Characterization of the EGFR interactome reveals associated protein complex networks and intracellular receptor dynamics

Growth factor receptor mediated signaling is meanwhile recognized as a complex signaling network, which is initiated by recruiting specific patterns of adaptor proteins to the intracellular domain of epidermal growth factor receptor (EGFR). Approaches to globally identify EGFR‐binding proteins are required to elucidate this network. We affinity‐purified EGFR with its interacting proteins by coprecipitation from lysates of A431 cells. A total of 183 proteins were repeatedly detected in high‐resolution MS measurements. For 15 of these, direct interactions with EGFR were listed in the iRefIndex interaction database, including Grb2, shc‐1, SOS1 and 2, STAT 1 and 3, AP2, UBS3B, and ERRFI. The newly developed Cytoscape plugin ModuleGraph allowed retrieving and visualizing 93 well‐described protein complexes that contained at least one of the proteins found to interact with EGFR in our experiments. Abundances of 14 proteins were modulated more than twofold upon EGFR activation whereof clathrin‐associated adaptor complex AP‐2 showed 4.6‐fold enrichment. These proteins were further annotated with different cellular compartments. Finally, interactions of AP‐2 proteins and the newly discovered interaction of CIP2A could be verified. In conclusion, a powerful technique is presented that allowed identification and quantitative assessment of the EGFR interactome to provide further insight into EGFR signaling.     

Synthesis of 3′-O-Propargylthymidine as a Candidate Antiretroviral Agent

Abstract

3′-O-Propargylthymidinc, which may be viewed as a stnictural analogue of the potent antiretroviral agent 3′-azido-3′-deoxythymidine (AZT), was synthesized from 5′-O-(4,4′-dimethoxytritylthymidine by reaction with propargyl bromide followed by gentle acidolysis. The 3′-O-propargyl derivative was tested for antiretroviral activity in SC-1 mouse fibroblasts infected with Rauscher murine leukemia virus (MuLV). No inhibition of MuLV proliferation was observed at concentrations of 3′-O-propargylthymidine from 0.001 to 100 μM. whereas the IC₅₀ against the host cells was 30 μM. By comparison, AZT had an IC₅₀ for MuLV growth of 0.01 μM and an IC₅₀ for cell growth of >100 μM. Thus, replacement of the 3′-N-N≡N group in AZT by a 3′-OCH₂C≡CH group increased cytotoxicity but decreased antiretroviral activity relative to AZT.     

Synthesis of 2′-Deoxyformycin B and 2′-Deoxyoxoformycin B

Abstract

3-β-D-Ribofuranosylpyazolo[4,3-d]pyrimidines (formycins)¹ modified in the heteroaromatic moiety are of biological interest as analogues of adenosine and guanosine, and have been the objects of intensive synthetic chemical effort by several groups.^2-9 2′-Deoxynucleosides^2c,2d,7b,13 and other analogties of the formycins modified in the sugar moiety^10-12 are also of potential interest, but have been less extensively studied. Examples of the 2′-deoxyribonucleoside type known to date include the 2′-deoxy-6-thioguanosine analogue 1, the 2′-deoxyadenosine (dAdo) analogue 2 (2′-deoxyformycin A),^10,13 and the 2-chloro-2′-deoxyadenosine analogue 3.^7b Compound 2 was found to be 10-15 times more potent than 2′-deoxyadenosine as an inhibitor of the growth of S49 cells, a murine lymphoma line of T-cell origin.¹³ Activity depended on 5′- phosphorylation, since mutants lacking the enzymes adenosine kinase (AK) and deoxycytidine kinase (dCK) were insensitive to the drug. Furthermore, activity was comparable in the presence and absence of an AK inhibitor, suggesting that 2, unlike dAdo, may be a poor substrate for adenosine deaminase. That 5′-phosphorylation of 2 was mediated by AK rather than dCK was indicated by the fact that miitants lacking only dCK retained sensitivity. This contrasted with the behavior of dAdo, which is known to be n substrate for both AK and dCK.¹⁴     

Development of a set of genomic microsatellite markers in tea (Camellia L.) (Camelliaceae)

Tea (Camellia L.) is the world’s most consumed health drink and is also important economically. Due to its self-incompatible and outcrossing nature, tea is composed of highly heterogeneous germplasm. It is a perennial, slow-growing crop and hence the successful release of new improved cultivars following conventional breeding methods takes years. In this context, a DNA marker-based molecular breeding approach holds great promise in accelerating genetic improvement programs in tea. Here we describe the isolation of a set of highly polymorphic genomic microsatellite markers using the enrichment approach, which may be useful for phylogenetic and marker-assisted breeding programs in tea. The enriched library comprising 3,205 clones was screened for the presence of microsatellites using a three-primer-based colony PCR method. Four hundred positive clones were selected and sequenced, to reveal 153 sequences containing simple sequence repeats. Seventy-eight primer pairs were designed from repeat-positive sequences, out of which 40 primer pairs produced successful amplifications. Twenty-two of these primer pairs, when tested on a panel of 21 diverse tea clones and accessions, were found to be highly polymorphic, resulting in 137 alleles with an average of 6.76 alleles per primer pair. The polymorphic information content (PIC), expected heterozygosity (H _e) and observed heterozygosity (H _o) of the polymorphic markers ranged from 0.1 to 0.9, 0.1–0.9 and 0.0–0.8, with average values of 0.6 ± 0.18, 0.7 ± 0.17 and 0.5 ± 0.22, respectively. These markers can be applied for various diversity analyses, mapping programs and genotyping of tea crop.     

Antiviral properties of copper and its alloys to inactivate covid-19 virus: a review

BioMetals - Copper (Cu) and its alloys are prospective materials in fighting covid-19 virus and several microbial pandemics, due to its excellent antiviral as well as antimicrobial properties. Even...     

Green synthesis of silver nanoparticles from aqueous extract of Scutellaria barbata and coating on the cotton fabric for antimicrobial applications and wound healing activity in fibroblast cells (L929)

Scutellaria barbata is a perennial herb which was vastly prescribed in Chinese medicine to treat inflammations, infections and it is also used a detoxifying agent. We synthesized silver nanoparticles with Scutellaria barbata extract and characterized the nanoparticles with UV–Vis spectroscopic analysis, TEM, AFM, FTIR and XRD. The biofilm inhibiting property of synthesized silver nanoparticles were examined with XTT reduction assay and the antimicrobial property was examined with well diffusion method. The silver nanoparticles were also coated with cotton fabrics and their efficacy against antimicrobials was analyzed to prove its application. The cytotoxic property of synthesized silver nanoparticles was examined with L929 fibroblast cells using MTT assay. Finally we analyzed the wound healing property of synthesized silver nanoparticles with wound scratch assay. The result of our UV–Vis spectroscopic analysis confirms Scutellaria barbata aqueous extract reduced silver ions and synthesized silver nanoparticles. The characterization studies TEM, AFM, FTIR and XRD confirms the synthesized silver nanoparticles are in ideal shape and size to be utilized as a drug. The XTT reduction assay proves silver nanoparticles effectively inhibits the biofilm formation in both resistant and sensitive strains. Antimicrobial sensitivity tests confirms synthesized silver nanoparticles and cotton coated synthesized silver nanoparticles both are effective against gram positive, gram negative and fungal species. Further the results of MTT assay confirms the synthesized silver nanoparticles are non toxic and finally the wound healing potency of the nanoparticles was confirmed with wound scratch assay. Over all our results authentically confirms the silver nanoparticles synthesized with Scutellaria barbata aqueous extract is potent wound healing drug.     

Antifungal testing and high-throughput screening of compound library against Geomyces destructans, the etiologic agent of geomycosis (WNS) in bats

Bats in the northeastern U.S. are affected by geomycosis caused by the fungus Geomyces destructans (Gd). This infection is commonly referred to as White Nose Syndrome (WNS). Over a million hibernating bats have died since the fungus was first discovered in 2006 in a cave near Albany, New York. A population viability analysis conducted on little brown bats (Myotis lucifugus), one of six bat species infected with Gd, suggests regional extinction of this species within 20 years. The fungus Gd is a psychrophile ("cold loving"), but nothing is known about how it thrives at low temperatures and what pathogenic attributes allow it to infect bats. This study aimed to determine if currently available antifungal drugs and biocides are effective against Gd. We tested five Gd strains for their susceptibility to antifungal drugs and high-throughput screened (HTS) one representative strain with SpectrumPlus compound library containing 1,920 compounds. The results indicated that Gd is susceptible to a number of antifungal drugs at concentrations similar to the susceptibility range of human pathogenic fungi. Strains of Gd were susceptible to amphotericin B, fluconazole, itraconazole, ketoconazole and voriconazole. In contrast, very high MICs (minimum inhibitory concentrations) of flucytosine and echinocandins were needed for growth inhibition, which were suggestive of fungal resistance to these drugs. Of the 1,920 compounds in the library, a few caused 50%--to greater than 90% inhibition of Gd growth. A number of azole antifungals, a fungicide, and some biocides caused prominent growth inhibition. Our results could provide a theoretical basis for future strategies aimed at the rehabilitation of most affected bat species and for decontamination of Gd in the cave environment.     

Rapid isolation of DNA from Dioscorea species suitable for PCR,restriction digestion and pathogen screening

The methods employed for DNA extraction from many plants is difficult because of the metabolites that interfere with DNA isolation procedures. We have developed a reliable and efficient method for isolating genomic DNA free from polysaccharide, polyphenols and protein contaminants from Dioscorea spp. The method involves inactivation of contaminant proteins by using CTAB/Proteinase K and precipitation of polysaccharides in the presence of high concentration of salt. The purity of genomic DNA was confirmed by A260/280 and A260/230 ratios calculated from the spectrophotometric readings and further by restriction analysis of the isolated DNA using restriction enzymes Eco RI. The total genomic DNA extracted by the new protocol was used for polymerase chain reaction amplification, RAPD analysis, restriction digestion and pathogen screening. The new protocol can be successfully used for both small- and large-scale preparation of genomic DNA from different tissues of Dioscorea spp. The quarantine of seed tubers and use of pathogen-free tubers for planting is a prerequisite for integrated disease management strategy. The protocol can be used for the isolation of genomic DNA from other crop plants too.     

PCR-based approach for mining of resistant gene analogues in taro (Colocasia esculenta)

Primers based on the conserved motifs were used to isolate nucleotide-binding sites (NBS) type sequences in taro (Colocasia esculenta). Cloning and sequencing identified three taro NBS-type sequences called resistance gene analogues (RGAs) that depicted similarity to other cloned RGA sequences. The deduced amino acid sequences of the RGAs detected the presence of conserved domains, viz. P-loop, categorising them with the NBS–leucine-rich repeat class gene family. Phylogenetic characterisation of the taro RGAs along with RGAs of other plant species grouped them with the non-toll interleukin receptor subclasses of the NBS sequences. The isolation and characterisation of taro RGAs have been reported for the first time in this study. This will provide a starting point towards characterisation of candidate resistance genes in taro and can act as a reference guide for future studies.