Switchable tetraplex elements in the heterogeneous nuclear ribonucleoprotein K promoter: micro-environment dictated structural transitions of G/C rich elements

We have elucidated the hnRNP K promoter as a hotspot for tetraplex-based molecular switches receptive to micro-environmental stimuli. We have characterised the structural features of four tetraplex-forming loci and identified them as binding sites of transcription factors. These segments form either G-quadruplex or i-motif structures, the structural dynamicity of which has been studied in depth via several biophysical techniques. The tetraplexes display high dynamicity and are influenced by both pH and KCl concentrations in vitro. The loci complementary to these sequences form additional non-canonical secondary structures. In the cellular context, the most eminent observation of this study is the binding of hnRNP K to the i-motif forming sequences in its own promoter. We are the first to report a probable transcriptional autoregulatory function of hnRNP K in coordination with higher-order DNA structures. Herein, we also report the positive interaction of the endogenous tetraplexes with Sp1, a well-known transcriptional regulator. Treatment with tetraplex-specific small molecule ligands further uncovered G-quadruplexes' functioning as repressors and i-motifs as activators in this context. Together, our findings strongly indicate the critical regulatory role of the identified tetraplex elements in the hnRNP K promoter.Communicated by Ramaswamy H. Sarma.

G-quadruplex structural dynamics at MAPK12 promoter dictates transcriptional switch to determine stemness in breast cancer

P38γ (MAPK12) is predominantly expressed in triple negative breast cancer cells (TNBC) and induces stem cell (CSC) expansion resulting in decreased survival of the patients due to metastasis. Abundance of G-rich sequences at MAPK12 promoter implied the functional probability to reverse tumorigenesis, though the formation of G-Quadruplex (G4) structures at MAPK12 promoter is elusive. Here, we identified two evolutionary consensus adjacent G4 motifs upstream of the MAPK12 promoter, forming parallel G4 structures. They exist in an equilibria between G4 and duplex, regulated by the binding turnover of Sp1 and Nucleolin that bind to these G4 motifs and regulate MAPK12 transcriptional homeostasis. To underscore the gene-regulatory functions of G4 motifs, we employed CRISPR-Cas9 system to eliminate G4s from TNBC cells and synthesized a naphthalene diimide (NDI) derivative (TGS24) which shows high-affinity binding to MAPK12-G4 and inhibits MAPK12 transcription. Deletion of G4 motifs and NDI compound interfere with the recruitment of the transcription factors, inhibiting MAPK12 expression in cancer cells. The molecular basis of NDI-induced G4 transcriptional regulation was analysed by RNA-seq analyses, which revealed that MAPK12-G4 inhibits oncogenic RAS transformation and trans-activation of NANOG. MAPK12-G4 also reduces CD44High/CD24Low population in TNBC cells and downregulates internal stem cell markers, arresting the stemness properties of cancer cells.

A beginner's handbook to identify and characterize i-motif DNA

Genomic DNA exhibits an innate ability to manifest diverse sequence-dependent secondary structures, serving crucial functions in gene regulation and cellular equilibrium. While extensive research has confirmed the formation of G-quadruplex structures by guanine-rich sequences in vitro and in cells, recent investigations have turned the quadruplex community's attention to the cytosine (C)-rich complementary strands that can adopt unique tetra-stranded conformation, termed as intercalated motif or i-motif. I-motifs are stabilized by hemi-protonated C:CH+ base pairs under acidic conditions. Initially, the in vivo occurrence of i-motifs was underestimated because their formation is favored at non-physiological pH. However, groundbreaking research utilizing the structure-specific iMab antibody and high-throughput sequencing have recently detected their conserved dispersion throughout the genome, challenging previous assumptions. Given the evolving nature of this research field, it becomes imperative to conduct independent in vitro experiments aimed at identifying potential i-motif formation in C-rich sequences and consolidating the findings to address the properties of i-motifs. This chapter serves as an introductory guide for the swift identification of novel i-motifs, where we present an experimental framework for investigating and characterizing i-motif sequences in vitro. In this chapter, we selected a synthetic oligonucleotide (C7T3) sequence and outlined appropriate methodologies for annealing the i-motif structure into suitable buffers. Then, we validated its formation by CD (Circular Dichroism) and NMR (Nuclear Magnetic Resonance) spectroscopy. Finally, we provided a thorough account of the step-by-step procedures to investigate the effect of i-motif formation on the stalling or retardation of DNA replication using high resolution primer extension assays.

A new G-quadruplex-specific photosensitizer inducing genome instability in cancer cells by triggering oxidative DNA damage and impeding replication fork progression

Photodynamic therapy (PDT) ideally relies on the administration, selective accumulation and photoactivation of a photosensitizer (PS) into diseased tissues. In this context, we report a new heavy-atom-free fluorescent G-quadruplex (G4) DNA-binding PS, named DBI. We reveal by fluorescence microscopy that DBI preferentially localizes in intraluminal vesicles (ILVs), precursors of exosomes, which are key components of cancer cell proliferation. Moreover, purified exosomal DNA was recognized by a G4-specific antibody, thus highlighting the presence of such G4-forming sequences in the vesicles. Despite the absence of fluorescence signal from DBI in nuclei, light-irradiated DBI-treated cells generated reactive oxygen species (ROS), triggering a 3-fold increase of nuclear G4 foci, slowing fork progression and elevated levels of both DNA base damage, 8-oxoguanine, and double-stranded DNA breaks. Consequently, DBI was found to exert significant phototoxic effects (at nanomolar scale) toward cancer cell lines and tumor organoids. Furthermore, in vivo testing reveals that photoactivation of DBI induces not only G4 formation and DNA damage but also apoptosis in zebrafish, specifically in the area where DBI had accumulated. Collectively, this approach shows significant promise for image-guided PDT.

Spin-hedgehog-derived electromagnetic effects in itinerant magnets

In itinerant magnets, the indirect exchange coupling of Ruderman-Kittel-Kasuya-Yosida type is known to stabilize incommensurate spin spirals, whereas an account of higher order spin interactions favors the formation of a noncoplanar magnetic texture. This is manifested by the finite Berry phase the conduction electrons accumulate when their spins follow this texture, leading thus to the topological Hall effect. We herein utilize the effective spin model with bilinear-biquadratic exchange interactions for studying the formation of the magnetic hedgehog lattice, that represents a periodic array of magnetic anti- and monopoles and has been recently observed in the B20-type compounds, in a three-dimensional itinerant magnet. As opposed to widely used Monte Carlo simulations, we employ a neural-network-based approach for exploring the ground state spin configuration in a noncentrosymmetric crystal structure. Further, we address the topological Hall conductivity, associated with nonzero scalar spin chirality, in the itinerant magnet due to the coupling to the spin hedgehog lattice, and provide the evidence of a magneto-optic Kerr effect.

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.

Cutaneous aspergillosis masquerading in sporotrichoid morphology in an immunocompetent host

Primary cutaneous aspergillosis is an uncommon opportunistic infection, generally seen in immunocompromised individuals. However, many atypical presentations have been reported recently particularly with the increased domain of immunosuppression. Sporotrichoid pattern of aspergillosis where it invades deep lymphatics have rarely been reported and never in immunocompetent individuals previously. We hereby report a case of a 29 years old immunocompetent individual with no comorbidities who presented with multiple painful erythematous papules and nodules over the left upper limb in a sporotrichoid pattern. Microscopy revealed branched septate hyphae and culture on Sabouraud dextrose agar grew powdery greenish colonies which showed hyaline branched septate hyphae with brush-like conidiophores and globose conidia in chains. Histopathology from one of the nodules was consistent with deep fungal infection. A diagnosis of Aspergillus chivalieri was made based on 18S rRNA sequencing of the isolate. The patient showed a satisfactory response to oral Itraconazole over 12 weeks.

New-onset diabetic ketoacidosis with purpura fulminans in a child with COVID-19-related multisystem inflammatory syndrome

BACKGROUND

Coronavirus disease 2019 (COVID 19) usually causes a mild illness among children. However, in a minority of children, it may be associated with the life-threatening multisystem inflammatory syndrome (MIS-C), or thrombotic microangiopathy, or sequelae like type-1 diabetes mellitus (T1DM). We describe a previously healthy, 12-year-old boy with new-onset T1DM with diabetic ketoacidosis (DKA) in the setting of MIS-C, with a course complicated by thrombotic microangiopathy.

CASE PRESENTATION

The patient presented with four days history of fever, non-bilious vomiting, polyuria and polydipsia. On evaluation, he was noted to have diabetic ketoacidosis. Although Diabetic ketoacidosis with insulin and intravenous fluids, his hospital course was notable for shock requiring vasopressor, purpura fulminans with eschar formation, neurological manifestations (left hemiparesis due to right middle cerebral artery territory infarct, mononeuritis multiplex) and thrombotic microangiopathy. MIS-C-like illness secondary to COVID-19 was suspected due to diabetic ketoacidosis, thrombotic microangiopathy, elevated inflammatory markers, history of contact with COVID-19-infected individual and detectable COVID-19 IgG antibodies. He improved following management with methylprednisolone, intravenous immunoglobulin, low-molecular-weight heparin and aspirin, and was discharged on hospital day 48.

CONCLUSION

MIS-C-like illness should be considered in children and adolescents presenting with complex multisystem involvement in this era of COVID 19. Management with immunomodulatory agents can be lifesaving.

The Molecular Tête-à-Tête between G-Quadruplexes and the i-motif in the Human Genome

G-Quadruplex (GQ) and i-motif structures are the paradigmatic examples of nonclassical tetrastranded nucleic acids having multifarious biological functions and widespread applications in therapeutics and material science. Recently, tetraplexes emerged as promising anticancer targets due to their structural robustness, gene-regulatory roles, and predominant distribution at specific loci of oncogenes. However, it is arguable whether the i-motif evolves in the complementary single-stranded region after GQ formation in its opposite strand and vice versa. In this review, we address the prerequisites and significance of the simultaneous and/or mutually exclusive formation of GQ and i-motif structures at complementary and sequential positions in duplexes in the cellular milieu. We discussed how their dynamic interplay Sets up cellular homeostasis and exacerbates carcinogenesis. The review gives insights into the spatiotemporal formation of GQ and i-motifs that could be harnessed to design different types of reporter systems and diagnostic platforms for potential bioanalytical and therapeutic intervention.

Inosine 5'-diphosphate, a molecular decoy rescues Nucleoside diphosphate kinase from c-MYC G-Quadruplex unfolding

BACKGROUND

The transcription-inhibitory G-Quadruplex(Pu27-GQ) at c-MYC promoter is challenging to target due to structural heterogeneity. Nucleoside diphosphate kinase (NM23-H2) specifically binds and unfolds Pu27-GQ to increase c-MYC transcription. Here, we used Inosine 5'-diphosphate (IDP) to disrupt NM23-H2-Pu27-GQ interactions and arrest c-MYC transcription without compromising NM23-H2-mediated kinase properties.

METHODS

Site-directed mutagenesis,³¹P-NMR and STD-NMR studies delineate the epitope of NM23-H2-IDP complex and characterize specific amino acids in NM23-H2 involved in Pu27-GQ and IDP interactions. Immunoprecipitations and phosphohistidine-immunoblots reveal how IDP blocks NM23-H2-Pu27 association to downregulate c-MYC transcription in MDAMB-231 cells exempting NM23-H2-mediated kinase properties.

RESULTS

NMR studies show that IDP binds to the Guanosine diphosphate-binding pocket of NM23-H2 (K_D = 5.0 ± 0.276 μM). Arg88-driven hydrogen bonds to the terminal phosphate of IDP restricts P-O-P bond-rotation increasing its pKa (∆pKa = 0.85 ± 0.0025).9-inosinyl moiety of IDP is stacked over Phe60 phenyl ring driving trans-conformation of inosine and axial geometry of pyrophosphates. Chromatin immunoprecipitations revealed that these interactions rescue NM23-H2-driven Pu27-GQ unfolding, which triggers Nucleolin recruitment and lowers Sp1 occupancy at c-MYC promoter stabilizing Pu27-GQ. This silences c-MYC transcription that reduces c-MYC-Sp1 association amplifying Sp1 recruitment across P21 promoter stimulating P21 transcription and G₂/M arrest.

CONCLUSIONS

IDP synergizes the effects of Pu27-GQ-interacting compounds to abrogate c-MYC transcription and induce apoptosis in MDAMB-231 cells by disrupting NM23-H2-Pu27-GQ interactions without affecting NM23-H2-mediated kinase properties.

GENERAL SIGNIFICANCE

Our study provides a pragmatic approach for developing NM23-H2-targeting regulators to rescue NM23-H2 binding at structurally ambiguous Pu27-GQ that synergizes the anti-tumorigenic effects of GQ-based therapeutics with minimized off-target effects.

Response to Comment on "The role of electron-electron interactions in two-dimensional Dirac fermions"

Hesselmann et al question one of our conclusions: the suppression of Fermi velocity at the Gross-Neveu critical point for the specific case of vanishing long-range interactions and at zero energy. The possibility they raise could occur in any finite-size extrapolation of numerical data. Although we cannot definitively rule out this possibility, we provide mathematical bounds on its likelihood.

The tumor suppressor FBXO31 preserves genomic integrity by regulating DNA replication and segregation through precise control of cyclin A levels

F-box protein 31 (FBXO31) is a reported putative tumor suppressor, and its inactivation due to loss of heterozygosity is associated with cancers of different origins. An emerging body of literature has documented FBXO31's role in preserving genome integrity following DNA damage and in the cell cycle. However, knowledge regarding the role of FBXO31 during normal cell-cycle progression is restricted to its functions during the G₂/M phase. Interestingly, FBXO31 levels remain high even during the early G₁ phase, a crucial stage for preparing the cells for DNA replication. Therefore, we sought to investigate the functions of FBXO31 during the G₁ phase of the cell cycle. Here, using flow cytometric, biochemical, and immunofluorescence techniques, we show that FBXO31 is essential for maintaining optimum expression of the cell-cycle protein cyclin A for efficient cell-cycle progression. Stable FBXO31 knockdown led to atypical accumulation of cyclin A during the G₁ phase, driving premature DNA replication and compromised loading of the minichromosome maintenance complex, resulting in replication from fewer origins and DNA double-strand breaks. Because of these inherent defects in replication, FBXO31-knockdown cells were hypersensitive to replication stress-inducing agents and displayed pronounced genomic instability. Upon entering mitosis, the cells defective in DNA replication exhibited a delay in the prometaphase-to-metaphase transition and anaphase defects such as lagging and bridging chromosomes. In conclusion, our findings establish that FBXO31 plays a pivotal role in preserving genomic integrity by maintaining low cyclin A levels during the G₁ phase for faithful genome duplication and segregation.

Site-specific amino acid substitution in dodecameric peptides determines the stability and unfolding of c-MYC quadruplex promoting apoptosis in cancer cells

c-MYC proto-oncogene harbours a transcription-inhibitory quadruplex-forming scaffold (Pu27) upstream P₁ promoter providing anti-neoplastic therapeutic target. Previous reports showed the binding profile of human Cathelicidin peptide (LL37) and telomeric G-quadruplex. Here, we truncated the quadruplex-binding domain of LL37 to prepare a small library of peptides through site-specific amino acid substitution. We investigated the intracellular selectivity of peptides for Pu27 over other oncogenic quadruplexes and their role in c-MYC promoter repression by dual-luciferase assays. We analysed their thermodynamics of binding reactions with c-MYC quadruplex isomers (Pu27, Myc22, Pu19) by Isothermal Titration Calorimetry. We discussed how amino acid substitutions and peptide helicity enhanced/weakened their affinities for c-MYC quadruplexes and characterized specific non-covalent inter-residual interactions determining their selectivity. Solution NMR structure indicated that KR12C, the best peptide candidate, selectively stabilized the 5′-propeller loop of c-MYC quadruplex by arginine-driven electrostatic-interactions at the sugar-phosphate backbone while KR12A peptide destabilized the quadruplex inducing a single-stranded hairpin-like conformation. Chromatin immunoprecipitations envisaged that KR12C and KR12A depleted and enriched Sp1 and NM23-H2 (Nucleoside diphosphate kinase) occupancy at Pu27 respectively supporting their regulation in stabilizing and unfolding c-MYC quadruplex in MCF-7 cells. We deciphered that selective arresting of c-MYC transcription by KR12C triggered apoptotic-signalling pathway via VEGF-A-BCL-2 axis.

Patient experiences and health system responsiveness among internal migrants: A nationwide study in 13 Indian cities

OBJECTIVE

To report various components of health system responsiveness among poor internal migrants who availed the government health facilities in 13 Indian cities.

MATERIALS AND METHODS

Cluster random sampling was used to select 50,806 migrant households, of which 14,263 households avail the government health facility in last six months. In addition, 5072 women, who sought antenatal care and 3946 women who had delivery in government health facility during last six months were also included. Data on different domains of health system responsiveness were collected using an interviewer-administered questionnaire, developed based on the World Health Survey of WHO.

RESULTS

Of the eight domains of responsiveness, namely, autonomy, communication, confidentiality, dignity, choice, quality of basic facilities, prompt attention and access to family and community, seven domains, except the 'choice', are assessed, and they are moderate. Only about 30% of participants said that doctor discussed on treatment options (autonomy). And 50-60% of participants said positively for questions of clarity of communication. About 59% of participants acknowledged the confidentiality. Not more than 40% of participants said they were treated with dignity, and privacy is respected (dignity). The responses to quality basic amenities, prompt attention and access to family and community domains are fairly satisfactory.

CONCLUSIONS

This study has implications as many urban poor, including migrants do not utilize the services of public healthcare facilities. Hence, a responsive health system is required. There should be a policy in place to train and orient healthcare workers on some of the domains of health system responsiveness.

Truncated G-Quadruplex Isomers Cross-Talk with the Transcription Factors To Maintain Homeostatic Equilibria in c-MYC Transcription

The nuclease hypersensitive element III1 (NHE III1) upstream c-MYC promoter harbors a transcription-silencing G-quadruplex (Pu27) element. Dynamic turnover of various transcription factors (TFs) across Pu27 to control c-MYC transcription homeostasis is enigmatic. Here, we reveal that native Pu27 evolves truncated G-quadruplex isomers (Pu19, Pu22, Pu24, and Pu25) in cells that are optimal intracellular targets of specific TFs in a sequence- and structure-dependent manner. Nuclear magnetic resonance and isothermal titration calorimetry envisaged that NM23-H2 (nucleoside diphosphate kinase) and nucleolin induce conformational fluctuations in Pu27 to sample specific conformationally restricted conformer(s). Structural investigations revealed that the flanking guanines at 5'-Pu27 control solvent exposure at G-quartets upon NM23-H2 and nucleolin binding driving Pu27 unfolding and folding, respectively. Transient chromatin immunoprecipitations confirmed that NM23-H2 drives the conformation switch to Pu24 that outcompetes nucleolin recruitment. Similarly, nucleolin arrests Pu27 in the Pu22 conformer minimizing NM23-H2 binding at Pu27. hnRNPK (heterogeneous nuclear ribonucleoprotein K) positively regulates NM23-H2 and nucleolin association at Pu27 despite their antagonism. On the basis of these results, we simulated the transcription kinetics in a feed-forward loop in which the transcription output responds to hnRNPK-induced early activation via NM23-H2 association, which favors Pu24 formation at NHE III1 reducing nucleolin occupancy and driving quadruplex unfolding to initiate transcription. NM23-H2 further promotes hnRNPK deposition across NHE III1 altering Pu27 plasticity that finally enriches the nucleolin abundance to drive Pu22 formation and weaken NM23-H2 binding to extinguish transcription. This mechanism involves three positive feedback loops (NM23-H2-hnRNPK, NM23-H2-CNBP, and hnRNPK-nucleolin) and one negative feedback loop (NM23-H2-nucleolin) controlling optimal turnover and residence time of TFs at Pu27 to homeostatically regulate c-MYC transcription.

Traces of statistical learning in the brain's functional connectivity after artificial language exposure

Our environment is full of statistical regularities, and we are attuned to learn about these regularities by employing Statistical Learning (SL), a domain-general ability that enables the implicit detection of probabilistic regularities in our surrounding environment. The role of brain connectivity on SL has been previously explored, highlighting the relevance of structural and functional connections between frontal, parietal, and temporal cortices. However, whether SL can induce changes in the functional connections of the resting state brain has yet to be investigated. To address this question, we applied a pre-post design where participants (n = 38) were submitted to resting-state fMRI acquisition before and after in-scanner exposure to either an artificial language stream (formed by 4 concatenated words) or a random audio stream. Our results showed that exposure to an artificial language stream significantly changed (corrected p < 0.05) the functional connectivity between Right Posterior Cingulum and Left Superior Parietal Lobule. This suggests that functional connectivity between brain networks supporting attentional and working memory processes may play an important role in statistical learning.

Ultrasound Quantification of Anterior Soft Tissue Thickness Fails to Predict Difficult Laryngoscopy in Obese Patients

Morbid obesity is associated with difficult laryngoscopy and intubation. In the general population, bedside indices for predicting difficult intubation (i.e. Mallampati classification, thyromental distance, sternomental distance, mouth-opening and Wilson risk score) have poor-to-moderate sensitivity (20-62%) and moderate-to-fair specificity (82-97%). In the obese population, although the risk of difficult intubation after a positive Mallampati test is 34%, it is still not sufficient to be used as a single predictive test. An abundance of pretracheal soft tissue anterior to the vocal cords, as quantified by ultrasound, was a better predictor of difficult laryngoscopy than body mass index (BMI) in Israeli patients. Obesity is a growing problem in the United States: therefore we sought to confirm this finding in the obese population in the United States. We used ultrasound to quantify the neck soft tissue, from the skin to the anterior aspect of the trachea at the vocal cords, in 64 obese patients (BMI >35). We assessed thyromental distance, mouth-opening, jaw movement, limited neck mobility, modified Mallampati score, abnormal upper teeth, neck circumference, confirmed obstructive sleep apnoea, BMI, age, race and gender as predictors. Twenty patients were classified as difficult laryngoscopy; they were older (47±9 vs 42±1 years; P=0.048; mean±SD) and had less soft pretracheal tissue (20.4±3.0 vs 22.3±3.8 mm; P=0.049) than did easy laryngoscopy patients. Multivariate regression indicated that none of the factors was an independent predictor of difficult laryngoscopy. We conclude that the thickness of pretracheal soft tissue at the level of the vocal cords is not a good predictor of difficult laryngoscopy in obese patients in the United States.

4′-Guanidinium-modified siRNA: a molecular tool to control RNAi activity through RISC priming and selective antisense strand loading

We present synthesis, biochemical, biophysical and computational evaluation of 4′ gunanidino modified siRNA.

Correction: 4′-Guanidinium-modified siRNA: a molecular tool to control RNAi activity through RISC priming and selective antisense strand loading

Correction for ‘4′-Guanidinium-modified siRNA: a molecular tool to control RNAi activity through RISC priming and selective antisense strand loading’ by Ganesh N. Nawale et al., Chem. Commun., 2019, 55, 9112–9115.

Assessment of trace metal contamination of wetland sediments from eastern and western coastal region of India dominated with mangrove forest

Ecosystem and biodiversity of India's coastal areas dominated with mangrove forest have been threatened by growing anthropogenic activities. The present work aims to investigate the contamination of wetland sediments with trace elements and assess the sediment quality at different sampling locations in eastern and western costal region dominated with mangrove forest. The longitudinal profile of trace elements in sediments from different sampling locations analyzed by employing Energy Dispersive X-ray Fluorescence (EDXRF) spectrometer shows variations in distribution of elements like Al, Si, K, Ca, V, Cr, Mn, Fe, Ni, Cu, Zn and Pb. The enrichment factor (EF) and Geo-accumulation index (I_geo) values suggested depletion of clay minerals and enrichment of heavy metals like Cr, Cu Fe and Mn. Depending on the variations in Igeo values, the elements are put into I_geo Class 0 to 3 levels of contamination. Contamination factor (Cf) and pollution load index (PLI) suggested deterioration of sediments analyzed in the present study. Assessment of ecological risk potential of elements suggests that few elements (Cr and Cu) are moderately contaminated and may cause environmental stress on the exposed flora and fauna.

Deep urban groundwater vulnerability in India revealed through the use of emerging organic contaminants and residence time tracers

Demand for groundwater in urban centres across Asia continues to rise with ever deeper wells being drilled to avoid shallow contamination. The vulnerability of deep alluvial aquifers to contaminant migration is assessed in the ancient city of Varanasi, India, using a novel combination of emerging organic contaminants (EOCs) and groundwater residence time tracers (CFC and SF₆). Both shallow and intermediate depth private sources (<100 m) and deep (>100 m) municipal groundwater supplies were found to be contaminated with a range of EOCs including pharmaceuticals (e.g. sulfamethoxazole, 77% detection frequency, range <0.0001-0.034 μg L^-1), perfluoroalkyl substances (e.g. PFOS, range <0.0001-0.033 μg L^-1) as well as a number of pesticides (e.g. phenoxyacetic acid, range <0.02-0.21 μg L^-1). The profile of EOCs found in groundwater mirror those found in surface waters, albeit at lower concentrations, and reflect common waste water sources with attenuation in the subsurface. Mean groundwater residence times were found to be comparable between some deep groundwater and shallow groundwater sources with residence times ranging from >70 to 30 years. Local variations in aquifer geology influence the extent of modern recharge at depth. Both tracers provide compelling evidence of significant inputs of younger groundwater to depth >100 m within the aquifer system.

SMAR1 inhibits Wnt/β-catenin signaling and prevents colorectal cancer progression

Reduced expression of Scaffold/Matrix Attachment Region Binding Protein 1 (SMAR1) is associated with various cancers resulting in poor prognosis of the diseases. However, the precise underlying mechanism elucidating the loss of SMAR1 requires ongoing study. Here, we show that SMAR1 is highly downregulated during aberrant Wnt3a signaling due to proteasomal degradation and predicted poor prognosis of colorectal cancer. However, substitution mutation (Arginine and Lysine to Alanine) in the D-box elements of SMAR1 viz. "RCHL" and "RQRL" completely abrogated its proteasomal degradation despite Wnt3a activity. SMAR1 inhibited Wnt/β-catenin signaling by recruiting Histone deacetylase-5 to β-catenin promoter resulting in reduced cell migration and invasion. Consequently, reduced tumor sizes in in-vivo NOD-SCID mice were observed that strongly associated with suppression of β-catenin. However, loss of SMAR1 led to enriched H3K9 Acetylation in the β-catenin promoter that further increased Wnt/β-catenin signaling activities and enhanced colorectal cancer progression drastically. Using docking and isothermal titration calorimetric studies we show that small microbial peptides viz. AT-01C and AT-01D derived from Mycobacterium tuberculosis mask the D-box elements of SMAR1. These peptides stabilized SMAR1 expression that further inhibited metastatic SW480 colorectal cancer cell migration and invasion. Drastically reduced subcutaneous tumors were observed in in-vivo NOD-SCID mice upon administration of these peptides (25 mg/kg body weight) intraperitoneally. Taken together our structural studies, in-vitro and in-vivo results strongly suggest that the D-box elements of SMAR1 represent novel druggable targets, where the microbial peptides hold promise as novel colorectal cancer therapeutics.

LINCRNA00273 promotes cancer metastasis and its G-Quadruplex promoter can serve as a novel target to inhibit cancer invasiveness

Discovery of anti-metastatic drugs is of immense clinical significance as metastasis is responsible for 90% of all cancer deaths. Here we report the inhibitory effect of a bis schiff base (M2) on cancer cell migration and invasion in vitro and in vivo. M2 has shown good solubility and permeability across the intestinal cell wall and hence can be classified as BCS (Biopharmaceutical classification system) class I. Microarray studies identified a long non coding intergenic RNA, LINC00273 as a novel molecular target of M2. We report that LINC00273 harbors a unique (4n-1) parallel G-Quadruplex structure in its promoter as validated by DMS footprint. M2 is proposed to stabilize this G-quadruplex structure resulting in the down-regulation of LINC00273 expression. Dual Luciferase reporter assay also suggests inhibition of LINC00273 promoter activity by M2. Involvement of this linc in metastasis is proven by siRNA and shRNA mediated knock down of LINC00273 in vitro and in vivo in nude mice which significantly decelerates cancer cell migration and invasion and also makes the cells unresponsive to TGF-β's pro-metastatic effects. Furthermore, the real time expression of LINC00273 in thirty seven human clinical samples is found to be positively correlated with the histopathological staging of metastasis.

In Silico Screening and Binding Characterization of Small Molecules toward a G-Quadruplex Structure Formed in the Promoter Region of c-MYC Oncogene

Overexpression of c-MYC oncogene is associated with cancer pathology. Expression of c-MYC is regulated by the G-quadruplex structure formed in the G-rich segment of nuclease hypersensitive element (NHE III₁), that is, "Pu27", which is localized in the promoter region. Ligand-induced stabilization of the Pu27 structure has been identified as a novel target for cancer therapeutics. Here, we have explored the library of synthetic compounds against the predefined binding site of Pu27. Three compounds were selected based on the docking analyses; they were further scrutinized using all atom molecular dynamics simulations in an explicit water model. Simulated trajectories were scrutinized for conformational stability and ligand binding free energy estimation; essential dynamic behavior was determined using principal component analysis. One of the molecules, "TPP (1-(3-(4-(1,2,3-thiadiazol-4-yl)phenoxy)-2-hydroxypropyl)-4-carbamoylpiperidinium)", with the best results was considered for further evaluation. The theoretical observations are supported well by biophysical analysis using circular dichroism, isothermal titration calorimetry, and high-resolution NMR spectroscopy indicating association of TPP with Pu27. The in vitro studies were then translated into c-MYC overexpression in the T47D breast cancer cell line. Biological evaluation through the MTT assay, flow cytometric assay, RT-PCR, and reporter luciferase assay suggests that TPP downregulates the expression of c-MYC oncogene by arresting its promoter region. In silico and in vitro observations cumulatively suggest that the novel skeleton of TPP could be a potential anticancer agent by stabilizing the G-quadruplex formed in the Pu27 and consequently downregulating the expression of c-MYC oncogene. Derivation of new molecules on its skeleton may confer anticancer therapeutics for the next generation.

Decline in sperm count in European men during the past 50 years

Purpose:

To investigate whether the sperm concentration of European men is deteriorating over the past 50 years of time.

Materials and Methods:

We analysed the data published in English language articles in the past 50 years in altering sperm concentration in European men.

Results:

A time-dependent decline of sperm concentration ( r = −0.307, p = 0.02) in the last 50 years and an overall 32.5% decrease in mean sperm concentration was noted.

Conclusion:

This comprehensive, evidence-based meta-analysis concisely presents the evidence of decreased sperm concentration in European male over the past 50 years to serve the scientific research zone related to male reproductive health.

Chelerythrine down regulates expression of VEGFA, BCL2 and KRAS by arresting G-Quadruplex structures at their promoter regions

A putative anticancer plant alkaloid, Chelerythrine binds to G-quadruplexes at promoters of VEGFA, BCL2 and KRAS genes and down regulates their expression. The association of Chelerythrine to G-quadruplex at the promoters of these oncogenes were monitored using UV absorption spectroscopy, fluorescence anisotropy, circular dichroism spectroscopy, CD melting, isothermal titration calorimetry, molecular dynamics simulation and quantitative RT-PCR technique. The pronounced hypochromism accompanied by red shifts in UV absorption spectroscopy in conjunction with ethidium bromide displacement assay indicates end stacking mode of interaction of Chelerythrine with the corresponding G-quadruplex structures. An increase in fluorescence anisotropy and CD melting temperature of Chelerythrine-quadruplex complex revealed the formation of stable Chelerythrine-quadruplex complex. Isothermal titration calorimetry data confirmed that Chelerythrine-quadruplex complex formation is thermodynamically favourable. Results of quantative RT-PCR experiment in combination with luciferase assay showed that Chelerythrine treatment to MCF7 breast cancer cells effectively down regulated transcript level of all three genes, suggesting that Chelerythrine efficiently binds to in cellulo quadruplex motifs. MD simulation provides the molecular picture showing interaction between Chelerythrine and G-quadruplex. Binding of Chelerythrine with BCL2, VEGFA and KRAS genes involved in evasion, angiogenesis and self sufficiency of cancer cells provides a new insight for the development of future therapeutics against cancer.

Restriction of telomerase capping by short non-toxic peptides via arresting telomeric G-quadruplex

The stabilization of a G-quadruplex structure in human telomeric DNA has become a promising strategy in the development of cancer therapeutics.

Myricetin arrests human telomeric G-quadruplex structure: a new mechanistic approach as an anticancer agent

The use of small molecules to arrest G-quadruplex structure has become a potential strategy for the development and design of a new class of anticancer therapeutics.

Interaction-Driven Metal-Insulator Transition in Strained Graphene

The question of whether electron-electron interactions can drive a metal to insulator transition in graphene under realistic experimental conditions is addressed. Using three representative methods to calculate the effective long-range Coulomb interaction between π electrons in graphene and solving for the ground state using quantum Monte Carlo methods, we argue that, without strain, graphene remains metallic and changing the substrate from SiO_{2} to suspended samples hardly makes any difference. In contrast, applying a rather large-but experimentally realistic-uniform and isotropic strain of about 15% seems to be a promising route to making graphene an antiferromagnetic Mott insulator.

Transient Loss of Vision after Coronary Angiogram - A Case Report

A 50-year old, diabetic, hypertensive patient with post-CABG status developed complete loss of vision about one hour after coronary angiogram (CAG). Thorough ophthalmological and neurological examination as well as magnetic resonance imaging of brain especially of the occipital region revealed no abnormality. The patient had complete recovery of vision about 48 hours later. We could not document any specific cause or mechanism for the visual loss, although the selective vulnerability of occipital lobes to contrast agent toxicity (Cortical blindness) was the most likely underlying mechanism.

Metals and female reproductive toxicity

Research into occupational exposure of metals and consequences of reproductive systems has made imperative scientific offerings in the preceding few decades. Early research works focused on possible effects on the reproductive functions rather than the complete reproductive health of the woman. Later, it was realized that metals, as reproductive toxins, may also induce hormonal changes affecting other facets of reproductive health such as the menstrual cycle, ovulation, and fertility. Concern is now shifting from considerations for the pregnant woman to the entire spectrum of occupational health threats and thus reproductive health among women.

Eccrine spiradenoma in knee

Eccrine spiradenoma is an uncommon benign adnexal tumor of the eccrine sweat glands. Although it can occur at any age, it is most common in young adults without any sex predilection. Malignant transformation is rare, presenting as rapid increase in size of a long-standing lesion. Here, we report a case of eccrine spiradenoma in a 35-year-old man who presented with swelling over the right knee, with cytological atypia but no recurrence until date.

Health-related morphological characteristics and physiological fitness in connection with nutritional, socio-economic status, occupational workload of tea garden workers

BACKGROUND

Reports on the cardiorespiratory fitness and body composition of male workers engaged in processing of tea leaves in factories within the tea-estates of West Bengal, under the influence of physiological workload, are quite scanty.

OBJECTIVES

This cross-sectional study was conducted to evaluate morphometric characteristics based on physiological status and physical fitness of tea factory laborers who are continuously exposed to tea dust in their work environment for more than two years.

METHODS

Subjects were divided into control and tea garden workers groups. Height and weight were measured and the body mass index (BMI) was computed. Physiological parameters such as resting heart rate, blood pressure, fitness variables like physical fitness index (PFI), energy expenditure (EE), handgrip strength and anthropometric parameters like mid-upper arm (MUAC), thigh circumference (TC), head circumference (HC) and waist-to-hip ratio (WHR) were measured.

RESULTS

Body surface area (BSA), BMI, body fat percentage and fitness variables (PFI, EE) showed significant difference (p < 0.05) between the two groups. Anthropometric measures (MUAC, TC, HC, WHR) reflected poor status among laborers.

CONCLUSIONS

The present study shows that the majority of workers had ectomorph stature, good physical fitness, but had poor nutritional status (BMI and WHR).

Thoracic cord compression by extramedullary hematopoiesis in thalassemia

Extramedullary hematopoiesis (EMH) refers to hematopoiesis occurring outside the medulla of bone. It may be physiologic or due to pathological conditions like hematopoietic disorders. EMH can involve liver, spleen, thorax, and lymph nodes. It can involve paraspinal tissues with extension and involvement of spinal canal. In our case, the diagnosis was confirmed by the history of the patient stating underlying hematological condition and by magnetic resonance imaging (MRI) findings showing large soft tissue masses in paraspinal areas with involvement of spinal canal and leading to cord compression.

Comparing the Physiological, Socio-economic and Nutritional Status among Male and Female Undergraduate College Students of Metropolitan City of Kolkata

BACKGROUND

In the present days, increasing trend of eating disorders are noticed among college students (both male and female) which can disturb their overall physiological and health status. It is more prevalent in metropolitan cities, like Kolkata. But, the existing literature about the physiological and nutritional status of the undergraduate college students of Kolkata is insufficient.

AIM

Thus, the objective of this small-scale cross-sectional study is to report and compare the prevalence of malnutrition (both obesity and undernutrition) among undergraduate male and female college students of Kolkata, based on body mass index (BMI) and some direct and derived anthropometric measures describing the body composition of the subjects.

SUBJECTS AND METHODS

This cross-sectional study conducted in October-December 2011. The present investigation was carried out in randomly selected male (mean age 20.9 [2.25]) and female college students (mean age 20.3 [2.34]) of Kolkata. A total of 100 students of different colleges has participated, having the age of 18-22 years. Measures included a total of 24 variables which included thirteen direct anthropometric measures and 11 derived variables.

RESULTS

Analysis of collected data showed significantly higher BMI, fat mass, body adiposity index, but, lower waist-to-hip ratio, conicity index in female students. Anthropometric data also showed lower waist circumference and abdominal extension in female college students. Conversely, male students showed a higher fat free mass (FFM), mid-upper arm circumference (MUAC) and thigh circumferences (TCs).

CONCLUSION

Based on the findings of the present study, it can be reported that higher body fat distribution and increased propensity of being overweight/obese was observed in female students, though they have shown lower abdominal fat distribution, which is a cue of female physical attractiveness. However, male students are found to have a higher FFM, MUAC and TCs, which is the indicator of strength and energy.

Relationship of body compositional and nutritional parameters with blood pressure in adults

BACKGROUND

Obesity has been regarded as a single best predictor and major controllable contributor to hypertension. The present study aimed to assess the relationship between body compositional and nutritional parameters with blood pressure in rural Bengalee adults.

METHODS

Anthropometric measures, blood pressure and nutritional parameters were measured in 522 rural Bengalee adults using standard protocols. Receiver operating characteristic analysis was carried out to identify cut-off values of body mass index (BMI) and percentage of body fat (BF%) as associated factors of hypertension and hypotension.

RESULTS

Most of the subjects were normotensive. However, a notable percentage had hypertension (males: 21.86%; females: 15.27%), although the prevalence of hypotension was low (males: 10.53%; females: 8.73%). Obesity indicators were significantly higher in hypertensive individuals than hypotensive and normotensive individuals. All anthropometric parameters and obesity indicators were significantly correlated (P < 0.001) with blood pressure. Blood pressure increased steadily from being underweight through to normal and then to overweight/obese individuals. There were significant differences in the percentage of hypertension and hypotension between nutritional categories. Blood pressure had significant positive correlation with energy, carbohydrate and fat intake, whereas protein and calcium were negatively associated with blood pressure. The suggested cut-off values of BMI and BF%, which were taken as associated factors of hypertension, were 21.86 kg m⁻² and 20.31%, and those of hypotension were 18.18 kg m⁻² and 13.3%, respectively.

CONCLUSIONS

In lean rural Bengalee populations, high BMI levels may be associated with an increased risk of hypertension. The cut-off values of BMI and BF% in the present study suggested associated factors for cardiovascular risk factors and these values may be of help with respect to reducing mean population blood pressure levels.

Screening obesity by direct and derived anthropometric indices with evaluation of physical efficiency among female college students of kolkata

BACKGROUND

The available information regarding the obesity pattern of the undergraduate female students of Kolkata is inadequate, though there are several reports which indicate the complications and/or awful consequences of obesity on female health particularly, during the reproductive years.

AIM

The present investigation has thus been carried out to report their present physiological status along with the prevalence of obesity, based on their body mass index (BMI), some direct and derived anthropometric indices, and physical fitness.

SUBJECTS AND METHODS

This small-scale cross-sectional study conducted in randomly selected 100 female students of different colleges of Kolkata with the age of 18-22 [mean age 20.4 (2.3)] years. Measurements of body composition included total 24 variables, with thirteen direct and eleven derived anthropometric variables; while physical efficiency parameters were physical fitness index, VO2max, energy expenditure and anaerobic power. The data of the experimental group were compared with those of the control group by t-test, using SPSS v.15.0 and MS-Excel v.2013.

RESULTS

Analysis of collected data showed majority of the students have normal range of BMI (67.95%), but, 21.95% of students found to be overweight and 3.84% are obese. They also showed higher fat mass [14.40 (4.11)], but, lower waist-to-hip ratio and conicity index. They were found to have poor to moderate physical fitness [57.60 (3.90)] and higher energy expenditure [5.61 (0.72)].

CONCLUSION

The findings of the present obesity screening reports almost one of four female students (24 out of 100 participants) are overweight/obese, indicated higher body fat distribution and increased propensity of being obese with age. Thus, the overall data along with their low physical fitness points out to health risks among female undergraduates of Kolkata.

Idiopathic hypertrophic cranial pachymenigitis - A long follow-up needed

Idiopathic hypertrophic cranial pachymenigitis is a rare clinical condition caused by localized or diffuse inflammatory thickening of dura matter. Described here is a person having diffuse thickening of dura matter of base of skull and he was on follow-up treatment for 5 years with us. Diagnosis was done by excluding other conditions and with biopsy. The patient responded to steroid and the MRI picture, which is given serially, shows improvement