Genome-wide identification of MATE and ALMT genes and their expression profiling in mungbean (Vigna radiata L.) under aluminium stress.

The Multidrug and toxic compound extrusion (MATE) and aluminium activated malate transporter (ALMT) gene families are involved in response to aluminium (Al) stress. In this study, we identified 48 MATE and 14 ALMT gene families in Vigna radiata genome and classified into 5 (MATE) and 3 (ALMT) clades by phylogenetic analysis. All the VrMATE and VrALMT genes were distributed across mungbean chromosomes. Tandem duplication was the main driving force for evolution and expansion of MATE gene family. Collinearity of mungbean with soybean indicated that MATE gene family is closely linked to Glycine max. Eight MATE transporters in clade 2 were found to be associated with previously characterized Al tolerance related MATEs in various plant species. Citrate exuding motif (CEM) was present in seven VrMATEs of clade 2. Promoter analysis revealed abundant plant hormone and stress responsive cis-elements. Results from quantitative real time-polymerase chain reaction (qRT-PCR) revealed that VrMATE19, VrMATE30 and VrALMT13 genes were markedly up-regulated at different time points under Al stress. Overall, this study offers a new direction for further molecular characterization of the MATE and ALMT genes in mungbean for Al tolerance.

Genome wide identification and expression profiling of ATP binding cassette (ABC) transporters gene family in lentil (Lens culinaris Medikus) under aluminium stress condition.

Adenosine triphosphate-binding cassette transporters (ABC transporters) are involved in regulating plant growth, development and tolerance to environmental stresses. In this study, a total of 138 ABC transporter genes were identified in the lentil genome that were classified into eight subfamilies. Four lentil ABC transporters from subfamily B and I were clustered together with the previously characterized ABC transporter proteins related to aluminium (Al) detoxification. Lentil ABC transporter genes were distributed across the chromosomes. Tandem duplication was the main driving force for expansion of the ABC gene family. Collinearity of lentil with soybean indicated that ABC gene family is closely linked to Glycine max. ABC genes in the same subfamily showed similar gene structure and conserved motifs. The ABC promoter regions harboured a large number of plant hormones and multiple stress responsive cis-regulatory elements. The qRT-PCR showed that ABC genes had varied expression in roots of lentil at different time points under Al stress. This is the first report on genome wide identification and expression analyses of genes encoding ABC transporter genes in lentil which has provided in-depth insight for future research on evolution and elucidation of molecular mechanisms for aluminium tolerance.

To be remembered: B cell memory response against SARS-CoV-2 and its variants in vaccinated and unvaccinated individuals.

COVID-19 disease has plagued the world economy and affected the overall well-being and life of most of the people. Natural infection as well as vaccination leads to the development of an immune response against the pathogen. This involves the production of antibodies, which can neutralize the virus during future challenges. In addition, the development of cellular immune memory with memory B and T cells provides long-lasting protection. The longevity of the immune response has been a subject of intensive research in this field. The extent of immunity conferred by different forms of vaccination or natural infections remained debatable for long. Hence, understanding the effectiveness of these responses among different groups of people can assist government organizations in making informed policy decisions. In this article, based on the publicly available data, we have reviewed the memory response generated by some of the vaccines against SARS-CoV-2 and its variants, particularly B cell memory in different groups of individuals.

Amyloidogenic Propensity of Metabolites in the Uric Acid Pathway and Urea Cycle Critically Impacts the Etiology of Metabolic Disorders.

Novel insights into the etiology of metabolic disorders have recently been uncovered through the study of metabolite amyloids. In particular, inborn errors of metabolism (IEMs), including gout, Lesch-Nyhan syndrome (LNS), xanthinuria, citrullinemia, and hyperornithinemia-hyperammonemia-homocitrullinuria (HHH) syndrome, are attributed to the dysfunction of the urea cycle and uric acid pathway. In this study, we endeavored to understand and mechanistically characterize the aggregative property exhibited by the principal metabolites of the urea cycle and uric acid pathway, specifically hypoxanthine, xanthine, citrulline, and ornithine. Employing scanning electron microscopy (SEM), transmission electron microscopy (TEM), and atomic force microscopy (AFM), we studied the aggregation profiles of the metabolites. Insights obtained through molecular dynamics (MD) simulation underscore the vital roles of π-π stacking and hydrogen bonding interactions in the self-assembly process, and thioflavin T (ThT) assays further corroborate the amyloid nature of these metabolites. The in vitro MTT assay revealed the cytotoxic trait of these assemblies, a finding that was substantiated by in vivo assays employing the Caenorhabditis elegans (C. elegans) model, which revealed that the toxic effects were more pronounced and dose-specific in the case of metabolites that had aged via longer preincubation. We hence report a compelling phenomenon wherein these metabolites not only aggregate but transform into a soft, ordered assembly over time, eventually crystallizing upon extended incubation, leading to pathological implications. Our study suggests that the amyloidogenic nature of the involved metabolites could be a common etiological link in IEMs, potentially providing a unified perspective to study their pathophysiology, thus offering exciting insights into the development of targeted interventions for these metabolic disorders.

Phytochemical Screening of Nyctanthes arbor-tristis Plant Extracts and Their Antioxidant and Antibacterial Activity Analysis.

Nyctanthes arbor-tristis, alias "Vishnu Parijat," is a medicinal plant used to treat various inflammation-associated ailments and to combat innumerable infections in the traditional system of medicine. In the present study, we collected the samples of N. arbor-tristis from the lower Himalayan region of Uttarakhand, India, and carried out their molecular identification through DNA barcoding. To examine the antioxidant and antibacterial activities, we prepared the ethanolic and aqueous extracts (from flowers and leaves) and performed their phytochemical analysis by using different qualitative and quantitative approaches. The phytoextracts showed marked antioxidant potential, as revealed by a comprehensive set of assays. The ethanolic leaf extract showed marked antioxidant potential towards DPPH, ABTS, and NO scavenging (IC50 = 30.75 ± 0.006, 30.83 ± 0.002, and 51.23 ± 0.009 µg/mL, respectively). We used TLC-bioautography assay to characterize different antioxidant constituents (based on their Rf values) in the chromatograms ran under different mobile phases. For one of the prominent antioxidant spots in TLC bioautography, GC-MS analysis identified cis-9-hexadecenal and n-hexadecanoic acid as the major constituents. Furthermore, in antibacterial study, the ethanolic leaf extract showed marked activity against Aeromonas salmonicida (113.40 mg/mL of extract was equivalent to 100 µg/mL of kanamycin). In contrast, the ethanolic flower extract showed considerable antibacterial activity against Pseudomonas aeruginosa (125.85 mg/mL of extract ≡100 µg/mL of kanamycin). This study presents the phylogenetic account and unravels the antioxidant-related properties and antibacterial potential of N. arbor-tristis.

Patterns and outcomes of weekend admission for acute ischemic stroke.

BACKGROUND AND OBJECTIVES: The "weekend effect" describes worse care delivery during off-hours or weekends and has been demonstrated in multiple sub-specialties. Off-hours care for acute ischemic stroke (AIS) has been associated with poorer outcomes. However, there is less data about the "weekend effect" on endovascular thrombectomy (ET) outcomes. METHODS: We used Medicare 100% sample datasets and included all AIS admissions from 2018-2019, using validated International Classification of Diseases, 10th Revision, Clinical Modification codes to identify AIS and comorbidities. Medicare provides the date of admission for all hospitalizations, and the day of the week was determined and assigned to weekend (Saturday or Sunday) or weekday (Monday through Friday). We defined 3 major outcomes: inpatient mortality, discharge home (vs. other destination), and 30-day mortality. RESULTS: Among 471427 AIS admissions,13.0% and 12.9% of all AIS admissions occurred on a Saturday and Sunday, respectively, less than the expected 14.3% occurring on any given day (p-value <0.0001). AIS admissions on a weekend were less likely to receive IV thrombolysis (13.6% on Saturday and 12.9% on Sunday) and ET (13.1% on Saturday and 13.2% on Sunday), p-value <0.0001. Among all AIS admissions, weekend admission was associated with worse outcomes, including higher odds of inpatient mortality (adjusted OR 1.04 [95% CI 1.01-1.08, p<0.0001]), lower odds of discharge home (0.94 [0.93-0.96, p<0.0001]), and higher odds of 30-day mortality (1.06 [1.04-1.08, p<0.0001]). However, among AIS patients treated with ET, there was no association of weekend admission with outcomes. CONCLUSIONS: In this national and contemporary dataset, we observed that the proportion of thrombolysis and ET cases was less over the weekend, and outcomes (inpatient mortality, 30-day mortality and odds of discharge home) were worse overall. We did not observe this association among AIS patients undergoing ET on a weekend vs. weekday.

A single site mutation can induce functional promiscuity in homoserine kinase.

L-Homoserine kinase is crucial in the biosynthesis of L-threonine, L-isoleucine, and L-methionine, where it catalyzes ATP-dependent phosphorylation of L-homoserine (Hse) to yield L-homoserine phosphate as its native activity. However, a single site mutation of H138 → L shows the emergence of ATPase activity as a secondary function. However, a previous mechanistic study proposes direct involvement of ATP and the substrate without any catalytic base; therefore, how the mutation of H138 → L causes the secondary function remains an enigma. Using computational tools herein, we provide new insight into the catalytic mechanism of L-homoserine kinase, showing direct involvement of H138 as a catalytic base. We show that mutation of H138 → L opens a new water channel connecting ATP, which facilitates the ATPase activity and reduces the native activity. The proposed mechanism agrees with the experimental finding that an H138 → L mutation reduces the kinase activity but enhances a promiscuous function, i.e. ATPase activity. Since homoserine kinase catalyzes the biosynthesis of amino acids, we believe that an accurate mechanism could be significant for enzyme engineering to synthesize amino acid analogs.

Patterns in the number of interventionalists for endovascular treatment of acute ischemic stroke in the US.

BACKGROUND: Endovascular thrombectomy (ET) has become the standard of stroke care for large vessel occlusion acute ischemic stroke (AIS) involving the anterior circulation. With continued eligibility expansion, the demand for neuro-intervention is growing. Current estimates indicate inadequate supply of interventionalists. However, there is limited data describing the number of interventionalists per hospital in the US, and correlations with outcomes. METHODS: We used Medicare 100% sample datasets and included all AIS admissions from 2018 to 2019, using validated International Classification of Diseases, 10th Revision, Clinical Modification codes to identify AIS and comorbidities. We utilized National Provider Identifier codes to identify distinct interventionalists at the hospital. We examined outcomes at the hospital level, including percent of AIS treated with thrombolysis, percent of AIS with inpatient mortality, percent of AIS with discharge home, and percent of AIS with death within 30 days. RESULTS: Among 471,427 AIS admissions, 16,253 received ET over the 2-year period of the study. Only 683 of 4576 AIS-treating institutions provided ET (14.9%). These ET centers most frequently only had one interventionalist performing ET and were clustered in large metropolitan areas with high AIS volumes. As AIS volumes, ET volumes, and mean NIHSS scores increased, so did the number of interventionalists. With each additional interventionalist, there was an increased likelihood of poor outcomes including inpatient mortality, discharge home, and 30-day mortality. CONCLUSIONS: We confirmed a relative lack of neuro-interventionalists among US hospitals, with a concentration of interventionalists in urban, high-volume centers. The greater likelihood of poor outcomes associated with increasing number of interventionalists is likely due to increasing complexity and severity of cases at high-volume ET centers, but further study is needed.

The Performance of Different Water Models on the Structure and Function of Cytochrome P450 Enzymes.

Modeling approaches and modern simulations to investigate the biomolecular structure and function rely on various methods. Since water molecules play a crucial role in all sorts of chemistry, the accurate modeling of water molecules is vital for such simulations. In cytochrome P450 (CYP450), in particular, water molecules play a key role in forming active oxidant that ultimately performs oxidation and metabolism. In the present study, we have highlighted the behavior of the three most widely used water models─TIP3P, SPC/E, and OPC─for three different CYP450 enzymes─CYP450BM3, CYP450OleT, and CYP450BSß─during MD simulations and QM/MM calculations. We studied the various properties, such as RMSD, RMSF, H-bond, water occupancy, and hydrogen atom transfer (HAT), using QM/MM calculations and compared them for all three water models. Our study shows that the stabilities of the enzyme complexes are well maintained in all three water models. However, the OPC water model performs well for the polar active sites, that is, in CYP450OleT and CYP450BSß, while the TIP3P water model is superior for the hydrophobic site, such as CYP450BM3.

Combined MD and QM/MM Calculations Reveal Allostery-Driven Promiscuity in Dipeptide Epimerases of Enolase Family.

The adaptability of the active site to amplify the secondary function is supposed to be the fundamental cause of the promiscuity and the evolution of new functions in enzymes. In most cases, mutations occur close to the active site and/or in the catalytic site to change the active site plasticity to accommodate the non-native substrate. In the present study, using MD simulations and hybrid QM/MM calculations, we have shown a way to enhance the promiscuity, i. e., the allostery-driven promiscuity. Using a case study of the AEE enzyme where the capping loop recognizes the substrate, herein, we show that a single site mutation (D321G) far from the capping loop can induce a large conformational change in the capping loop to recognize different substrates for different functions. The QM/MM calculations for the WT and mutated enzyme provide a first validation of the mechanism of 1,1-proton transfer and dehydration by the AEE enzyme. Since AEE epimerase possesses a highly conserved TIM-barrel fold, we believe that our study provides a crucial lead to understanding the mechanism of emergence of secondary function which can be useful to repurpose ancient enzymes for modern usage.

A facile synthesis of palladium nanoparticles decorated bismuth oxybromide nanostructures with exceptional photo-antimicrobial activities.

Assessing the interaction between microbes and nanocatalysts for finding an inclusive, proactive and deep understanding of nanoparticles-based toxicity is vital for discovering their broad range of applications. Palladium based photocatalysts owing to their unique fundamental characteristics and brilliant physicochemical potential have gained immense interest in environment remediation as disinfection system. In the present study, we report synthesis of a novel palladium nanoparticles decorated bismuth oxybromide (Pd/BiOBr) nanostructures using an energy efficient solution-based method, having excellent photocatalytic antibacterial action. The synthesized nanomaterials was thoroughly characterized using various analytical techniques. The photocatalytic antibacterial efficiency of Pd/BiOBr was evaluated against some common pathogenic strains of Gram-positive and Gram-negative bacteria (Pseudomonas fluorescens, Pseudomonas aeruginosa, Escherichia coli, Aeromonas salmonicida, Salmonella typhimurium, Klebsiella pneumoniae, Bacillus subtilis). In our results Pd/BiOBr showed excellent photocatalytic disinfection efficacy with > 99.9% bacterial inactivation. A very low concentration of Pd/BiOBr (0.5 µg/mL) effectively inhibited the bacterial growth in response to just 2 h of visible light irradiation, while 1 µg/mL of Pd/BiOBr completely killed all the tested bacterial strains proving their magnificent bactericidal potential. The developed materials with exceptional antibacterial broad range efficiency can be used in different photocatalytic disinfection systems including water purification systems, biofilm exclusion and combating differential antibiotic resistance.

A Review of Anti-Cancer and Related Properties of Lichen-Extracts and Metabolites.

BACKGROUND: Lichens are a composite consortium of a fungus and an alga. The symbiotic organisms are naturally equipped with distinct characteristics as compared to constituting organisms separately. Lichens, due to their peculiar anatomy and physiology, are the reservoir of more than 600 unique secondary metabolites, also known as 'lichen substances'. Since ancient times, many ethnic groups from various parts of the world have known about the applications of lichens as major provenance of food/fodder, medicine, dyes, spices, perfumes, etc. Lichen substances have shown impressive antioxidant, antimicrobial, antiviral, anti-tumor, and antiinflammatory activities under experimental conditions. Usnic acid, a well-known metabolite found in several species of lichens, possesses potent antioxidant and anti-inflammatory activities. It also has significant antiproliferative potential, as revealed through testing in different cancer cell lines. Atranorin, Lecanoric acid, Norstictic acid, Lobaric acid, Stictic acid, Ramalin, Gyrophoric acid, Salazinic acid, Protolichesterinic, and Fumarprotocetraric acid are some of the other purified lichen-metabolites with potent anti-cancer activities. OBJECTIVE: This study presents an overview of lichen-derived extracts and compounds showing anti-cancer (or related) properties. METHOD: The review comprehends different studies (in vivo and in vitro) backing up the possibility of lichenextracts and metabolites towards their use as antioxidant, anti-proliferative, anti-inflammatory, and Epithelialmesenchymal transition (EMT) -inhibiting agents. RESULTS: Various studies carried out to date show that lichen-extracts and metabolites have a range of anti-cancer and related properties that include anti-oxidative, anti-inflammatory, anti-proliferative, pro-apoptotic, and the potential of inhibition of cancer-associated EMT that is responsible for drug resistance and metastasis of cancer cells in a substantial proportion of cases. CONCLUSION: Lichens are the repertoire of a plethora of lichen-metabolites with significant anti-cancer potential. However, some of the critical 'anti-cancer related' properties, such as the ability of EMT-inhibition and the potential of induction of apoptosis, are relatively less studied for several lichen compounds. Additionally, many lichen compounds need to be purified at a larger scale to explore their anti-cancer potential.

Adhesins in the virulence of opportunistic fungal pathogens of human.

Aspergillosis, candidiasis, and cryptococcosis are the most common cause of mycoses-related disease and death among immune-compromised patients. Adhesins are cell-surface exposed proteins or glycoproteins of pathogens that bind to the extracellular matrix (ECM) constituents or mucosal epithelial surfaces of the host cells. The forces of interaction between fungal adhesins and host tissues are accompanied by ligand binding, hydrophobic interactions and protein-protein aggregation. Adherence is the primary and critical step involved in the pathogenesis; however, there is limited information on fungal adhesins compared to that on the bacterial adhesins. Except a few studies based on screening of proteome for adhesin identification, majority are based on characterization of individual adhesins. Recently, based on their characteristic signatures, many putative novel fungal adhesins have been predicted using bioinformatics algorithms. Some of these novel adhesin candidates have been validated by in-vitro studies; though, most of them are yet to be characterised experimentally. Morphotype specific adhesin expression as well as tissue tropism are the crucial determinants for a successful adhesion process. This review presents a comprehensive overview of various studies on fungal adhesins and discusses the targetability of the adhesins and adherence phenomenon, for combating the fungal infection in a preventive or therapeutic mode.

Molecular and biological characterization of soybean yellow mottle mosaic virus severe strain infecting soybean in India.

The complete nucleotide sequence and genome organization of soybean yellow mottle mosaic virus severe strain causing bright yellow mosaic, mottling and puckering symptoms in soybean (Glycine max) from India was determined. The monopartite single stranded genomic RNA is 3974 nuclotides long and has the potential to encode six viral proteins viz., p25, p83, p8, p10, p39 and p25. The SYMMV-Sb isolate differed from mungbean strain with 69 nucleotides and nine aminoacids dispersed over the various ORFs. Comparative sequence analysis revealed that SYMMV-Sb shared 98% nt sequence identity at complete genome level and 96-100% at all ORFs level with SYMMV mungbean strain from India and 71-92% identity with SYMMV Korean soybean isolate, whereas it showed very low sequence identity with other tombusviridae members (2-53%). The phylogenetic analysis showed the clustering of SYMMV-Sb along with other members of genus Gammacarmovirus. The SYMMV-Sb isolate produced chlorotic blotches, mild and veinal mottling, necrosis and puckering symptoms in various leguminous host plants. The symptomatalogy of the soybean isolate was differed from mungbean strain as earlier induced severe symptoms on soybean and mild symptoms on mungbean. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02925-2.

Seed transmission of a distinct soybean yellow mottle mosaic virus strain identified from India in natural and experimental hosts.

Soybean yellow mottle mosaic virus (SYMMV) is a newly identified member of the genus Gammacarmovirus from grain legumes in India. As the modes of transmission of this virus have not been described, we assessed the possibility of SYMMV to be transmitted through seed collected from field infected mungbean plants and mechanically sap inoculated French bean plants using serological and molecular techniques followed by progeny assays. Direct antigen coated enzyme linked immunosorbent assay (DAC-ELISA) and reverse transcription polymerase chain reaction (RT-PCR) results are inconsistent with field infected mungbean seed tissues to ensure seed transmissibility irrespective of seed number used. Seed from mechanical sap inoculated French bean showed higher absorbance values in DAC-ELISA and amplification corresponding to replicase, movement and coat protein regions of SYMMV genome. The relative accumulation of SYMMV was higher in pod walls, immature seed and stamens and stigma of mechanical sap inoculated French bean. Progeny assays with infected seed revealed the seed transmissibility of SYMMV at the rate of 63.33% in mungbeanand 73.33% in French bean. Mechanical sap inoculation of mungbean progeny seedlings on French bean cv. Pusa Parvati produced characteristic symptoms of SYMMV. The results obtained from this study demonstrate that SYMMV is seed borne in nature and can be transmitted to next generation seedlings. This is the first report of seed transmission of SYMMV in mungbean and French bean.

Iodine-Catalyzed Aerobic Diazenylation-Amination of Indole Derivatives.

A mild strategy for consecutive diazenylation and amination of indole moieties has been demonstrated. The functionalization occurs at C3 and C2 carbon atoms, respectively, at the indole scaffold in the presence of catalytic iodine and air at 40 °C in the 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) solvent. It is noteworthy that the aromatic amines are generated in situ by the reaction of aryl hydrazine with iodine. In general, bright red products are obtained in moderate to good yield. Control reactions are conducted to establish the reaction mechanism.

Transformed yeast (Schizosaccharomyces pombe) overexpressing rice Tau class glutathione S-transferase (OsGSTU30 and OsGSTU41) shows enhanced resistance to hexavalent chromium.

Extensive use of hexavalent chromium [Cr(VI)] in leather tanning, stainless-steel production, wood preservatives and electroplating industries has resulted in widespread environmental pollution and poses a serious threat to human health. A plant's response to Cr(VI) stress results in growth inhibition and toxicity leading to changes in components of antioxidant systems. In a previous study, we observed that a large number of glutathione S-transferase (GST) genes were up-regulated under Cr(VI) stress in rice. In this study, two rice root-specific Tau class GST genes (OsGSTU30 and OsGSTU41) were introduced into yeast (Schizosaccharomyces pombe). Transformed yeast cells overexpressing OsGSTU30 and OsGSTU41 had normal growth, but had much higher levels of GST activities and showed enhanced resistance to Cr(VI) as compared to control cells (transformed with empty vector). Also, a higher accumulation of chromium was found in the transformed yeast cells as compared to the control cells. Manipulation of glutathione biosynthesis by exogenous application of buthionine sulfoximine abolishes the protective effect of OsGSTs against Cr(VI) stress. These results suggest that Tau class OsGSTs play a significant role in detoxification of Cr(VI), probably by chelating and sequestrating glutathione-Cr(VI) complexes into vacuoles.