RESUMEN
Bos indicus cattle breeds have been naturally selected for thousands of years for disease resistance and thermo-tolerance. However, the genetic mechanisms underlying these specific inherited characteristics must be elucidated. Hence, in this study, a whole-genome comparative analysis of the Bos indicus cattle breeds Kangayam, Tharparkar, Sahiwal, Red Sindhi, and Hariana of the Indian subcontinent was conducted. Genetic variant identification analysis revealed 155 851 012 SNPs and 10 062 805 InDels in the mapped reads across all Bos indicus cattle breeds. The functional annotation of 17 252 genes that comprised both SNPs and InDels, with high functional impact on proteins, was carried out. The functional annotation results revealed the pathways involved in the innate immune response, including toll-like receptors, retinoic acid-inducible gene I-like receptors, NOD-like receptors, Jak-STAT signaling pathways, and non-synonymous variants in the candidate immune genes. We also identified several pathways involved in the heat shock response, hair and skin properties, oxidative stress response, osmotic stress response, thermal sweating, feed intake, metabolism, and non-synonymous variants in the candidate thermo-tolerant genes. These pathways and genes directly or indirectly contribute to the disease resistance and thermo-tolerance adaptations of Bos indicus cattle breeds.
Asunto(s)
Resistencia a la Enfermedad , Termotolerancia , Animales , Bovinos/genética , Resistencia a la Enfermedad/genética , Genoma , Mutación INDEL , Polimorfismo de Nucleótido Simple , Termotolerancia/genéticaRESUMEN
Elucidation of the molecular pathogenesis underlying virus-host interactions is important for the development of new diagnostic and therapeutic strategies against highly pathogenic avian influenza (HPAI) virus infection in chickens. However, the pathogenesis of HPAI virus in chickens is not completely understood. To identify the intracellular signaling pathways and critical host proteins associated with influenza pathogenesis, we analyzed the lung proteome of a chicken infected with HPAI H5N1 virus (A/duck/India/02CA10/2011/Agartala). Mass spectrometry data sets were searched against the chicken UniProt reference database. At the local false discovery rate level of 5%, a total of 3313 proteins with the presence of at least one unique peptide were identified in the chicken lung proteome datasets. Differential expression analysis of these proteins showed that 247 and 1754 proteins were downregulated at 12 h and 48 h postinfection, respectively. We observed expression of proteins of the predominant signaling pathways, including Toll-like receptors (TLRs), retinoic acid-inducible gene I-like receptors (RLRs), NOD-like receptors (NLRs), and JAK-STAT signaling. Activation of these pathways is associated with the cytokine storm effect and thus may be the cause of the severity of HPAI H5N1 infection in chickens. We also observed the expression of myeloid differentiation primary response protein (MyD88), inhibitor of nuclear factor kappa B kinase subunit beta (IKBKB), interleukin 1 receptor associated kinase 4 (IRAK4), RELA proto-oncogene NF-κB subunit (RELA), and mitochondrial antiviral signaling protein (MAVS), which are involved in critical signaling pathways, as well as other, less-commonly identified proteins such as hepatocyte nuclear factor 4 alpha (HNF4A), ELAV-like RNA binding protein 1 (ELAVL1), fibronectin 1 (FN1), COP9 signalosome subunit 5 (COPS5), cullin 1 (CUL1), breast cancer type 1 susceptibility protein (BRCA1), and the FYN proto-oncogene Src family tyrosine kinase (FYN) as main hub proteins that might play important roles in influenza pathogenesis in chickens. In summary, we identified the signaling pathways and the proteomic determinants associated with disease pathogenesis in chickens infected with HPAI H5N1 virus.
Asunto(s)
Subtipo H5N1 del Virus de la Influenza A , Gripe Aviar , Animales , Pollos , Subtipo H5N1 del Virus de la Influenza A/genética , Gripe Aviar/genética , Pulmón , ProteómicaRESUMEN
In May 2021, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detected in Asiatic lions in a zoological park in India. Sequence and phylogenetic analyses showed the SARS-CoV-2 strains were the B.1.617.2 (Delta) variant. To reduce transmission of variants of concern, surveillance of SARS-CoV-2 in wild animal populations should be increased.
Asunto(s)
COVID-19 , Leones , Animales , Humanos , Filogenia , SARS-CoV-2RESUMEN
In this study, we report the complete genome sequence of swinepox virus from a clinical sample from a naturally occurring infection in India. The sequencing was done on a Nanopore MinION sequencer from Oxford Nanopore Technologies. Two new annotations were added to the genome. Three of the genes were found to have frameshifts, which might be of importance in relation to infection. When compared to the only other reported whole genome sequence of swinepox virus, which was obtained from an isolate from America in 1999, our sequence is only 98.19% identical at the nucleotide level. The average amino acid sequence identity of the viral proteins, based on the common 149 annotations, is also 98.19%, demonstrating that these viruses are distinctly divergent. Owing to the fact that swinepox virus infects only swine, it could not have entered America until the introduction of swine in the 16th century from Europe. The swinepox viruses in both continents have continued to evolve independently. The sequence divergence identified here indicates a Eurasian-lineage virus that is geographically distinct from the American-lineage swinepox virus.
Asunto(s)
Genoma Viral/genética , Infecciones por Poxviridae/veterinaria , Suipoxvirus/genética , Enfermedades de los Porcinos/virología , Animales , ADN Viral/genética , Variación Genética , India , Infecciones por Poxviridae/virología , Análisis de Secuencia de ADN , Homología de Secuencia , Suipoxvirus/clasificación , Suipoxvirus/aislamiento & purificación , Porcinos , Proteínas Virales/genéticaRESUMEN
MAIN CONCLUSIONS: Low temperature decreases PSII damage in vivo, confirming earlier in vitro results. Susceptibility to photoinhibition differs among Arabidopsis accessions and moderately decreases after 2-week cold-treatment. Flavonols may alleviate photoinhibition. The rate of light-induced inactivation of photosystem II (PSII) at 22 and 4 °C was measured from natural accessions of Arabidopsis thaliana (Rschew, Tenela, Columbia-0, Coimbra) grown under optimal conditions (21 °C), and at 4 °C from plants shifted to 4 °C for 2 weeks. Measurements were done in the absence and presence of lincomycin (to block repair). PSII activity was assayed with the chlorophyll a fluorescence parameter Fv/Fm and with light-saturated rate of oxygen evolution using a quinone acceptor. When grown at 21 °C, Rschew was the most tolerant to photoinhibition and Coimbra the least. Damage to PSII, judged from fitting the decrease in oxygen evolution or Fv/Fm to a first-order equation, proceeded more slowly or equally at 4 than at 22 °C. The 2-week cold-treatment decreased photoinhibition at 4 °C consistently in Columbia-0 and Coimbra, whereas in Rschew and Tenela the results depended on the method used to assay photoinhibition. The rate of singlet oxygen production by isolated thylakoid membranes, measured with histidine, stayed the same or slightly decreased with decreasing temperature. On the other hand, measurements of singlet oxygen from leaves with Singlet Oxygen Sensor Green suggest that in vivo more singlet oxygen is produced at 4 °C. Under high light, the PSII electron acceptor QA was more reduced at 4 than at 22 °C. Singlet oxygen production, in vitro or in vivo, did not decrease due to the cold-treatment. Epidermal flavonols increased during the cold-treatment and, in Columbia-0 and Coimbra, the amount correlated with photoinhibition tolerance.
Asunto(s)
Arabidopsis/fisiología , Complejo de Proteína del Fotosistema II/metabolismo , Oxígeno Singlete/metabolismo , Aclimatación , Arabidopsis/efectos de la radiación , Clorofila A/análisis , Frío , Fluorescencia , Complejo de Proteína del Fotosistema II/efectos de la radiación , Hojas de la Planta/fisiología , Hojas de la Planta/efectos de la radiación , Oxígeno Singlete/efectos de la radiaciónRESUMEN
MicroRNAs (miRNAs) are small noncoding RNAs that are crucial posttranscriptional regulators for host mRNAs. Recent studies indicate that miRNAs may modulate host response during RNA virus infection. However, the role of miRNAs in immune response against H5N1 infection is not clearly understood. In this study, we showed that expression of cellular miRNA miR-324-5p was downregulated in A549 cells in response to infection with RNA viruses H5N1, A/PR8/H1N1, and Newcastle disease virus (NDV) and transfection with poly(I·C). We found that miR-324-5p inhibited H5N1 replication by targeting the PB1 viral RNA of H5N1 in host cells. In addition, transcriptome analysis revealed that miR-324-5p enhanced the expression of type I interferon, type III interferon, and interferon-inducible genes (ISGs) by targeting CUEDC2, the negative regulator of the JAK1-STAT3 pathway. Together, these findings highlight that the miR-324-5p plays a crucial role in host defense against H5N1 by targeting viral PB1 and host CUEDC2 to inhibit H5N1 replication.IMPORTANCE Highly pathogenic influenza A virus (HPAIV) continues to pose a pandemic threat globally. From 2003 to 2017, H5N1 HPAIV caused 453 human deaths, giving it a high mortality rate (52.74%). This work shows that miR-324-5p suppresses H5N1 HPAIV replication by directly targeting the viral genome (thereby inhibiting viral gene expression) and cellular CUEDC2 gene, the negative regulator of the interferon pathway (thereby enhancing antiviral genes). Our study enhances the knowledge of the role of microRNAs in the cellular response to viral infection. Also, the study provides help in understanding how the host cells utilize small RNAs in controlling the viral burden.
Asunto(s)
Proteínas Portadoras/genética , Interacciones Huésped-Patógeno , Subtipo H1N1 del Virus de la Influenza A/genética , Subtipo H5N1 del Virus de la Influenza A/genética , Proteínas de la Membrana/genética , MicroARNs/genética , Virus de la Enfermedad de Newcastle/genética , Proteínas Virales/genética , Células A549 , Proteínas Adaptadoras Transductoras de Señales , Animales , Proteínas Portadoras/inmunología , Pollos , Regulación de la Expresión Génica , Células HEK293 , Células HeLa , Humanos , Subtipo H1N1 del Virus de la Influenza A/inmunología , Subtipo H5N1 del Virus de la Influenza A/inmunología , Gripe Humana/genética , Gripe Humana/inmunología , Gripe Humana/virología , Interferones/genética , Interferones/inmunología , Janus Quinasa 1/genética , Janus Quinasa 1/inmunología , Proteínas de la Membrana/inmunología , MicroARNs/inmunología , Virus de la Enfermedad de Newcastle/inmunología , Infecciones por Orthomyxoviridae/genética , Infecciones por Orthomyxoviridae/inmunología , Infecciones por Orthomyxoviridae/virología , Poli I-C/genética , Poli I-C/inmunología , Factor de Transcripción STAT3/genética , Factor de Transcripción STAT3/inmunología , Transducción de Señal , Carga Viral , Proteínas Virales/inmunología , Replicación ViralRESUMEN
Cold acclimation modifies the photosynthetic machinery and enables plants to survive at sub-zero temperatures, whereas in warm habitats, many species suffer even at non-freezing temperatures. We have measured chlorophyll a fluorescence (ChlF) and CO2 assimilation to investigate the effects of cold acclimation, and of low temperatures, on a cold-sensitive Arabidopsis thaliana accession C24. Upon excitation with low intensity (40 µmol photons m- 2 s- 1) ~ 620 nm light, slow (minute range) ChlF transients, at ~ 22 °C, showed two waves in the SMT phase (S, semi steady-state; M, maximum; T, terminal steady-state), whereas CO2 assimilation showed a linear increase with time. Low-temperature treatment (down to - 1.5 °C) strongly modulated the SMT phase and stimulated a peak in the CO2 assimilation induction curve. We show that the SMT phase, at ~ 22 °C, was abolished when measured under high actinic irradiance, or when 3-(3, 4-dichlorophenyl)-1, 1- dimethylurea (DCMU, an inhibitor of electron flow) or methyl viologen (MV, a Photosystem I (PSI) electron acceptor) was added to the system. Our data suggest that stimulation of the SMT wave, at low temperatures, has multiple reasons, which may include changes in both photochemical and biochemical reactions leading to modulations in non-photochemical quenching (NPQ) of the excited state of Chl, "state transitions," as well as changes in the rate of cyclic electron flow through PSI. Further, we suggest that cold acclimation, in accession C24, promotes "state transition" and protects photosystems by preventing high excitation pressure during low-temperature exposure.
Asunto(s)
Arabidopsis/metabolismo , Fotosíntesis/fisiología , Aclimatación , Clorofila A/metabolismo , Frío , TemperaturaRESUMEN
Pigeon paramyxovirus type 1 (PPMV-1) is an antigenic variant of avian paramyxovirus type 1 (APMV-1), which infects pigeons. The virus causes high morbidity and mortality, creating an alarming state for the poultry industry. The present work describes the molecular and pathogenic characterization of a PPMV-1 strain isolated from pigeon in Bhopal, India. Complete genome sequence analysis revealed a genome of 15,192 nucleotides encoding six genes organized in the order 3'-N-P-M-F-HN-L-5'. The fusion gene sequence analysis showed the presence of multiple basic amino acids 112R-R-Q-K-R-F117 at the cleavage site corresponding to pathogenic strains. The mean death time and intracerebral pathogenicity index values indicated a mesogenic nature for the PPMV-1 isolate. On phylogenetic analysis, the strain clustered with genotype VI viruses, including isolates from pigeon and dove. The Bhopal strain showed significant intra and inter-genotype evolutionary distance, suggesting the emergence of a new sub-genotype, VIj.
Asunto(s)
Columbidae/virología , Enfermedad de Newcastle/virología , Virus de la Enfermedad de Newcastle/clasificación , Animales , Genoma Viral , Genotipo , India , Virus de la Enfermedad de Newcastle/genética , Virus de la Enfermedad de Newcastle/aislamiento & purificación , Filogenia , Proteínas Virales/genéticaRESUMEN
The jungle crow (Corvus macrorhynchos) belongs to the order Passeriformes of bird species and is important for avian ecological and evolutionary genetics studies. However, there is limited information on the transcriptome data of this species. In the present study, we report the characterization of the lung transcriptome of the jungle crow using GS FLX Titanium XLR70. Altogether, 1,510,303 high-quality sequence reads with 581,198,230 bases was de novo assembled into 22,169 isotigs (isotig represents an individual transcript) and 784,009 singletons. Using these isotigs and 581,681 length-filtered (greater than 300 bp) singletons, 20,010 unique protein-coding genes were identified by BLASTx comparison against a nonredundant (nr) protein sequence database. Comparative analysis revealed that 46,604 (70.29%) and 51,642 (72.48%) of the assembled transcripts have significant similarity to zebra finch and chicken RefSeq proteins, respectively. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Transcripts putatively involved in the immune response were identified. Furthermore, 20,599 single nucleotide polymorphisms (SNPs) and 7525 simple sequence repeats (SSRs) were retrieved from the assembled transcript database. This resource should lay an important base for future ecological, evolutionary, and conservation genetic studies on this species and in other related species.
Asunto(s)
Cuervos/genética , Pulmón/metabolismo , Transcriptoma , Animales , Proteínas Aviares/genética , Pollos/genética , Cuervos/metabolismo , Pinzones/genética , Perfilación de la Expresión Génica , Ontología de Genes , Marcadores Genéticos , Fenómenos del Sistema Inmunológico/genéticaRESUMEN
MicroRNAs (miRNAs) play a crucial role in cancer progression by selectively inducing translational degradation of messenger RNA (mRNA) via sequence-specific interactions with the 3'-untranslated region (3'-UTR). The potential targeting of miRNA has been recognized as a significant avenue for investigating the biological progression of diverse cancer types. Consequently, targeting of pri-miRNA and pre-miRNA by phytochemicals emerges as a viable strategy in the realm of anticancer therapies. Among phytochemicals, triterpenoids have garnered significant recognition for their chemotherapeutic and chemopreventive capabilities in combating multiple cancers. To date, there is a dearth of literature about the molecular interactions between triterpenoids and miRNAs. The primary objective of this investigation is to discern the potential triterpenoids that can function as modulators for specific miRNAs, namely pri-miRNA-19b-2, pre-miR21, microRNA 20b, pri-miRNA-208a, pri-miRNA-378a, pri-miRNA-320b-2, and pri-miRNA-300, achieved through the use of in silico investigations. The study primarily focused on performing drug-likeness, computer-aided toxicity, and pharmacokinetic prediction studies for triterpenoids. Furthermore, molecular docking and simulation techniques were employed to investigate these compounds. The triterpenoids studied were shown to have drug-likeness characteristics, although asiatic acid, lupeol, and pristimerin were able to pass all toxicity tests. Among the triterpenoids that underwent docking, pristimerin had a significant binding energy of -10.9 kcal/mol during its interaction with pri-miR-378a. The stable interaction between the pristimerin and miRNA complex was demonstrated by molecular dynamics simulation. As a result, pristimerin has the potential to act as a modulator of carcinogenic miRNAs, making it a promising candidate for cancer prevention and treatment due to its tailored modulation of miRNA activity.
Asunto(s)
MicroARNs , Neoplasias , Triterpenos Pentacíclicos , Triterpenos , Humanos , Procesamiento Postranscripcional del ARN , Triterpenos/farmacología , Angiogénesis , Simulación del Acoplamiento Molecular , Precursores del ARN/metabolismo , MicroARNs/metabolismo , Neoplasias/tratamiento farmacológico , Neoplasias/genética , Proliferación CelularRESUMEN
Green synthesis methods offer a cost-effective and environmentally friendly approach to producing nanoparticles (NPs), particularly metal-based oxides. This study explores the green synthesis of copper oxide nanoparticles using Aloe vera (Aloe barbadensis Miller) leaf extract. The characterization revealed a unique sago-shaped morphology revealed by field-emission scanning electron microscopy and X-ray diffraction analysis. Distinctive metal-oxygen bonds at 521 and 601 cm-1 were confirmed by Fourier-transform infrared (FT-IR) spectroscopy. Furthermore, UV-visible spectroscopy revealed absorbance at 248 nm, suggesting electron transitions across energy bands and varying surface conduction electrons. The band gap value indicated the presence of quantum confinement effects, which were probably caused by the distinctive morphology and surface structure of the biogenic NPs. Additionally, molecular docking studies were carried out against key proteins of Salmonella typhi and Listeria monocytogenes, namely, listeriolysin O (PDB ID: 4CDB), internalin (InlA) (PDB ID: 1O6T), Salmonella effector protein (SopB) (PDB ID: 4DID), and YfdX (PDB ID: 6A07) using AutoDock 4.2. The results revealed binding energies against S. typhi and L. monocytogenes proteins, indicating potential interactions establishing the foundation for further in-depth understanding of the molecular basis underlying the observed antibacterial effects in vitro against S. typhi, Klebsiella pneumoniae, Pseudomonas aeruginosa, and L. monocytogenes. Antibacterial activity evaluation yielded impressive results, with CuO NPs displaying significant activity against S. typhi and L. monocytogenes, exhibiting zones of inhibition values of 13 ± 0.02 and 15 ± 0.04 mm, respectively. Moreover, the CuO NPs demonstrated remarkable photocatalytic efficacy, resulting in the degradation of 77% of the methylene blue dye when exposed to UV irradiation. This study highlighted the potential of green-synthesized CuO NPs derived from A. vera with their unique morphology, interesting spectroscopic properties, and promising antibacterial and photocatalytic activities.
RESUMEN
Domestic ducks (Anas platyrhynchos domesticus) are resistant to most of the highly pathogenic avian influenza virus (HPAIV) infections. In this study, we characterized the lung proteome and phosphoproteome of ducks infected with the HPAI H5N1 virus (A/duck/India/02CA10/2011/Agartala) at 12 h, 48 h, and 5 days post-infection. A total of 2082 proteins were differentially expressed and 320 phosphorylation sites mapping to 199 phosphopeptides, corresponding to 129 proteins were identified. The functional annotation of the proteome data analysis revealed the activation of the RIG-I-like receptor and Jak-STAT signaling pathways, which led to the induction of interferon-stimulated gene (ISG) expression. The pathway analysis of the phosphoproteome datasets also confirmed the activation of RIG-I, Jak-STAT signaling, NF-kappa B signaling, and MAPK signaling pathways in the lung tissues. The induction of ISG proteins (STAT1, STAT3, STAT5B, STAT6, IFIT5, and PKR) established a protective anti-viral immune response in duck lung tissue. Further, the protein-protein interaction network analysis identified proteins like AKT1, STAT3, JAK2, RAC1, STAT1, PTPN11, RPS27A, NFKB1, and MAPK1 as the main hub proteins that might play important roles in disease progression in ducks. Together, the functional annotation of the proteome and phosphoproteome datasets revealed the molecular basis of the disease progression and disease resistance mechanism in ducks infected with the HPAI H5N1 virus.
RESUMEN
BACKGROUND: Over the last three years, the coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has had a global impact. COVID-19 has led to diagnostic and treatment delays in head and neck squamous cell cancers (HNSCCs). Both cancer and COVID-19 trigger systemic inflammatory responses that can result in cytokine storms, creating a favorable tumor microenvironment that supports tumor growth. Various studies have shown a positive association between increasing neutrophil-to-lymphocyte ratio (NLR) and disease severity in COVID-19. Studies have also shown that high NLR is associated with poor survival outcomes in cancer patients. Our aim is to investigate whether an increased NLR is linked to rapid tumor progression in patients with HNSCC who have also been affected by infections like COVID-19 in the pre-operative period. METHODS: This was a retrospective analysis of patients of HNSCC who were scheduled for surgery and had contracted COVID-19 in their pre-operative period between April 2021 and May 2021. The study analyzed pre- and post-COVID NLR in relation to disease progression in HNSCC. Statistical analysis was presented as an interquartile range and numbered with the percentage. Statistical Package for the Social Sciences (IBM SPSS Statistics for Windows, IBM Corp., Version 26.0, Armonk, NY) was utilized for the analysis. RESULTS: We evaluated 200 operable cases of which 38/200 (20%) patients with HNSCC were COVID-19 positive. Out of those COVID-19-positive patients, 27/38 (71%) patients got operated. Around, 11/38 (28.9%) patients were inoperable. And, 14/27 (53.8%) operated patients also had a change in treatment plan. The mean duration from the joint clinic treatment plan to the date of surgery was 25.18 days. Patients who had contracted COVID-19 and had a change in their treatment plan due to disease progression exhibited mean NLR values of 3.84 (pre-COVID) and 11.11 (post-COVID), with respective medians of 3.04 and 10.50. These differences showed a statistically significant p-value of 0.000. In contrast, patients who had no change in treatment plan displayed mean NLR values of 4.51 (pre-COVID) and 9.70 (post-COVID), with respective medians of 3.47 and 3.42, resulting in with a non-significant p-value of 0.082. CONCLUSION: This is a one-of-its-kind study that has evaluated the role of elevated NLR in patients with a COVID-19 virus infection and its relationship with the clinical progression of the disease. The findings suggest that elevated NLR in patients with HNSCC, along with concurrent SARS-CoV2 infection, may contribute to accelerated disease progression with an increase in tumor burden and nodal metastasis.
RESUMEN
The 2D Ruddlesden-Popper (RP) perovskites Cs2PbI2Cl2 (Pb-based, n = 1) and Cs2SnI2Cl2 (Sn-based, n = 1) stand out as unique and rare instances of entirely inorganic constituents within the more expansive category of organic/inorganic 2D perovskites. These materials have recently garnered significant attention for their strong UV-light responsiveness, exceptional thermal stability, and theoretically predicted ultrahigh carrier mobility. In this study, we synthesized Pb and Sn-based n = 1 2D RP perovskite films covering millimeter-scale areas for the first time, utilizing a one-step chemical vapor deposition (CVD) method under atmospheric conditions. These films feature perovskite layers oriented horizontally relative to the substrate. Multilayered Cs3Pb2I3Cl4 (Pb-based, n = 2) and Cs3Sn2I3Cl4 (Sn-based, n = 2) films were also obtained for the first time, and their crystallographic structures were refined by combining X-ray diffraction (XRD) and density functional theory (DFT) calculations. DFT calculations and experimental optical spectroscopy support band-gap energy shifts related to the perovskite layer thickness. We demonstrate bias-free photodetectors using the Sn-based, n = 1 perovskite with reproducible photocurrent and a fast 84 ms response time. The present work not only demonstrates the growth of high-quality all-inorganic multilayered 2D perovskites via the CVD method but also suggests their potential as promising candidates for future optoelectronic applications.
RESUMEN
The availability of rapid and reliable tools for monitoring of plants' cold tolerance is a prerequisite for research aimed at breeding of cold-tolerant crop plants. Therefore, we have tested the capacity of metabolomics-based methods employing ultra-high-performance liquid chromatography (UHPLC)-mass spectrometry and direct analysis in real time-mass spectrometry for high-throughput screening of cold tolerance in eight differentially cold-tolerant accessions of Arabidopsis thaliana. Metabolomic fingerprinting of leaf tissues was performed in methanolic extracts for (1) 6-week-old non-acclimated (NAC) plants grown at room temperature, (2) NAC plants cold-acclimated (ACC) at 4 °C for 2 weeks, and (3) cold-acclimated plants given sub-zero-temperature treatments by slow cooling at -4 °C for 8 h. The generated chromatograms and mass spectra were processed with the use of multivariate statistical analysis employing principal component analysis (PCA) and linear discriminant analysis. The PCA of metabolomic fingerprints classified the investigated A. thaliana accessions into three categories with low, intermediate, and high cold tolerance for both the cold-acclimated and the sub-zero-temperature-treated plants. This indicates the potential application of metabolomics-based fingerprinting for measuring cold tolerance in the cold-acclimated state, i.e., without treating plants at freezing temperatures that is required by currently available methods. Furthermore, we employed UHPLC coupled to the quadrupole-time-of-flight mass spectrometry to identify characteristic metabolites in ACC state and found the abundance of gluconapin and flavon-3-ol glycosides, respectively, in the cold-sensitive and the cold-tolerant accessions.
Asunto(s)
Arabidopsis/química , Cromatografía Líquida de Alta Presión/métodos , Espectrometría de Masas/métodos , Metabolómica/métodos , Arabidopsis/metabolismo , Biomarcadores/química , Biomarcadores/metabolismo , FríoRESUMEN
Differently expressed genes (DEGs) across cervical (CC), endometrial (EC), and vulvar carcinoma (VC) may serve as potential biomarkers for these progressive tumor conditions. In this study, DEGs of cervical (CC), endometrial (EC), and vulvar carcinoma (VC) were identified by microarray analysis. The interaction network between the identified 124 DEGs was constructed and analyzed to identify the hub genes and genes with high stress centrality. DEGs, namely, CDK1 and MMP9, were found to show highest degree and highest stress centrality respectively from the gene interaction network of 124 nodes and 1171 edges. DEG CDK1 is found to be overlapping in both cervical and endometrial carcinomic conditions while DEG MMP9 is found in vulvar carcinomic condition. Further, as it is studied that many phytochemicals play an important role as medicinal drugs, we have identified phytochemicals from few widely available medicinal plants and performed comprehensive computational study to identify a multi-targeted phytochemical against the identified DEGs, which are crucially responsible for the progression of these carcinomic conditions. Virtual screening of the phytochemicals against the target DEG protein structures with PDB IDs 4Y72 and 1GKC resulted in identifying the multi-targeted phytochemical against both the proteins. The molecular docking and dynamics simulation studies reveal that luteolin can act as a multi-targeted agent. Thus, the interactional and structural insights of luteolin toward the DEG proteins signify that it can be further explored as a multi-targeted agent against the cervical, endometrial, and vulvar carcinoma.
Asunto(s)
Carcinoma , Plantas Medicinales , Metaloproteinasa 9 de la Matriz , Simulación del Acoplamiento Molecular , Luteolina , Biomarcadores , Fitoquímicos/farmacología , Carcinoma/genética , Biología Computacional/métodos , Perfilación de la Expresión Génica/métodos , Biomarcadores de Tumor/genética , Regulación Neoplásica de la Expresión GénicaRESUMEN
The chemical structure of a compound directly affects its biological activity, as different functional groups can change a compound's activity. With this in mind, the current study aims to predict the likely mechanism of action of several podophyllotoxin derivatives whose biological activities have already been documented. The interactions of the derivatives of podophyllotoxin with tubulin (PDB ID: 6NNG) and topoisomerase II (PDB ID: 3QX3), the two recognised targets of podophyllotoxin, were examined using molecular docking experiments. According to the molecular docking result, tubulin, and the investigated variants of podophyllotoxin interact more effectively than topoisomerase. The greatest docking score of the compounds was -12.200 against tubulin and -4.511 against topoisomerase, indicating that tubulin is the target of these drugs. Further to ascertain the strength of the interaction between the best-docked derivatives and the target protein, additional molecular dynamics investigations were also incorporated. With tubulin, the derivatives engage steadily, while with topoisomerase, the ligands shift from the protein's initial binding site to its DNA binding site. MMPBSA analysis was used to examine the stability of their relationship.Communicated by Ramaswamy H. Sarma.
RESUMEN
Lung cancer is still the most frequent cause of cancer-related death, accounting for nearly two million cases yearly. As cancer is a multifactorial disease, developing novel molecular therapeutics that can simultaneously target multiple associated cellular processes has become necessary. Ion channels are diverse regulators of cancer-related processes such as abnormal proliferation, invasion, migration, tumor progression, inhibition of apoptosis, and chemoresistance. Among the various families of ion channels, the transient receptor potential canonical channel family steps out in the context of lung cancer, as several members have been postulated as prognostic markers for lung cancer. Phytochemicals have been found to have health benefits in the treatment of a variety of diseases and disorders. Among phytochemicals, monoterpenes are effective in treating both the early and late stages of cancer. The molecular docking interaction analysis was conducted to evaluate the binding potential of selected monoterpenes with TRPC3, TRPC4, TRPC5, and TRPC6 involved in different phases of carcinogenesis. Amongst the selected monoterpenes, thymoquinone exhibited the highest binding energy of -6.7 kcal/mol against the TRPC4 channel, and all amino acid binding residues were similar to those of the known inhibitor for TRPC4. In addition, molecular-dynamic simulation results parameters, such as RMSD, RMSF, and Rg, indicated that thymoquinone did not impact the protein compactness and exhibited stability during the interaction. The average interaction energy between thymoquinone and TRPC4 protein was -26.85 kJ/mol. In-silico Drug-likeness and ADMET profiling indicated that thymoquinone is a druggable candidate with minimal toxicity. We propose further investigation and evaluation of thymoquinone for lead optimization and drug development.Communicated by Ramaswamy H. Sarma.
Thymoquinone exhibited the highest BE −6.7 kcal/mol against the TRPC4 channel.Thymoquinone passed all drug-likeness parameters.Thymoquinone showed 99.38% of intestinal absorption in ADMET analysis.MD confirms thymoquinone forms stable molecular interaction with TRPC4.
RESUMEN
Neolamarckia cadamba is an Indian traditional medicinal plant having various therapeutic potentials. In the present study, we did solvent-based extraction of Neolamarckia cadamba leaves. The extracted samples were screened against liver cancer cell line (HepG2) and bacteria (Escherichia coli). MTT cytotoxic assay was performed for in vitro analysis of extracted samples against the HepG2 cell lines and the normal human prostate PNT2 cell line. Chloroform extract of Neolamarckia cadamba leaves showed better activity with IC50 value 69 µg/ml. DH5α strain of Escherichia coli (E. coli) was cultured in Luria Bertani (LB) broth media and minimum inhibitory concentration (MIC) and Minimum bactericidal concentration (MBC) were calculated. Solvent extract chloroform showed better activity in MTT analysis and antibacterial screening and it was taken for characterization of phytocomposition by Fourier transform infrared (FTIR) and gas chromatography mass spectrometry (GC-MS). The identified phytoconstituents were docked with potential targets of liver cancer and E. coli. The phytochemical 1-(5-Hydroxy-6-hydroxymethyl-tetrahydropyran-2-yl)-5-methyl-1H-pyrimidine-2,4-dione shows highest docking score against the targets PDGFRA (PDB ID: 6JOL) and Beta-ketoacyl synthase 1(PDB ID: 1FJ4) and their stability was further confirmed by molecular dynamics simulation studies.
Asunto(s)
Extractos Vegetales , Rubiaceae , Masculino , Humanos , Extractos Vegetales/farmacología , Rubiaceae/química , Escherichia coli , Cloroformo , Antibacterianos/farmacologíaRESUMEN
Wastewater management has emerged as an uprising concern that demands immediate attention from environmentalists worldwide. Indiscriminate and irrational release of industrial and poultry wastes, sewage, pharmaceuticals, mining, pesticides, fertilizers, dyes and radioactive wastes, contribute immensely to water pollution. This has led to the aggravation of critical health concerns as evident from the uprising trends of antimicrobial resistance, and the presence of xenobiotics and pollutant traces in humans and animals due to the process of biomagnification. Therefore, the development of reliable, affordable and sustainable technologies for the supply of fresh water is the need of the hour. Conventional wastewater treatment often involves physical, chemical, and biological processes to remove solids from the effluent, including colloids, organic matter, nutrients, and soluble pollutants (metals, organics). Synthetic biology has been explored in recent years, incorporating both biological and engineering concepts to refine existing wastewater treatment technologies. In addition to outlining the benefits and drawbacks of the current technologies, this review addresses novel wastewater treatment techniques, especially those using dedicated rational design and engineering of organisms and their constituent parts. Furthermore, the review hypothesizes designing a multi-bedded wastewater treatment plant that is highly cost-efficient, sustainable and requires easy installation and handling. The novel setup envisages removing all the major wastewater pollutants, providing water fit for household, irrigation and storage purposes.