands, while the isothermal titration calorimetry results showed selective interactions of TCZ and TCA to c-MYC and BCL-2 GQs, respectively. The aldehyde group in TCA favors stacking interactions with the tetrad of BCL-2 GQ, whereas TCZ provides selective groove interactions with c-MYC GQ. Dual-luciferase assay and chromatin immunoprecipitation (ChIP) showed that these molecules interfere with the recruitment of specific transcription factors at c-MYC and BCL-2 promoters and stabilize the promoter GQ structures to inhibit their constitutive transcription in cancer cells. Their intrinsic turn-on fluorescence response with longer lifetimes upon GQ binding allowed real-time visualization of GQ structures at subcellular compartments. Confocal microscopy revealed the uptake of these ligands in the nucleoli, resulting in nucleolar stress. ChIP studies further confirmed the inhibition of Nucleolin occupancy at multiple GQ-enriched regions of ribosomal DNA (rDNA) promoters, which arrested rRNA biogenesis. Therefore, carbazole ligands act as the "double-edged swords" to arrest c-MYC and BCL-2 overexpression as well as rRNA biogenesis, triggering synergistic inhibition of multiple oncogenic pathways and apoptosis in cancer cells.

A mutual response between surface temperature and black carbon mass concentration during the daytime

The mutual response between surface temperature and the mass concentration of regional black carbon (BC) aerosols has still remained far from understanding due to its complex nature. A detailed analysis presented in this study using long-term data indicates a significant pattern of mutual response between surface temperature and BC in restricted background weather conditions (water vapor, cloud cover and wind speeds). The analysis shows that a fall in surface temperature which naturally occurs daily after the sunrise, leads to the development of a stronger inversion in the near-surface level and this, in turn, contributes to the enhancement of BC fumigation peak. Further, the enhanced fumigation peak (especially during pre-monsoon) is found positively influencing the mid-day temperature rise possibly due to the immediate impact of the direct radiative forcing of BC aerosols. These observations lead us to consider a hypothesis that 'an extra fall in the morning hour surface temperature contributes to the enhancement of BC fumigation peak and can degrade the morning hour air quality which gives positive feedback to the mid-day temperature rise over a region'. A substantial in situ data [over Gadanki (13.5°N, 79.2°E)] along with MERRA-2 and ERA-5 data are used in this methodical analysis. Moreover, the validity of the hypothesis has been tested over other locations. Regional weather and seasonal cycle are found to have apparent interference with the feature of the observed mutual response pattern. The results from this study clearly indicate that the approach used, can be executed location independently.

Germline-focussed analysis of tumour-only sequencing: recommendations from the ESMO Precision Medicine Working Group

It is increasingly common in oncology practice to perform tumour sequencing using large cancer panels. For pathogenic sequence variants in cancer susceptibility genes identified on tumour-only sequencing, it is often unclear whether they are of somatic or constitutional (germline) origin. There is wide-spread disparity regarding both the extent to which systematic 'germline-focussed analysis' is carried out upon tumour sequencing data and for which variants follow-up analysis of a germline sample is carried out. Here we present analyses of paired sequencing data from 17 152 cancer samples, in which 1494 pathogenic sequence variants were identified across 65 cancer susceptibility genes. From these analyses, the European Society of Medical Oncology Precision Medicine Working Group Germline Subgroup has generated (i) recommendations regarding germline-focussed analyses of tumour-only sequencing data, (ii) indications for germline follow-up testing and (iii) guidance on patient information-giving and consent.

Metal catalyst-free photo-induced alkyl C–O bond borylation

Tertiary alkyl boronates were prepared via the C–O bond borylation of the corresponding oxalates under catalyst-free/(DMF)₂–B₂cat₂ initiated visible light-induced conditions.

Tetrazolylpyrene unnatural nucleoside as a human telomeric multimeric G-quadruplex selective switch-on fluorescent sensor

Specific sensing of dimeric H45 G-quadruplex DNA using a fluorescence light-up probe, tetrazolylpyrene nucleoside (^TzPyB_Do), is reported.

Expression of the ZNT1 Zinc Transporter from the Metal Hyperaccumulator Noccaea caerulescens Confers Enhanced Zinc and Cadmium Tolerance and Accumulation to Arabidopsis thaliana

Prompt regulation of transition metal transporters is crucial for plant zinc homeostasis. NcZNT1 is one of such transporters, found in the metal hyperaccumulator Brassicaceae species Noccaea caerulescens. It is orthologous to AtZIP4 from Arabidopsis thaliana, an important actor in Zn homeostasis. We examined if the NcZNT1 function contributes to the metal hyperaccumulation of N. caerulescens. NcZNT1 was found to be a plasma-membrane located metal transporter. Constitutive overexpression of NcZNT1 in A. thaliana conferred enhanced tolerance to exposure to excess Zn and Cd supply, as well as increased accumulation of Zn and Cd and induction of the Fe deficiency response, when compared to non-transformed wild-type plants. Promoters of both genes were induced by Zn deficiency in roots and shoots of A. thaliana. In A. thaliana, the AtZIP4 and NcZNT1 promoters were mainly active in cortex, endodermis and pericycle cells under Zn deficient conditions. In N. caerulescens, the promoters were active in the same tissues, though the activity of the NcZNT1 promoter was higher and not limited to Zn deficient conditions. Common cis elements were identified in both promoters by 5' deletion analysis. These correspond to the previously determined Zinc Deficiency Responsive Elements found in A. thaliana to interact with two redundantly acting transcription factors, bZIP19 and bZIP23, controlling the Zn deficiency response. In conclusion, these results suggest that NcZNT1 is an important factor in contributing to Zn and Cd hyperaccumulation in N. caerulescens. Differences in cis- and trans-regulators are likely to account for the differences in expression between A. thaliana and N. caerulescens. The high, constitutive NcZNT1 expression in the stele of N. caerulescens roots implicates its involvement in long distance root-to-shoot metal transport by maintaining a Zn/Cd influx into cells responsible for xylem loading.

Donor/acceptor chromophores-decorated triazolyl unnatural nucleosides: synthesis, photophysical properties and study of interaction with BSA

We report the syntheses and photophysical properties of some triazolyl donor/acceptor unnatural nucleosides and studies on the interaction of one of the fluorescent nucleosides with BSA.

Evolving Strategies for Therapeutically Targeting Cancer Stem Cells

Cancer is a multifactor and multistep process that is affected intrinsically by the genetic and epigenetic makeup of tumor cells and extrinsically by the host microenvironment and immune system. A key component of cancer involves a unique subpopulation of highly malignant cancerous cells referred to as cancer stem cells (CSCs). CSCs are positioned at the apex of the tumor hierarchy with an ability to both self-renew and also generate non-CSC/differentiated progeny, which contribute to the majority of the tumor mass. CSCs undergo functional changes and show plasticity that is stimulated by specific microenvironmental cues and interactions in the tumor niche, which contribute to the complexity and heterogeneity of the CSC population. The prognostic value of CSCs in the clinic is evident since there are many examples in which CSCs serve as markers for poor patient prognosis. CSCs are innately resistant to many standard therapies and they display anoikis resistance, immune evasion, tumor dormancy, and field cancerization, which may result in metastasis and relapse. Many academic laboratories and biotechnology companies are currently focusing on strategies that target CSCs. Combination therapies, epigenetic modifiers, stemness inhibitors, CSC surface marker-based therapies, and immunotherapy-based CSC-targeting drugs are currently undergoing clinical trials. Potential new targets/strategies in CSC-targeted therapy include MDA-9/Syntenin (SDCBP), Patched (PTCH), epigenetic targets, noncoding RNAs, and differentiation induction. Defining ways of targeting and destroying CSCs holds potential to impact significantly on cancer therapy, including prevention of metastasis and cancer recurrence.

Serological diagnosis of dengue in laboratory practice in Kolkata

PURPOSE

To find out the most suitable serological investigative procedures to diagnose dengue cases effectively in the laboratory practice identifying primary and secondary cases as well as period of suffering.

MATERIALS AND METHODS

Dengue suspected cases sent to the laboratory in 2012 in central Kolkata by the local physicians were categorised into seven panels according to the investigations asked for such as (1) only dengue-specific NS1 antigen (2) only IgM antibodies, (3) NS1+IgM+IgG antibodies, (4) only IgM and IgG, (5) NS1+IgM, (6) NS1+IgG and (7) only IgG.

RESULTS

Out of 1892 suspected cases, dengue was diagnosed in 725 (38.3%). Through panels I, II, III, IV, V, VI and VII, it was possible to diagnose dengue in (I) 35.98% (435/1209), (II) 37.5% (24/60), (III) 49% (173/354), (IV) 30.8% (68/221), (V) 60.5% (23/38), (VI) 40% (2/5) and (VII) 0 of cases respectively. Detail information such as confirmed diagnosis, duration of the disease (whether early or prolonged) and classification of primary and secondary dengue in such early or prolonged stages would only be possible in panel III, which information would be helpful for effective monitoring and treatment of dengue patients. In all other panels, merely fragmentary information would be obtained.

CONCLUSIONS

Serodiagnostic tests dengue-specific NS1 antigen and IgM and IgG antibodies when conducted simultaneously would be able to diagnose confirmed dengue cases categorising primary and secondary dengue along with the duration of the disease, whether early or prolonged.

Design and synthesis of triazolyl-donor/acceptor unnatural nucleosides and oligonucleotide probes containing triazolyl-phenanthrene nucleoside

In the context of abasic DNA or DNA duplex stabilization, several unnatural nucleosidic/non-nucleosidic base surrogates have been reported. Toward this end, we have designed and synthesized triazolyl-aromatic donor chomophores as unnatural nucleoside analogs. These modifications display markedly higher thermal stabilization of abasic DNA duplex in comparison to the stabilization offered by other nucleoside/non-nucleoside base surrogates reported in the literature. The same oligonucleotide probe containing triazolylphenanthrene nucleotide also offers very good stability of the self-pair duplex via π-π stacking interaction and hetero-pair duplex via charge transfer interaction when paired against triazolyl acceptor aromatic nucleoside. Moreover, the probe in the reverse sequence containing triazolylphenanthrene nucleotide has shown FRET efficiency in a chimeric DNA duplex. The triazolyl nucleotides would expectedly show stability toward exonuclease activity. This unit describes protocols for chemical synthesis of unnatural triazolyl nucleosides and one oligonucleotide probe. The unit also provides a summary of various thermal and photophysical applications of triazolylphenantherene-containing oligonucleotides.

Triazolyl donor/acceptor chromophore decorated unnatural nucleosides and oligonucleotides with duplex stability comparable to that of a natural adenine/thymine pair

We report the design and synthesis of triazolyl donor/acceptor unnatural nucleosides via click chemistry and studies on the duplex stabilization of DNA containing two such new nucleosides. The observed duplex stabilization among the self-pair/heteropair has been found to be comparable to that of a natural A/T pair. Our observations on the comparable duplex stabilization has been explained on the basis of possible π-π stacking and/or charge transfer interactions between the pairing partners. The evidence of ground-state charge transfer complexation came from the UV-vis spectra and the static quenching of fluorescence in a heteropair. We have also exploited one of our unnatural DNAs in stabilizing abasic DNA.

Arabidopsis thaliana transcription factors bZIP19 and bZIP23 regulate the adaptation to zinc deficiency

Zinc is an essential micronutrient for all living organisms. When facing a shortage in zinc supply, plants adapt by enhancing the zinc uptake capacity. The molecular regulators controlling this adaptation are not known. We present the identification of two closely related members of the Arabidopsis thaliana basic-region leucine-zipper (bZIP) transcription factor gene family, bZIP19 and bZIP23, that regulate the adaptation to low zinc supply. They were identified, in a yeast-one-hybrid screening, to associate to promoter regions of the zinc deficiency-induced ZIP4 gene of the Zrt- and Irt-related protein (ZIP) family of metal transporters. Although mutation of only one of the bZIP genes hardly affects plants, we show that the bzip19 bzip23 double mutant is hypersensitive to zinc deficiency. Unlike the wild type, the bzip19 bzip23 mutant is unable to induce the expression of a small set of genes that constitutes the primary response to zinc deficiency, comprising additional ZIP metal transporter genes. This set of target genes is characterized by the presence of one or more copies of a 10-bp imperfect palindrome in their promoter region, to which both bZIP proteins can bind. The bZIP19 and bZIP23 transcription factors, their target genes, and the characteristic cis zinc deficiency response elements they can bind to are conserved in higher plants. These findings are a significant step forward to unravel the molecular mechanism of zinc homeostasis in plants, allowing the improvement of zinc bio-fortification to alleviate human nutrition problems and phytoremediation strategies to clean contaminated soils.

Bioinformatic approaches for identification and characterization of olfactomedin related genes with a potential role in pathogenesis of ocular disorders

PURPOSE

To identify olfactomedin domain containing proteins, which are expressed in the eye and have similarity to myocilin, to test as potential candidates for eye diseases. Most of the mutations in myocilin causing primary open angle glaucoma are located in the olfactomedin domain. In vitro experiments demonstrated interaction between optimedin and myocilin through the conserved olfactomedin domains of the proteins in rats, and it was speculated that optimedin might have a role in the pathogenesis of ocular disorders. Hence, we aimed to identify myocilin related human proteins having conserved olfactomedin domains with potential to interact between them and examine the expression patterns in the eye by bioinformatics approaches. This endeavor would have the potential to identify new candidate genes for eye diseases in general and glaucoma in particular to be tested by wet-lab experiments.

METHODS

Proteins with homology to myocilin were selected by BLASTp at the NCBI server. cDNA sequences and corresponding genomic contigs were retrieved. Pairwise BLAST was done to investigate the gene structure. The human EST database and NEIBank were searched against the selected cDNAs to look for tissue specific expression of the transcripts.

RESULTS

The study led to the identification of three groups of proteins encoded by three different genes; Noelin 1 (9q34.3), Noelin 2 (19p13.2), and Noelin 3 (1p22) encompassing 45,575 bp, 82,679 bp, and 1,93,421 bp of the genomic sequence, respectively. Genomic structures, alternate usage of exons, and molecular evolution of the Noelins were determined. Similar structures of the genes, splicing patterns and high levels of homology shed light on the relatedness and molecular evolution of this group of olfactomedin related proteins. Strikingly, however, Noelin 1 and Noelin 3 were found to be expressed as multiple splice variants while only a single spliced transcript could be identified for Noelin 2. A human EST database search suggested the expression of all three Noelin genes in the brain but only two (Noelin 1 and Noelin 2) in the eye despite experimental evidence for expression of Noelin 3 in ocular tissue. Myocilin was determined to have similar levels (60-61%) of homology with all three Noelin gene products (Noelin 1_v1, Noelin 2_v1, and Noelin 3_v1) at the conserved olfactomedin domains.

CONCLUSIONS

Mammalian Noelin 1 evolved from its precursor, followed by evolution of Noelin 3 and Noelin 2 by gene duplication events. Myocilin might have evolved from Noelin 2 by gene duplication followed by exon fusion. Noelin 1 and Noelin 2 could be tested as candidate genes for eye diseases based on their expressions in the eye and shared olfactomedin domains with Myocilin in the C-termini of the respective proteins.

Polymer-supported benzotriazoles as catalysts in the synthesis of tetrahydroquinolines by condensation of aldehydes with aromatic amines

Four polymer-supported benzotriazoles were prepared by linkage of 5-(hydroxymethyl)benzotriazole and benzotrizaole-5-carboxylic acid with Wang resin, Merrifield resin, and (monomethoxy)poly(ethylene glycol). The solid-phase and liquid-phase syntheses of tetrahydroquinolines were achieved by two-pair coupling reactions of aldehydes and aromatic amines using these polymer-supported benzotriazoles as the promoters. The ether-type benzotriazole prepared by loading 5-(hydroxymethyl)benzotriazole onto Merrifield resin turned out to be the catalyst of choice. Thus, a series of tetrahydroquinoline products were obtained in high purity by simple filtration, and the resin was recovered for reuse without loss of activity.

Generation of reactive low-valent titanium species using metal--arenes as efficient organic reductants for TiCl(3): applications to organic synthesis

A comprehensive study on the use of metal-arene systems as organic reductants for TiCl(3) has resulted in an efficient method for the generation of highly reactive low-valent titanium (LVT) reagents. The activated titanium species could be prepared by refluxing a mixture of substoichiometric amounts of arenes, TiCl(3), and Li/Mg in THF or DME. Among the LVT reagents screened, TiCl(3)--Li--naphthalene--THF (reagent I) was the best for coupling of carbonyls to olefins. The reagent could carry out the McMurry olefination of both aromatic and aliphatic substrates at a lower temperature and in a much reduced time as compared to the conventional procedures. Subtle changes in the method of preparation of the LVT reagents influenced the stereoisomeric ratio of the olefins. The reagent was also useful for the synthesis of O- and N- heterocycles and vicinal diamines via intramolecular carbonyl coupling and reductive duplication of imines, respectively.

Eighth nerve involvement in meningo-encephalitis

Seventy-two patients suffering from meningo-encephalitis were studied, clinically, biochemically, microbiologically and virologically. Evidence of rising titre in serum and CSF of antibodies to Japanese encephalitis were present in 50% of cases, and recent past infection in 20% of cases. Cranial nerve involvement particularly the "8th" was present in 70% of cases though there was a 2.5% involvement of the 2nd, 3rd and 6th nerves. All the patients belonged to plain Tribal population and all had a history of eating pork 7-10 days prior to development of the infection.