DNA methylation-dependent and -independent binding of CDX2 directs activation of distinct developmental and homeostatic genes.

Precise spatiotemporal and cell type-specific gene expression is essential for proper tissue development and function. Transcription factors (TFs) guide this process by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. In turn, DNA and chromatin modifications direct the genomic binding of TFs. However, how TFs navigate various chromatin features and selectively bind a small portion of the millions of possible genomic target loci is still not well understood. Here we show that Cdx2 - a pioneer TF that binds distinct targets in developing versus adult intestinal epithelial cells - has a preferential affinity for a non-canonical CpG-containing motif in vivo. A higher frequency of this motif at embryonic and fetal Cdx2 target loci and the specifically methylated state of the CpG during development allows selective Cdx2 binding and activation of developmental enhancers and linked genes. Conversely, demethylation at these enhancers prohibits ectopic Cdx2 binding in adult cells, where Cdx2 binds its canonical motif without a CpG. This differential Cdx2 binding allows for corecruitment of Ctcf and Hnf4, facilitating the establishment of intestinal superenhancers during development and enhancers mediating adult homeostatic functions, respectively. Induced gain of DNA methylation in the adult mouse epithelium or cultured cells causes ectopic recruitment of Cdx2 to the developmental target loci and facilitates cobinding of the partner TFs. Together, our results demonstrate that the differential CpG motif requirements for Cdx2 binding to developmental versus adult target sites allow it to navigate different DNA methylation profiles and activate cell type-specific genes at appropriate times.

Efficacy of Levetiracetam in neonatal seizures: a systematic review.

BACKGROUND: Neonatal seizures represent the most frequent presenting sign of any neurological abnormality secondary to various etiologies in the neonatal period. Phenobarbitone (PB) has been used as first-line anti-epileptic drug in the treatment of seizures but concerns have been raised regarding its neuro-apoptotic effects over the developing brain. Levetiracetam (LEV) is a newer anti-epileptic drug with neuroprotective property and has been used in adults and pediatric patient but its use in neonates have very limited experience. Recently many neonatal studies have sought the role of LEV in the management of neonatal seizures. AIMS AND OBJECTIVE: To evaluate the efficacy of Levetiracetam in the management of neonatal seizures. SEARCH METHODS: The literature search was done for this systematic review by searching the Cochrane Central Register of Controlled Trials (CENTRAL), and other various electronic databases including PubMed and various sites for ongoing trials and abstracts of conferences. RESULTS: Two eligible studies were analyzed that fulfilled the inclusion criteria of the systematic review. Fifteen studies were excluded due to the non-fulfillment of inclusion criteria. The primary outcome of both studies was to see the efficiency of LEV in controlling neonatal seizures when compared to PB. Better seizure control after a single loading dose of LEV was seen. Rates of seizure cessation at 24 h was also better in the LEV arm. Neonatal seizures secondary to hypoxic-ischemic encephalopathy (HIE) and receiving therapeutic hypothermia were better controlled with LEV. The side effect of LEV was significantly less when compared to PB. CONCLUSION: Levetiracetam has shown to have promising anti-epileptic properties for the management of neonatal seizure with better efficacy and less or no side effects. There is a need to conduct more randomized controlled trials seeking the role of LEV in the acute management of neonatal seizures and also for assessing its neuroprotective role and neurodevelopmental outcome in these neonates.

High-throughput virtual screening of drug databanks for potential inhibitors of SARS-CoV-2 spike glycoprotein.

COVID-19, which is caused by a novel coronavirus known as SARS-CoV-2, has spread rapidly around the world, and it has infected more than 29 million individuals as recorded on 16 September 2020. Much effort has been made to stop the virus from spreading, and there are currently no approved pharmaceutical products to treat COVID-19. Here, we apply an in silico approach to investigate more than 3800 FDA approved drugs on the viral RBD S1-ACE2 interface as a target. The compounds were investigated through flexible ligand docking, ADME property calculations and protein-ligand interaction maps. Molecular dynamics (MD) simulations were also performed on eleven compounds to study the stability and the interactions of the protein-ligand complexes. The MD simulations show that bagrosin, chidamide, ebastine, indacaterol, regorafenib, salazosulfadimidine, silodosin and tasosartan are relatively stable near the C terminal domain (CTD1) of the S1 subunit of the viral S protein. The relative MMGBSA binding energies show that silodosin has the best binding to the target. The constant velocity steered molecular dynamics (SMD) simulations show that silodosin preferentially interacts with the RBD S1 and has potential to act as an interfering compound between viral spike-host ACE2 interactions. Communicated by Ramaswamy H. Sarma.

Genetic variations at loci involved in the immune response are risk factors for hepatocellular carcinoma.

UNLABELLED: Primary liver cancer is the third most common cause of cancer-related death worldwide, with a rising incidence in Western countries. Little is known about the genetic etiology of this disease. To identify genetic factors associated with hepatocellular carcinoma (HCC) and liver cirrhosis (LC), we conducted a comprehensive, genome-wide variation analysis in a population of unrelated Asian individuals. Copy number variation (CNV) and single nucleotide polymorphisms (SNPs) were assayed in peripheral blood with the high-density Affymetrix SNP6.0 microarray platform. We used a two-stage discovery and replication design to control for overfitting and to validate observed results. We identified a strong association with CNV at the T-cell receptor gamma and alpha loci (P < 1 × 10(-15)) in HCC cases when contrasted with controls. This variation appears to be somatic in origin, reflecting differences between T-cell receptor processing in lymphocytes from individuals with liver disease and healthy individuals that is not attributable to chronic hepatitis virus infection. Analysis of constitutional variation identified three susceptibility loci including the class II MHC complex, whose protein products present antigen to T-cell receptors and mediate immune surveillance. Statistical analysis of biologic networks identified variation in the "antigen presentation and processing" pathway as being highly significantly associated with HCC (P = 1 × 10(-11)). SNP analysis identified two variants whose allele frequencies differ significantly between HCC and LC. One of these (P = 1.74 × 10(-12)) lies in the PTEN homolog TPTE2. CONCLUSION: Combined analysis of CNV, individual SNPs, and pathways suggest that HCC susceptibility is mediated by germline factors affecting the immune response and differences in T-cell receptor processing.

Tetrasubstituted 2-imidazolones via Ag(I)-catalyzed cycloisomerization of propargylic ureas.

A one-pot protocol based on a Ag(I)-catalyzed cycloisomerization of propargylic ureas, derived from secondary propargylamines and isocyanates, was developed for the generation of the 2-imidazolone core.

N-heterocyclic carbene catalyzed aroylation of 3,5-dichloro-2(1H)-pyrazinones.

The N-heterocyclic carbene catalyzed chemoselective C3-aroylation of 3,5-dichloro-2(1H)-pyrazinones with various aldehydes is reported. We herein describe results of this remarkable mild and efficient procedure.

Pyrolysis of waste expanded polystyrene and reduction of styrene via in-situ multiphase pyrolysis of product oil for the production of fuel range hydrocarbons.

Upgraded fuel oil was produced from the waste expanded polystyrene (WEPS) using pyrolysis and in-situ selective aromatization in a specially designed reactor. The catalytic pyrolysis of WEPS was performed keeping the catalyst in three different types of catalyst arrangements inside the reactor i.e., A-type/catalyst in liquid phase, B-type/catalyst in vapour phase, and AB-type or Multiphase/catalyst in both liquid and vapour phases, respectively. The ZSM-5 ammonium powder was used as a catalyst with varying feed to catalyst ratio and 20:1 was found to be optimum. Aromatics of fuel range like benzene, toluene, and ethylbenzene (BTE) were significantly increased and styrene got reduced by many folds when AB-type/multiphase catalytic pyrolysis was performed. The thermal pyrolysis produced maximum liquid yield of 94.37 wt% at a temperature of 650 °C and a heating rate of 15 °C/min. The maximum liquid yield of 88.05 wt%, 78.85 wt%, and 75.11 wt% were obtained for the A-type, B-type, and AB-type catalytic pyrolysis at the temperature of 600 °C, 550 °C and 550 °C, respectively using the same heating rate. The liquid oil of thermal pyrolysis contains very low amount of fuel range aromatics i.e., BTE of 11.38 wt% and the highest amount of styrene (84.74 wt%). In contrarily, BTE content for the catalytic process increased progressively in the order of 18.98 wt% (A-type) < 24.27 wt% (B-type) < 28.12 wt% (AB-type). The styrene content significantly decreased to a very low value of 46.30 wt% for AB-type/multiphase pyrolysis at the temperature of 550 °C.

Pathogenicity of Fusarium oxysporum against the larvae of Culex quinquefasciatus (Say) and Anopheles stephensi (Liston) in laboratory.

The entomopathogenic fungi Fusarium oxysporum are the next generation mosquito controlling agent. F. oxysporum basically contains unique toxin and can be a selectively good agent in tropical countries. We are reporting here the efficacy of the metabolites of F. oxysporum against the larvae of Anopheles stephensi and Culex quinquefasciatus in the laboratory. F. oxysporum was grown on Czapek Dox broth. The bioassays were run at five different concentrations (1.30, 1.60, 1.77, 1.90, and 2.00 ppm). The LC(50), LC(90), and LC(99) values with 95% fiducial limits and probit equations were calculated by probit analysis. The mortality was observed after 24, 48, and 72 h against all instars. The LC(90) values in the case of C. quinquefasciatus after 48 h when calculated were 1.85, 1.92, 1.87, and 1.87 ppm, respectively, while LC(99) values calculated were 2.24, 2.25, 2.18, and 2.19 ppm. Moreover, after 48 h in the case of A. stephensi, the LC(50) values for the first, second, third, and fourth instars were recorded as 1.48, 1.51, 1.71, and 1.50 ppm, respectively. The LC(90) values recorded were 1.88, 1.91, 1.93, and 1.89 ppm and LC(99) values observed were 2.36, 2.23, 2.26, and 2.21 ppm. The results obtained 24, 48, and 72 h have been compared and it was observed significantly that 48 h after exposure the metabolite has more pathogenicity. The results of the metabolites of F. oxysporum may be considered as a new bio-control agent for vector mosquitoes if the field trial succeeds.

Molecular level investigation of curcumin self-assembly induced by trigonelline and nanoparticle formation.

Nanoparticle-facilitated drug delivery forms the core of medicine nowadays with the drug being delivered right at the target, reducing side effects and enhancing therapeutic value. Nanoparticles derived from natural compounds are further a point of focus being biocompatible and safe by and large. In this study, we have performed HF/6-31G calculations coupled with intermolecular interaction calculations and nanoscale molecular dynamics simulations to investigate self-assemblage in curcumin induced by trigonelline. Similar to recently reported self-assemblage in curcumin induced by sugar, trigonelline, a natural antidiabetic derived from fenugreek, can also induce auto-catalyzed self-assemblage in curcumin to form nanoparticles. It has been shown that these nanoparticles may be utilized for the delivery of drugs with severe side effects especially for diabetic patients with triple benefit of being antidiabetic, biocompatible and safe. As an example, carriage of antidiabetic drug pioglitazone and anticancer drug taxol have been depicted utilizing nanoparticles of curcumin and trigonelline. Twenty five taxol molecules could be comfortably carried in a 50 nm nanoparticle with an average overall root mean square deviation of 2.89 Å with reference to initial positions. For the first time, this study shows the possibility of developing antidiabetic nanoparticles with plethora of opportunities for diabetic patients. The study is expected to motivate experimental verification and has a long lasting impact in medicinal chemistry.

Role of Asp190 in the Phosphorylation of the Antibiotic Kanamycin Catalyzed by the Aminoglycoside Phosphotransferase Enzyme: A Combined QM:QM and MD Study.

The aminoglycoside phosphotransferase (APH(3')-IIIa) kinases form a clinically central group of antibiotic-resistant enzymes. Computationally, we have studied the catalytic mechanism of the APH(3')-IIIa enzyme at the atomic-level. The proposed reaction mechanism involves protonation of Asp190 by the kanamycin 3'-hydroxyl group mediated through an explicit neighboring water molecule, which leads to a simultaneous nucleophilic attack on the γ-phosphate of the ATP by the deprotonated kanamycin 3'-hydroxyl group. The second step is a proton abstraction from the protonated Asp190 to the phosphate group of the phosphorylated kanamycin mediated by an explicit water molecule. The calculated Gibbs energy of activation (ΔG⧧) of the rate-determining step for the phosphorylation reaction is 77 kJ mol-1 at the M06-2X/6-311++G(2df,p)//ONIOM(M06-2X/6-31+G(d):HF/6-31G(d)) level of theory. This study has provided a new understanding of the APH(3')-IIIa catalytic mechanism that agrees with the available experimental data (ΔG⧧ = 75 ± 4 kJ mol-1) and could provide a starting point for the rational design of mechanism-based inhibitors of aminoglycoside modifying enzyme to circumvent antibiotic resistance.

Role of kangaroo mother care in growth and breast feeding rates in very low birth weight (VLBW) neonates: a systematic review.

OBJECTIVE: To evaluate the role of kangaroo mother care (KMC) on growth and breast feeding rates in very low birth weight (VLBW) neonates. MATERIALS AND METHODS: A literature search was done to identify eligible studies using various electronic database searches including PubMed and EMBASE, various Web of Science including Scopus, Index Copernicus, African Index Medicus (AIM), Thomson Reuters (ESCI), Chemical Abstracts Service (CAS), SCIWIN (Scientific World Index), Google Scholar, Latin American and Caribbean Health Sciences Information System (LILACS), Index Medicus for the Eastern Mediterranean Region (IMEMR), Index Medicus for the South-East Asian Region (IMSEAR), and Western Pacific Region Index Medicus (WPRIM) and various clinical trial registries. RESULTS: Thirteen studies that evaluated the role of KMC in VLBW infants in improvement of growth outcome (weight/length/head circumference) or breast feeding rates as their primary or secondary outcome, were included in this systematic review. Seven studies evaluated both growth and breast feeding rates, four studies evaluated breast feeding rates and two studies evaluated growth outcome. All included studies except one either showed positive effect or no effect on growth and breast feeding rates. CONCLUSIONS: KMC has a positive effect on growth of the VLBW infants and also leads to increase in the breast-feeding rates. KMC should be an integral part of neonatal care and should be promoted as an essential newborn care component.

Four tyrosine residues of the rice immune receptor XA21 are not required for interaction with the co-receptor OsSERK2 or resistance to Xanthomonas oryzae pv. oryzae.

Tyrosine phosphorylation has emerged as an important regulator of plasma membrane-localized immune receptors activity. Here, we investigate the role of tyrosine phosphorylation in the regulation of rice XANTHOMONAS RESISTANCE 21 (XA21)-mediated immunity. We demonstrate that the juxtamembrane and kinase domain of Escherichia coli-expressed XA21 (XA21JK) autophosphorylates on tyrosine residues. Directed mutagenesis of four out of the nine tyrosine residues in XA21JK reduced autophosphorylation. These sites include Tyr698 in the juxtamembrane domain, and Tyr786, Tyr907, and Tyr909 in the kinase domain. Rice plants expressing XA21-GFP fusion proteins or proteins with these tyrosine residues individually mutated to phenylalanine (XA21YF-GFP), which prevents phosphorylation at these sites, maintain resistance to Xanthomonas oryzae pv. oryzae. In contrast, plants expressing phosphomimetic XA21 variants with tyrosine mutated to aspartate (XA21YD-GFP) were susceptible. In vitro purified XA21JKY698F, XA21JKY907F, and XA21JKY909F variants are catalytically active, whereas activity was not detected in XA21JKY768F and the four XA21JKYD variants. We previously demonstrated that interaction of XA21 with the co-receptor OsSERK2 is critical for biological function. Four of the XA21JKYF variants maintain interaction with OsSERK2 as well as the XA21 binding (XB) proteins XB3 and XB15 in yeast, suggesting that these four tyrosine residues are not required for their interaction. Taken together, these results suggest that XA21 is capable of tyrosine autophosphorylation, but the identified tyrosine residues are not required for activation of XA21-mediated immunity or interaction with predicted XA21 signaling proteins.

Mono and dihydroxy coumarin derivatives: Copper chelation and reduction ability.

Due to the limited array of the currently available copper chelators, research of such compounds continues to be of clinical interest. Notably, o-dihydroxycoumarins have been previously shown to be potent iron chelators under neutral conditions. Within this study, the interaction of a series of natural coumarins and their synthetic analogs with copper has been evaluated in order to obtain structure-activity relationships under different pathophysiological pH conditions. Both competitive and non-competitive methods have been employed. Analysis of cupric ion reduction has also been performed. Under mildly competitive conditions, cupric chelation was observed for o-dihydroxycoumarins, and partially for o-diacetoxycoumarin. Non-competitive studies showed that cuprous ions are not chelated at all and that the stoichiometries of the most active 6,7- and 7,8-dihydroxycoumarins to cupric ions ranged from 1:1 to 2:1 depending on pH and concentration. Interestingly, under highly competitive conditions, coumarins were not capable of chelating cupric ions, either. Reduction experiments have shown that 13 out of the 15 coumarins included in this study reduced cupric ions. However, significant differences depending on their structures were apparent in their potencies. O-dihydroxycoumarins were the most potent ones again. CONCLUSION: O-dihydroxycoumarins are moderately active cupric ion chelators with potent copper reducing properties.

Non-covalent carriage of anticancer agents by humanized antibody trastuzumab.

This article explores the internalization and non-covalent carriage of small molecule anticancer agents like vinca alkaloids by humanized monoclonal antibody trastuzumab. Such carriage is marked by significant reduction in side effects and increased therapeutic value of these anticancer agents. This study is coherent with few clinical observations of enhanced efficiency of these anticancer agents when co-administered with therapeutic antibodies. This study will also serve as the foundation for screening a database of anticancer agents for possible compounds that may be co-delivered alongwith the antibody. Based on this study vincristine conformation inside antibody and its charge environment may be used as descriptors for screening purposes.

Bridging Links between Long Noncoding RNA HOTAIR and HPV Oncoprotein E7 in Cervical Cancer Pathogenesis.

Human Papillomavirus (HPV) type 16 oncoprotein E7 plays a major role in cervical carcinogenesis by interacting with and functionally inactivating various host regulatory molecules. Long noncoding RNA (lncRNA) HOTAIR is one such regulator that recruits chromatin remodelling complex PRC2, creating gene silencing H3K27 me3 marks. Hence, we hypothesized that HOTAIR could be a potential target of E7, in HPV16 related cervical cancers (CaCx). We identified significant linear trend of progressive HOTAIR down-regulation through HPV negative controls, HPV16 positive non-malignants and CaCx samples. Majority of CaCx cases portrayed HOTAIR down-regulation in comparison to HPV negative controls, with corresponding up-regulation of HOTAIR target, HOXD10, and enrichment of cancer related pathways. However, a small subset had significantly higher HOTAIR expression, concomitant with high E7 expression and enrichment of metastatic pathways. Expression of HOTAIR and PRC2-complex members (EZH2 and SUZ12), showed significant positive correlation with E7 expression in CaCx cases and E7 transfected C33A cell line, suggestive of interplay between E7 and HOTAIR. Functional inactivation of HOTAIR by direct interaction with E7 could also be predicted by in silico analysis and confirmed by RNA-Immunoprecipitation. Our study depicts one of the causal mechanisms of cervical carcinogenesis by HPV16 E7, through modulation of HOTAIR expression and function.