Design, Synthesis and Catalytic Activity of Protein Containing Thiotyrosine as an Active Site Residue.

Native chemical ligation is a key reaction in the toolbox of chemical methods for the synthesis of native and modified proteins. The catalysis of ligation is commonly performed by using small aryl-thiol molecules added at high concentrations. In this work, we incorporated thiotyrosine, a non-canonical amino acid containing an aryl-thiol moiety, into a designed cyclic protein « sans queue ni tête ¼. Importantly, the protein environment reduced the pKa of the thiol group to 5.8-5.9, which is significantly lower than the previously reported value for thiotyrosine in a short peptide (pKa 6.4). Furthermore, we demonstrated the catalytic activity of this protein both as hydrolase and in native chemical ligation of peptides. These results will be useful for the development of efficient protein catalysts (enzymes) for protein synthesis and modification.

Comparison of the performance of SWAT and hybrid M5P tree models in rainfall-runoff simulation.

Stream flow forecasting is a crucial aspect of hydrology and water resource management. This study explores stream flow forecasting using two distinct models: the Soil and Water Assessment Tool (SWAT) and a hybrid M5P model tree. The research specifically targets the daily stream flow predictions at the MH Halli gauge stations, located along the Hemvati River in Karnataka, India. A 14-year dataset spanning from 2003 to 2017 is divided into two subsets for model calibration and validation. The SWAT model's performance is evaluated by comparing its predictions to observed stream flow data. Residual time series values resulting from this comparison are then resolved using the M5P model tree. The findings reveal that the hybrid M5P tree model surpasses the SWAT model in terms of various evaluation metrics, including root-mean-square error, coefficient of determination (R2), Nash-Sutcliffe efficiency, and degree of agreement (d) for the MH Halli stations. In conclusion, this study shows the effectiveness of the hybrid M5P tree model in stream flow forecasting. The research contributes valuable insights into improved water resource management and underscores the importance of selecting appropriate models based on their performance and suitability for specific hydrological forecasting tasks.

Modulation of terpenoid indole alkaloid pathway via elicitation with phytosynthesized silver nanoparticles for the enhancement of ajmalicine, a pharmaceutically important alkaloid.

MAIN CONCLUSION: The use of silver nanoparticles as elicitors in cell cultures of Rauwolfia serpentina resulted in increased levels of ajmalicine, upregulated structural and regulatory genes, elevated MDA content, and reduced activity of antioxidant enzymes. These findings hold potential for developing a cost-effective method for commercial ajmalicine production. Plants possess an intrinsic ability to detect various stress signals, prompting the activation of defense mechanisms through the reprogramming of metabolites to counter adverse conditions. The current study aims to propose an optimized bioprocess for enhancing the content of ajmalicine in Rauwolfia serpentina callus through elicitation with phytosynthesized silver nanoparticles. Initially, callus lines exhibiting elevated ajmalicine content were established. Following this, a protocol for the phytosynthesis of silver nanoparticles using seed extract from Rauwolfia serpentina was successfully standardized. The physicochemical attributes of the silver nanoparticles were identified, including their spherical shape, size ranging from 6.7 to 28.8 nm in diameter, and the presence of reducing-capping groups such as amino, carbonyl, and amide. Further, the findings indicated that the presence of 2.5 mg L-1 phytosynthesized silver nanoparticles in the culture medium increased the ajmalicine content. Concurrently, structural genes (TDC, SLS, STR, SGD, G10H) and regulatory gene (ORCA3) associated with the ajmalicine biosynthetic pathway were observed to be upregulated. A notable increase in MDA content and a decrease in the activities of antioxidant enzymes were observed. A notable increase in MDA content and a decrease in the activities of antioxidant enzymes were also observed. Our results strongly recommend the augmentation of ajmalicine content in the callus culture of R. serpentina through supplementation with silver nanoparticles, a potential avenue for developing a cost-effective process for the commercial production of ajmalicine.

Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq.

Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-increasing ncRNAs under study, it is essential to identify, categorize and annotate these ncRNAs on a genome-wide scale. The use of high-throughput RNA sequencing (RNA-seq) technologies provides a broader picture of the non-coding component of transcriptome, enabling the comprehensive identification and annotation of all major ncRNAs across samples. However, the detection of known and emerging class of ncRNAs from RNA-seq data demands complex computational methods owing to their unique as well as similar characteristics. Here, we discuss major plant endogenous, regulatory ncRNAs in an RNA sample followed by computational strategies applied to discover each class of ncRNAs using RNA-seq. We also provide a collection of relevant software packages and databases to present a comprehensive bioinformatics toolbox for plant ncRNA researchers. We assume that the discussions in this review will provide a rationale for the discovery of all major categories of plant ncRNAs.

Musashi-2 causes cardiac hypertrophy and heart failure by inducing mitochondrial dysfunction through destabilizing Cluh and Smyd1 mRNA.

Regulation of RNA stability and translation by RNA-binding proteins (RBPs) is a crucial process altering gene expression. Musashi family of RBPs comprising Msi1 and Msi2 is known to control RNA stability and translation. However, despite the presence of MSI2 in the heart, its function remains largely unknown. Here, we aim to explore the cardiac functions of MSI2. We confirmed the presence of MSI2 in the adult mouse, rat heart, and neonatal rat cardiomyocytes. Furthermore, Msi2 was significantly enriched in the heart cardiomyocyte fraction. Next, using RNA-seq data and isoform-specific PCR primers, we identified Msi2 isoforms 1, 4, and 5, and two novel putative isoforms labeled as Msi2 6 and 7 to be expressed in the heart. Overexpression of Msi2 isoforms led to cardiac hypertrophy in cultured cardiomyocytes. Additionally, Msi2 exhibited a significant increase in a pressure-overload model of cardiac hypertrophy. We selected isoforms 4 and 7 to validate the hypertrophic effects due to their unique alternative splicing patterns. AAV9-mediated overexpression of Msi2 isoforms 4 and 7 in murine hearts led to cardiac hypertrophy, dilation, heart failure, and eventually early death, confirming a pathological function for Msi2. Using global proteomics, gene ontology, transmission electron microscopy, seahorse, and transmembrane potential measurement assays, increased MSI2 was found to cause mitochondrial dysfunction in the heart. Mechanistically, we identified Cluh and Smyd1 as direct downstream targets of Msi2. Overexpression of Cluh and Smyd1 inhibited Msi2-induced cardiac malfunction and mitochondrial dysfunction. Collectively, we show that Msi2 induces hypertrophy, mitochondrial dysfunction, and heart failure.

PTPAMP: prediction tool for plant-derived antimicrobial peptides.

The emergence of antimicrobial peptides (AMPs) as a potential alternative to conventional antibiotics has led to the development of efficient computational methods for predicting AMPs. Among all organisms, the presence of multiple genes encoding AMPs in plants demands the development of a plant-based prediction tool. To this end, we developed models based on multiple peptide features like amino acid composition, dipeptide composition, and physicochemical attributes for predicting plant-derived AMPs. The selected compositional models are integrated into a web server termed PTPAMP. The designed web server is capable of classifying a query peptide sequence into four functional activities, i.e., antimicrobial (AMP), antibacterial (ABP), antifungal (AFP), and antiviral (AVP). Our models achieved an average area under the curve of 0.95, 0.91, 0.85, and 0.88 for AMP, ABP, AFP, and AVP, respectively, on benchmark datasets, which were ~ 6.75% higher than the state-of-the-art methods. Moreover, our analysis indicates the abundance of cysteine residues in plant-derived AMPs and the distribution of other residues like G, S, K, and R, which differ as per the peptide structural family. Finally, we have developed a user-friendly web server, available at the URL: http://www.nipgr.ac.in/PTPAMP/ . We expect the substantial input of this predictor for high-throughput identification of plant-derived AMPs followed by additional insights into their functions.

Microscopic and Transcriptomic Analyses of Dalbergoid Legume Peanut Reveal a Divergent Evolution Leading to Nod-Factor-Dependent Epidermal Crack-Entry and Terminal Bacteroid Differentiation.

Root nodule symbiosis (RNS) is the pillar behind sustainable agriculture and plays a pivotal role in the environmental nitrogen cycle. Most of the genetic, molecular, and cell-biological knowledge on RNS comes from model legumes that exhibit a root-hair mode of bacterial infection, in contrast to the Dalbergoid legumes exhibiting crack-entry of rhizobia. As a step toward understanding this important group of legumes, we have combined microscopic analysis and temporal transcriptome to obtain a dynamic view of plant gene expression during Arachis hypogaea (peanut) nodule development. We generated comprehensive transcriptome data by mapping the reads to A. hypogaea, and two diploid progenitor genomes. Additionally, we performed BLAST searches to identify nodule-induced yet-to-be annotated peanut genes. Comparison between peanut, Medicago truncatula, Lotus japonicus, and Glycine max showed upregulation of 61 peanut orthologs among 111 tested known RNS-related genes, indicating conservation in mechanisms of nodule development among members of the Papilionoid family. Unlike model legumes, recruitment of class 1 phytoglobin-derived symbiotic hemoglobin (SymH) in peanut indicates diversification of oxygen-scavenging mechanisms in the Papilionoid family. Finally, the absence of cysteine-rich motif-1-containing nodule-specific cysteine-rich peptide (NCR) genes but the recruitment of defensin-like NCRs suggest a diverse molecular mechanism of terminal bacteroid differentiation. In summary, our work describes genetic conservation and diversification in legume-rhizobia symbiosis in the Papilionoid family, as well as among members of the Dalbergoid legumes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The landscape of chimeric RNAs in non-diseased tissues and cells.

Chimeric RNAs and their encoded proteins have been traditionally viewed as unique features of neoplasia, and have been used as biomarkers and therapeutic targets for multiple cancers. Recent studies have demonstrated that chimeric RNAs also exist in non-cancerous cells and tissues, although large-scale, genome-wide studies of chimeric RNAs in non-diseased tissues have been scarce. Here, we explored the landscape of chimeric RNAs in 9495 non-diseased human tissue samples of 53 different tissues from the GTEx project. Further, we established means for classifying chimeric RNAs, and observed enrichment for particular classifications as more stringent filters are applied. We experimentally validated a subset of chimeric RNAs from each classification and demonstrated functional relevance of two chimeric RNAs in non-cancerous cells. Importantly, our list of chimeric RNAs in non-diseased tissues overlaps with some entries in several cancer fusion databases, raising concerns for some annotations. The data from this study provides a large repository of chimeric RNAs present in non-diseased tissues, which can be used as a control dataset to facilitate the identification of true cancer-specific chimeras.

Hsp70-nucleotide exchange factor (NEF) Fes1 has non-NEF roles in degradation of gluconeogenic enzymes and cell wall integrity.

Fes1 is a conserved armadillo repeat-containing Hsp70 nucleotide exchange factor important for growth at high temperature, proteasomal protein degradation and prion propagation. Depleting or mutating Fes1 induces a stress response and causes defects in these processes that are ascribed solely to disruption of Fes1 regulation of Hsp70. Here, we find Fes1 was essential for degradation of gluconeogenic enzymes by the vacuole import and degradation (Vid) pathway and for cell wall integrity (CWI), which is crucial for growth at high temperature. Unexpectedly, Fes1 mutants defective in physical or functional interaction with Hsp70 retained activities that support Vid and CWI. Fes1 and the Fes1 mutants bound to the Vid substrate Fbp1 in vitro and captured Slt2, a signaling kinase that regulates CWI, from cell lysates. Our data show that the armadillo domain of Fes1 binds proteins other than Hsp70, that Fes1 has important Hsp70-independent roles in the cell, and that major growth defects caused by depleting Fes1 are due to loss of these functions rather than to loss of Hsp70 regulation. We uncovered diverse functions of Fes1 beyond its defined role in regulating Hsp70, which points to possible multi-functionality among its conserved counterparts in other organisms or organelles.

The potential application of genome editing by using CRISPR/Cas9, and its engineered and ortholog variants for studying the transcription factors involved in the maintenance of phosphate homeostasis in model plants.

Phosphorus (P), an essential macronutrient, is pivotal for growth and development of plants. Availability of phosphate (Pi), the only assimilable P, is often suboptimal in rhizospheres. Pi deficiency triggers an array of spatiotemporal adaptive responses including the differential regulation of several transcription factors (TFs). Studies on MYB TF PHR1 in Arabidopsis thaliana (Arabidopsis) and its orthologs OsPHRs in Oryza sativa (rice) have provided empirical evidence of their significant roles in the maintenance of Pi homeostasis. Since the functional characterization of PHR1 in 2001, several other TFs have now been identified in these model plants. This raised a pertinent question whether there are any likely interactions across these TFs. Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has provided an attractive paradigm for editing genome in plants. Here, we review the applications and challenges of this technique for genome editing of the TFs for deciphering the function and plausible interactions across them. This technology could thus provide a much-needed fillip towards engineering TFs for generating Pi use efficient plants for sustainable agriculture. Furthermore, we contemplate whether this technology could be a viable alternative to the controversial genetically modified (GM) rice or it may also eventually embroil into a limbo.

From current knowledge to best practice: A primer on viral diagnostics using deep sequencing of virus-derived small interfering RNAs (vsiRNAs) in infected plants.

Plants have evolved many defense strategies for combating viral infections. One major surveillance strategy adopted by them is manipulating viral sequences to generate distinct small RNA products via Dicer-like enzymes (DCL), and thereby restricting virus multiplication through the RNA interference (RNAi) mechanism. The power of high-throughput sequencing technologies, with diverse computational tools to handle small RNA sequencing (sRNA-Seq) data, bestows unprecedented opportunities to answer fundamental questions in plant virology. Here, we present some basic concepts of virus-derived, small interfering RNA (vsiRNA) biogenesis in plants, optimization strategies, caveats, and best practices for efficient discovery and diagnosis of known as well as novel plant viruses/viroids using deep sequencing of small RNA (sRNA) pools.

Fluorescence enhancement of a single germanium vacancy center in a nanodiamond by a plasmonic Bragg cavity.

Germanium vacancy (GeV) centers in diamonds constitute a promising platform for single-photon sources to be used in quantum information technologies. Emission from these color centers can be enhanced by utilizing a cavity that is resonant at the peak emission wavelength. We investigate circular plasmonic Bragg cavities for enhancing the emission from single GeV centers in nanodiamonds (NDs) at the zero phonon line. Following simulations of the enhancement for different configuration parameters, the appropriately designed Bragg cavities together with out-coupling gratings composed of hydrogen silsesquioxane ridges are fabricated around the NDs containing nitrogen vacancy centers deposited on a silica-coated silver surface. We characterize the fabricated configurations and finely tune the cavity parameters to match the GeV emission. Finally, we fabricate the cavity containing a single GeV-ND and compare the total decay-rate before and after cavity fabrication, finding a decay-rate enhancement of ∼5.5 and thereby experimentally confirming the feasibility of emission enhancement with circular plasmonic cavities.

E-cigarettes and vaping - a panacea or a bane to smoking in current times?

OBJECTIVE: Use of electronic cigarettes has increased across the world in the last decade with heavy investment from the tobacco industry targeting younger population through well-designed marketing campaigns portraying e-cigarettes as harmless, less addictive and effective in smoking cessation while delivering higher nicotine concentration. The safety profile of e-cigarettes is reviewed in this paper. CONCLUSIONS: The safety of e-cigarettes and the chemicals they contain have not been evaluated rigorously. Emerging data suggest e-cigarette use could do severe harm. People with serious mental illness, already the highest nicotine consumers, could be exploited by the tobacco industry.

Court-ordered assessments and routine access to confidential health information: findings from a regional forensic mental health service.

Health Assessors undertaking court ordered assessments are granted access to material related to the alleged They do not have access to defendant's confidential health records. Defendant's consent must be obtained for their health information to be accessed. One hundred files of court ordered reports were audited, to see whether Health Assessors in a New Zealand regional forensic mental health service had obtained such consent. The results were categorised as follows: Category 1: Consent was provided and health record accessed, c (n = 76). Category 2: Consent was not provided and health information not accessed (n = 5) - included defendants deemed unfit to stand trial and unable to give informed consent (n = 2). Category 3: Consent was not provided but health information accessed (n = 19). Ethical and medico-legal implications of Health Assessors accessing defendant's confidential health records are discussed. Recommendations are made for improving services so that public trust in the integrity of confidential information can be maintained.

Selenolysine: A New Tool for Traceless Isopeptide Bond Formation.

Despite their biological importance, post-translationally modified proteins are notoriously difficult to produce in a homogeneous fashion by using conventional expression systems. Chemical protein synthesis or semisynthesis offers a solution to this problem; however, traditional strategies often rely on sulfur-based chemistry that is incompatible with the presence of any cysteine residues in the target protein. To overcome these limitations, we present the design and synthesis of γ-selenolysine, a selenol-containing form of the commonly modified proteinogenic amino acid, lysine. The utility of γ-selenolysine is demonstrated with the traceless ligation of the small ubiquitin-like modifier protein, SUMO-1, to a peptide segment of human glucokinase. The resulting polypeptide is poised for native chemical ligation and chemoselective deselenization in the presence of unprotected cysteine residues. Selenolysine's straightforward synthesis and incorporation into synthetic peptides marks it as a universal handle for conjugating any ubiquitin-like modifying protein to its target.

Global Access to 3/4-Phosphorylated Heterocycles via a Carbene-Catalyzed Stetter Reaction of Vinylphosphonates and Aldehydes.

The first global method for the preparation of 3-phosphorylated-pyrroles, -furans, -thiophenes, and 4-phosphorylated 2,5-dihydropyridazines is reported. To achieve this, the first protocol for the direct synthesis of α-phosphorylated 1,4-diketones has been developed through a carbene-catalyzed Stetter reaction of vinylphosphonates and aldehydes. This is the first synthetic method for accessing 4-phosphorylated 2,5-dihydropyridazines. This process is metal-free and produces multifunctionalized heterocycles.

Design, synthesis, in vitro and in silico studies of 2, 3-diaryl benzofuran derivatives as antitubercular agents.

As a part of our drug discovery program for anti-tubercular agents, a total of seventeen 2, 3-diaryl benzofuran hybrids were designed, synthesized and screened for their anti-tubercular potential against Mycobacterium tuberculosis H37Ra avirulent strain. Out of seventeen, four derivatives showed significant activity against M. tuberculosis H37Ra avirulent strain (ATCC 25177) with MIC value ranging from 12.5 to 50 µg/mL but out of four, one derivative (9E) was significantly active (MIC 12.5 µg/mL), which was further supported by the molecular docking energy (-8.4 kcal/mol) with respect to the first line anti-tubercular drug, isoniazid (-6.2 kcal/mol) on the target Polyketide Synthase-13. All the derivatives were also evaluated for their cytotoxicity against the normal lung cell line L-132 by the MTT assay and no toxicity was observed up to 27.4 µg/mL concentration. This report on the antitubercular potential of benzofuran derivatives may be of great help in anti-tubercular drug development.

Dopamine acts through Cryptochrome to promote acute arousal in Drosophila.

The fruit fly, Drosophila melanogaster, is generally diurnal, but a few mutant strains, such as the circadian clock mutant Clk(Jrk), have been described as nocturnal. We report here that increased nighttime activity of Clk mutants is mediated by high levels of the circadian photoreceptor CRYPTOCHROME (CRY) in large ventral lateral neurons (l-LN(v)s). We found that CRY expression is also required for nighttime activity in mutants that have high dopamine signaling. In fact, dopamine signaling is elevated in Clk(Jrk) mutants and acts through CRY to promote the nocturnal activity of this mutant. Notably, dopamine and CRY are required for acute arousal upon sensory stimulation. Because dopamine signaling and CRY levels are typically high at night, this may explain why a chronic increase in levels of these molecules produces sustained nighttime activity. We propose that CRY has a distinct role in acute responses to sensory stimuli: (1) circadian responses to light, as previously reported, and (2) noncircadian effects on arousal, as shown here.

Maxillofacial injuries in pregnancy following domestic abuse: A challenge in management.

Domestic violence against women remains one of the most difficult obstacles in the growth of civilization. The maxillofacial region is commonly involved, and injuries are complex to characterize and manage due to diverse presentations, underlying physiological changes and sometimes an association with pregnancy complications, creating a challenge for the operating surgeon. This case report discusses the clinical presentation of maxillofacial injuries sustained by a pregnant woman who also had obstetric complications. The management of such trauma by a multidisciplinary squad led by the maxillofacial surgery team is outlined. Increasing awareness among oral healthcare providers for the early identification of interpersonal abuse along with timely intervention and adequate referral is important. Close monitoring and follow-up are also mandatory.

Role of Platelet-rich Plasma in the Healing of Impacted Third Molar Socket: A Comparative Study on Central India Population.

AIM: The aim of the study was to compare the healing and osseous regeneration of mandibular third molar extraction sockets with and without platelet-rich plasma (PRP) with the evaluation of clinical objectives such as pain, swelling, trismus, soft tissue healing, pocket depth distal to second molar and radiological evaluation of the bony density in the postextracted third molar socket. MATERIALS AND METHODS: In this prospective study, 100 patients were selected by the random sampling method from the outpatient department of oral and maxillofacial surgery in the year 2016-2017. Patients were equally allocated into intervention (transalveolar extraction followed by PRP placement) and nonintervention (transalveolar extraction without PRP placement) group as group I and group II, respectively, and evaluation parameters were considered accordingly. The statistical analysis was done using SPSS (Statistical Package for Social Sciences) Version 15.0 (IBM, USA) statistical analysis software. RESULTS: The pain score of patients of group I (non-PRP) was found to be higher as compared to group II (with PRP). Mean trismus of patients of group II was found to be higher than that of group I at postoperative day 7, but this difference was not found to be statistically significant. Swelling at T-Sn (Tragus-Subnasale) and T-Pog (Tragus-Pogonion) was higher among patients of group I as compared to group II. Healing in group II was two to three times faster than group I. Healing among patients of group I and group II was found to be statistically significant. The mean pocket depth of patients of group I was found to be significantly higher than that of group II at follow-up of 1 and 2 months. The bone density of patients of group II was found to be significantly higher than that of group I at 3 months and 6 months follow-up. CONCLUSION: The procedure of PRP preparation is simple and cost-effective, and can be prepared at the point of care. It had a significant impact on the postoperative healing of the third molar socket. CLINICAL SIGNIFICANCE: The use of PRP application increases the bone density, healing process, and improvement in the pain and swelling, and there was a definite reduction in trismus and periodontal probing depth after the impacted mandibular wisdom teeth extraction.