Genome sequencing and assembly of Indian golden silkmoth, Antheraea assamensis Helfer (Saturniidae, Lepidoptera).

Muga silkworm (Antheraea assamensis), one of the economically important wild silkmoths, is unique among saturniid silkmoths. It is confined to the North-eastern part of India. Muga silk has the highest value among the other silks. Unlike other silkmoths, A. assamensis has a low chromosome number (n = 15), and ZZ/ZO sex chromosome system. Here, we report the first high-quality draft genome of A. assamensis, assembled by employing the Illumina and PacBio sequencing platforms. The assembled genome of A. assamensis is 501.18 Mb long, with 2697 scaffolds and an N50 of 683.23 Kb. The genome encompasses 18,385 protein-coding genes, 86.29% of which were functionally annotated. Phylogenetic analysis of A. assamensis revealed its divergence from other Antheraea species approximately 28.7 million years ago. Moreover, an investigation into detoxification-related gene families, CYP450, GST, and ABC-transporter, revealed a significant expansion in A. assamensis as compared to the Bombyx mori. This expansion is comparable to Spodoptera litura, suggesting adaptive responses linked to the polyphagous behavior observed in these insects. This study provides valuable insights into the molecular basis of evolutionary divergence and adaptations in muga silkmoth. The genome assembly reported in this study will significantly help in the functional genomics studies on A. assamensis and other Antheraea species along with comparative genomics analyses of Bombycoidea insects.

Molecular-iodine catalyzed selective construction of cyclopenta[b]indoles from indoles and acetone: a green gateway to indole-fused cycles.

Molecular-iodine catalyzed access to an important class of bio-relevant indole derivatives, cyclopenta[b]indoles, has been achieved via a cascade addition/intramolecular cyclization reaction of indoles and acetone. Explorations of diverse substitution patterns revealed an essential substrate-control in the reaction. The high-density electronic core of indole is pivotal in favouring the formation of indolyl-cyclopenta[b]indole derivatives; in contrast, the electron deficiency of the core hindered the cyclization process, directing the formation of bis(indolyl)propanes. Investigations on the mechanistic pathway revealed that bis(indolyl)alkanes were the intermediates for the addition-cyclization process. This simple experimental method provides sustainable synthetic access to cyclopentannulated indoles.

RNAinsecta: A tool for prediction of precursor microRNA in insects and search for their target in the model organism Drosophila melanogaster.

INTRODUCTION AND BACKGROUND: Pre-MicroRNAs are the hairpin loops from which microRNAs are produced that have been found to negatively regulate gene expression in several organisms. In insects, microRNAs participate in several biological processes including metamorphosis, reproduction, immune response, etc. Numerous tools have been designed in recent years to predict novel pre-microRNA using binary machine learning classifiers where prediction models are trained with true and pseudo pre-microRNA hairpin loops. Currently, there are no existing tool that is exclusively designed for insect pre-microRNA detection. AIM: Application of machine learning algorithms to develop an open source tool for prediction of novel precursor microRNA in insects and search for their miRNA targets in the model insect organism, Drosophila melanogaster. METHODS: Machine learning algorithms such as Random Forest, Support Vector Machine, Logistic Regression and K-Nearest Neighbours were used to train insect true and false pre-microRNA features with 10-fold Cross Validation on SMOTE and Near-Miss datasets. miRNA targets IDs were collected from miRTarbase and their corresponding transcripts were collected from FlyBase. We used miRanda algorithm for the target searching. RESULTS: In our experiment, SMOTE performed significantly better than Near-Miss for which it was used for modelling. We kept the best performing parameters after obtaining initial mean accuracy scores >90% of Cross Validation. The trained models on Support Vector Machine achieved accuracy of 92.19% while the Random Forest attained an accuracy of 80.28% on our validation dataset. These models are hosted online as web application called RNAinsecta. Further, searching target for the predicted pre-microRNA in Drosophila melanogaster has been provided in RNAinsecta.

Halogen bonding assisted site-selective C-3 triaryl methylation of indoles and N-triaryl methylation of imidazoles.

Halogen bonding triggered by the Lewis basic nature of acetonitrile catalyzes the site-selective C-3 triaryl methylation of indoles and N-triaryl methylation of imidazoles with trityl chlorides under catalyst-, metal-, and additive-free conditions at room temperature. This method generates a quaternary carbon centre appended to a heterocyclic moiety. UV-Vis and FT-IR analyses indicate the existence of halogen bonding which is the driving force of the reaction. This approach is suitable for a wide range of substrates, furnishing moderate to excellent yields (up to 100%) of triaryl methylated products under ambient reaction conditions. Equimolar amounts of reactants are sufficient to obtain the optimum yield and in some cases pure products can be obtained without column chromatography.

Papaya latex mediated synthesis of prism shaped proteolytic gold nanozymes.

Beyond natural enzymes, the artificially synthesized nanozymes have attracted a significant interest as it can overcome the limitations of the former. Here, we report synthesis of shape controlled nanozymes showing proteolytic activity using Carica papaya L. (papaya) latex. The nanozymes synthesized under optimized reaction conditions exhibited sharp SPR peak around 550 nm with high abundance (45.85%) of prism shaped particles. FTIR analysis and coagulation test indicated the presence of papaya latex enzymes as capping agents over the gold nanoprisms. The milk clot assay and the inhibition test with egg white confirmed the proteolytic activity of the nanozymes and the presence of cysteine protease on it, respectively. The nanozymes were found to be biocompatible and did not elicit any toxic response in both in-vitro and in-vivo study. Based on our findings, we envisage that these biocompatible, shape-specific nanozymes can have potential theragnostic applications.

N,N'-Dimethylurea as an efficient ligand for the synthesis of pharma-relevant motifs through Chan-Lam cross-coupling strategy.

N,N'-Dimethylurea (DMU) is introduced as a ligand to aid the Chan-Lam N-arylation of primary amides, amines, and 3-aminophenols with arylboronic acids and its ester derivative as the arylating associate. The developed methodology is catalyzed by Cu and its in situ complexation with DMU brings about efficient synthesis of N-arylated anilines, 3-aminophenols, and primary amides in moderate to good yields (50-90%). The [Cu2(OAc)4(DMU)2] complex is synthesized and characterized by single crystal structure elucidation. The catalyst is cheap, free from prior synthesis of a metal complex, provides chemoselectivity towards the N-arylation of 3-aminophenols, and is suitable for mono-arylation of primary amides. The synthetic utility of the methodology is tested in the post-modification of two active pharmaceutical ingredients (APIs). The developed catalytic system extends the scope of N,N'-dimethylurea as an auxiliary in inexpensive and versatile Cu catalysis.

Towards integrated sustainable biofuel and chemical production: An application of banana pseudostem ash in the production of biodiesel and recovery of lignin from bamboo leaves.

This study investigated an integrated approach to the biowaste transformation and valorization of byproducts. Biochar obtained from the banana pseudostem was calcined to synthesize a heterogeneous catalyst and sustainably prepare a highly alkaline solution. The ash was utilized directly as a heterogeneous catalyst in biodiesel production from waste cooking oil. At the same time, an alkaline solution prepared from the ash was used for delignification and recovery of lignin from bamboo leaves by the hydrothermal reaction. Techniques like Fourier-transform infrared spectroscopy (FTIR), Field emission scanning electron microscopy (FESEM), Brunauer-Emmett-Teller (BET), Transmission electron microscopy (TEM), and Energy dispersive X-ray (EDX) were applied to characterized the catalyst. The alkaline solution was analyzed with Atomic absorption spectroscopy (AAS). The Response surface methodology (RSM) technique was considered for the optimization of different parameters in the transesterification and hydrothermal reaction. Under the optimized condition, waste cooking oil (WCO) to Fatty acid methyl ester (FAME) conversion was 97.56 ± 0.11%, and lignin recovery was 43.20 ± 0.45%. While at the best operating pyrolysis temperature, the liquid fraction yield from the banana pseudostem (500 °C) was 38.10 ± 0.31 wt%. This integrated study approach encourages the inexpensive, sustainable, and environment-friendly pathway for synthesizing catalysts and preparing a highly alkaline solution for the valorization of biowaste into biofuel and biochemicals.

Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies.

Uziflies (Family: Tachinidae) are dipteran endoparasites of sericigenous insects which cause major economic loss in the silk industry globally. Here, we are presenting the first full mitogenome of Blepharipa sp. (Acc: KY644698, 15,080 bp, A + T = 78.41%), a dipteran parasitoid of Muga silkworm (Antheraea assamensis) found in the Indian states of Assam and Meghalaya. This study has confirmed that Blepharipa sp. mitogenome gene content and arrangement is similar to other Tachinidae and Sarcophagidae flies of Oestroidea superfamily, typical of ancestral Diptera. Although, Calliphoridae and Oestridae flies have undergone tRNA translocation and insertion, forming unique intergenic spacers (IGS) and overlapping regions (OL) and a few of them (IGS, OL) have been conserved across Oestroidea flies. The Tachinidae mitogenomes exhibit more AT content and AT biased codons in their protein-coding genes (PCGs) than the Oestroidea counterpart. About 92.07% of all (3722) codons in PCGs of this new species have A/T in their 3rd codon position. The high proportion of AT and repeats in the control region (CR) affects sequence coverage, resulting in a short CR (Blepharipa sp.: 168 bp) and a smaller tachinid mitogenome. Our research unveils those genes with a high AT content had a reduced effective number of codons, leading to high codon usage bias. The neutrality test shows that natural selection has a stronger influence on codon usage bias than directed mutational pressure. This study also reveals that longer PCGs (e.g., nad5, cox1) have a higher codon usage bias than shorter PCGs (e.g., atp8, nad4l). The divergence rates increase nonlinearly as AT content at the 3rd codon position increases and higher rate of synonymous divergence than nonsynonymous divergence causes strong purifying selection. The phylogenetic analysis explains that Blepharipa sp. is well suited in the family of insectivorous tachinid maggots. It's possible that biased codon usage in the Tachinidae family reduces the effective number of codons, and purifying selection retains the core functions in their mitogenome, which could help with efficient metabolism in their endo-parasitic life style and survival strategy.

Revisiting the synthesis of aryl nitriles: a pivotal role of CAN.

Facilitated by the dual role of Ceric Ammonium Nitrate (CAN), herein we report a cost-effective approach for the cyanation of aryl iodides/bromides with CAN-DMF as an addition to the existing pool of combined cyanation sources. In addition to being an oxidant, CAN acts as a source of nitrogen in our protocol. The reaction is catalyzed by a readily available Cu(ii) salt and the ability of CAN to generate ammonia in the reaction medium is utilized to eliminate the additional requirement of a nitrogen source, ligand, additive or toxic reagents. The mechanistic study suggests an evolution of CN- leading to the synthesis of a variety of aryl nitriles in moderate to good yields. The proposed mechanism is supported by a series of control reactions and labeling experiments.

Towards sustainable biodiesel and chemical production: Multifunctional use of heterogeneous catalyst from littered Tectona grandis leaves.

Waste biomass derived heterogeneous catalyst is an excellent alternative to chemically synthesized catalysts. In this work, calcined Tectona grandis leaves were proposed as an eco-friendly, renewable and low cost heterogeneous base catalyst. The prepared catalyst was examined by FTIR, XRD, XPS, SEM, EDX, TEM, TGA, BET and Hammett indicator test. The catalyst has an appealing nature towards various chemical transformations due to its basic surface sites provided by alkali and alkaline earth metals. The efficiency of the catalyst was successfully investigated by its application in biodiesel production. The products were confirmed by 1H and 13C NMR. 100% FAME conversion was attained using a catalyst loading of 2.5 wt% under optimized reaction parameters. The catalyst was further explored for Knoevenagel condensation reaction, in which it showed its effectiveness and recyclability towards the formation of benzylidenemalononitrile derivatives of aryl aldehydes. Thus, it is a potential 'green catalyst' derived from waste biomass without any addition of chemicals that can replace the industrial base catalysts used for biodiesel production and Knoevenagel reaction and makes the protocol environmentally benign.

Effect of Substrates on Catalytic Activity of Biogenic Palladium Nanoparticles in C-C Cross-Coupling Reactions.

This work describes a practical methodology for C-C bond formation reactions with the aid of biogenic palladium nanoparticles, which are synthesized by using phytochemicals extracted from two common plant species. Comparative studies have been done on the activity of two plant species (Ocimum sanctum and Aloe vera) in generation of palladium nanoparticles via ex situ and in situ methods. The structural and morphological characteristics of the nanoparticles are examined by UV/visible spectroscopy, powder X-ray diffraction, X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, and transmission electron microscopy analyses. We have observed a significant influence of the substrates on the catalytic activity of the palladium nanoparticles in Sonogashira and Suzuki cross-coupling reactions.

Molecular Iodine-Catalyzed Selective C-3 Benzylation of Indoles with Benzylic Alcohols: A Greener Approach toward Benzylated Indoles.

Iodine-catalyzed selective C-3 benzylation of indoles with benzylic alcohols is developed. The reaction proceeds with molecular iodine as the catalyst under ligand-, metal-, and base-free conditions and tolerates wide functionalities. The experimental observations account for the halogen-bond activation mechanistic pathway for the molecular iodine catalysis.

Phospholipases play multiple cellular roles including growth, stress tolerance, sexual development, and virulence in fungi.

Phospholipases are ubiquitous enzymes that hydrolyze phospholipids. Based on the cleavage site of the ester linkage in the substrate phospholipids, phospholipases are classified into four major types, phospholipase A (PLA), phospholipase B (PLB), phospholipase C (PLC), and phospholipase D (PLD), which are further classified into various subtypes. Phospholipases hydrolyze phospholipids into various signaling products including phosphatidic acid (PA), diacylglycerol (DAG), free fatty acids (FFAs), and lyso-phospholipids (LPLs). These signaling products regulate numerous processes such as cytoskeletal dynamics, growth, homeostasis, membrane remodeling, nutrient acquisition, secretion, signal transduction, stress tolerance, sexual development, and virulence in various organisms including fungi. Due to these key cellular roles, phospholipases are also promising targets in diagnostic and therapeutic applications. In this review, we discuss current knowledge about the cellular roles of different classes of phospholipases in fungi.

Greener Biogenic Approach for the Synthesis of Palladium Nanoparticles Using Papaya Peel: An Eco-Friendly Catalyst for C-C Coupling Reaction.

The development of a green and sustainable synthetic methodology still remains a challenge across the globe. Encouraging the prevailing challenge, herein, we have synthesized Pd nanoparticles (Pd NPs) in a green and environmentally viable route, using the extract of waste papaya peel without the assistance of any reducing agents, high-temperature calcination, and reduction procedures. The biomolecules present in the waste papaya peel extract reduced Pd(II) to nanosize Pd(0) in a one-pot green and sustainable process. As a catalyst, the new Pd NPs offer a simple and efficient methodology in direct Suzuki-Miyaura and Sonogashira coupling with excellent yields under mild reaction conditions.

The mitochondrial genome of Muga silkworm (Antheraea assamensis) and its comparative analysis with other lepidopteran insects.

Muga (Antheraea assamensis) is an economically important silkmoth endemic to the states of Assam and Meghalaya in India and is the producer of the strongest known commercial silk. However, there is a scarcity of genomic and proteomic data for understanding the organism at a molecular level. Our present study is on decoding the complete mitochondrial genome (mitogenome) of A. assamensis using next generation sequencing technology and comparing it with other available lepidopteran mitogenomes. Mitogenome of A. assamensis is an AT rich circular molecule of 15,272 bp (A+T content ~80.2%). It contains 37 genes comprising of 13 protein coding genes (PCGs), 22 tRNA and 2 rRNA genes along with a 328 bp long control region. Its typical tRNAMet-tRNAIle-tRNAGln arrangement differed from ancestral insects (tRNAIle-tRNAGln-tRNAMet). Two PCGs cox1 and cox2 were found to have CGA and GTG as start codons, respectively as reported in some lepidopterans. Interestingly, nad4l gene showed higher transversion mutations at intra-species than inter-species level. All PCGs evolved under strong purifying selection with highest evolutionary rates observed for atp8 gene while lowest for cox1 gene. We observed the typical clover-leaf shaped secondary structures of tRNAs with a few exceptions in case of tRNASer1 and tRNATyr where stable DHU and TΨC loop were absent. A significant number of mismatches (35) were found to spread over 19 tRNA structures. The control region of mitogenome contained a six bp (CTTAGA/G) deletion atypical of other Antheraea species and lacked tandem repeats. Phylogenetic position of A. assamensis was consistent with the traditional taxonomic classification of Saturniidae. The complete annotated mitogenome is available in GenBank (Accession No. KU379695). To the best of our knowledge, this is the first report on complete mitogenome of A. assamensis.

Electrospun silk-polyaniline conduits for functional nerve regeneration in rat sciatic nerve injury model.

The present study describes the fabrication of polyaniline-silk fibroin (PASF) nanocomposite-based nerve conduits and their subsequent implantation in a rat sciatic nerve injury model for peripheral nerve regeneration. This is the first in vivo study of polyaniline-based nerve conduits describing the safety and efficacy of the conduits in treating peripheral nerve injuries. The nanocomposite was synthesized by electrospinning a mixture of silk fibroin protein and polyaniline wherein the silk nanofibers were observed to be uniformly coated with polyaniline nanoparticles. Tubular shaped nerve conduits were subsequently formed by multiple rolling of the electrospun sheet over a stainless steel mandrel. The conduits were characterized in vitro for their physico-chemical properties as well as their compatibility with rat Schwann cells. Upon implantation in a 10 mm sciatic nerve injury model, the conduits were evaluated for their neuro-regenerative potential through extensive electrophysiological studies and monitoring of gait pattern over a course of 12 months. Gross examination, histological and ultra-structure analyses of the conduits and the regenerated nerve were also performed to evaluate morphological regeneration of transected nerve. PASF nanocomposite conduits seeded with Schwann cell (cell seeded PASF) exhibited excellent nerve conduction velocity (NCV) (50 m s-1), compound muscle action potential (CMAP) (12.8 mV), motor unit potential (MUP) (124 µV), growth of healthy tissue along the nerve gap and thick myelination of axons 12 months after implantation indicating enhanced neuro-regeneration. The excellent functional recovery achieved by animals implanted with cell seeded PASF conduits (86.2% NCV; 80.00% CMAP; 76.07% MUP) are superior to outcomes achieved previously with similar electrically conductive conduits. We believe that the present study would encourage further research in developing electrically active neural implants using synthetic conducting polymers and the in vivo applications of the same.

De novo transcriptome of the muga silkworm, Antheraea assamensis (Helfer).

Antheraea assamensis (Lepidoptera: Saturniidae), is a semi-domesticated silkworm known to be endemic to Assam and the adjoining hilly areas of Northeast India. It is the only producer of a unique, commercially important variety of golden silk called "muga silk". Herein, we report the de novo transcriptome of A. assamensis reared on Machilus bombycina leaves for the first time. Short reads generated by high throughput sequencing of cDNA libraries from multiple tissues, viz. alimentary canal, silk gland and residual body of the 5th instar of muga silkworm were assembled into transcripts via a de novo assembly pipeline followed by functional annotation and classification. A total of 1,21,433 transcripts were generated from ~231 million raw reads of which ~74% (89,583) were either allocated a functional annotation or categorized under Pfam/COG/KEGG categories. Identification of differentially expressed transcripts and their comparative sequence analysis revealed candidate genes related to silk synthesis, viz. silk gland factor-1 and 3, sericin-like transcript, etc. with conserved forkhead, homeo- and POU domains. Several candidate anti-microbial peptides which may have potential anti-bacterial, anti-fungal or anti-parasitic activity in A. assamensis were also identified. T/A and AT/TA were predicted to be the most abundant mono- and di-nucleotide simple sequence repeat markers in the transcriptome. Transcriptome validation was carried out by quantitative real-time PCR (qPCR) amplification of eight transcripts. The resources generated by this study will expand the periphery of existing genomic data on A. assamensis facilitating future in-depth studies on its unknown aspects.

DNA aptamer probes for detection of estrogen receptor α positive carcinomas.

Estrogen receptor alpha (ERα) also known as NR3A1 (nuclear receptor subfamily 3, group A, member 1) is a ligand-activated transcription factor. It is an important biomarker for breast cancer metastasis. In the present study, we report a novel DNA aptamer candidate against estrogen receptor (ER) alpha structure. The enriched aptamer candidate was obtained after 14 iterative cycles of in vitro protein-SELEX process. Isothermal calorimetry study suggests the nanomolar sensitivity of the candidate ER_Apt1 to its target protein. Fluorescence- and chemiluminescence-binding assays confirm the specificity of the candidate aptamer to ER alpha positive breast cancer cell line. Comparative analysis of ER_Apt1 to ER alpha monoclonal antibody was also performed to analyze the expression of ER alpha in various malignant cancer cell line. Cytochemical and immunohistochemistry assay indicates its potential use as a diagnostic agent against ERα positive carcinomas. The nucleotide aptamer sequences described in the present study can be used for the detection, treatment, prophylaxis and diagnosis of ERα-related disorder.

An immobilized symmetrical bis-(NHC) palladium complex as a highly efficient and recyclable Suzuki-Miyaura catalyst in aerobic aqueous media.

A bis-N-heterocyclic carbene (NHC) functionalized with chloropropyltriethoxysilane over silica was used to synthesize a well-defined immobilized palladium complex. This complex is a suitable and easily retrievable catalyst for Suzuki-Miyaura cross-coupling reactions under mild aqueous conditions. Excellent yields and conversions were obtained with low palladium loadings (down to 0.03 mol% Pd). The catalyst can be reused up to six cycles without the loss of its activity. The catalytic role of the NHC complex of palladium during coupling between bromobenzene and phenylboronic acid was investigated theoretically. The oxidative addition step is predicted to be endothermic in agreement with the experimental conditions.

A comprehensive view of the web-resources related to sericulture.

Recent progress in the field of sequencing and analysis has led to a tremendous spike in data and the development of data science tools. One of the outcomes of this scientific progress is development of numerous databases which are gaining popularity in all disciplines of biology including sericulture. As economically important organism, silkworms are studied extensively for their numerous applications in the field of textiles, biomaterials, biomimetics, etc. Similarly, host plants, pests, pathogens, etc. are also being probed to understand the seri-resources more efficiently. These studies have led to the generation of numerous seri-related databases which are extremely helpful for the scientific community. In this article, we have reviewed all the available online resources on silkworm and its related organisms, including databases as well as informative websites. We have studied their basic features and impact on research through citation count analysis, finally discussing the role of emerging sequencing and analysis technologies in the field of seri-data science. As an outcome of this review, a web portal named SeriPort, has been created which will act as an index for the various sericulture-related databases and web resources available in cyberspace.Database URL: http://www.seriport.in/.