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Origin Pro 9.1: Scientific Data Analysis and Graphing Software-Software Review
Abstract
OriginPro 9.1. OriginLab Corporation, One Roundhouse Plaza, Suite 303, Northampton, MA 01060, United States. 1800-969-7720. www.OriginLab.com. See Web site for pricing information.
... Every 1 ps, the trajectories produced by the MD simulations were stored, and they were then analysed using the AMBER 14 suit's CPPTRAJ [17] module. Using Chimera [11] and the Origin data analysis tool [18], all plots and visualizations were finished. These follow the previously published MD simulation procedure that we previously developed [19]. ...
... The DCCM matrix was carried out using the CPPTRAJ package in Amber 14, and the matrices were plotted and evaluated using Origin software (www.originlab.com) [18]. ...
For the past 50 years, antibiotics that target DNA gyrase have proven to be clinically successful. As a result, the search for novel gyrase inhibitors has intensified due to the rise in bacterial resistance. Since it is absent in eukaryotes yet essential in all bacteria, anti-bacterials target it aggressively. Although quinolones are a clinically approved medication, both Gram-positive and Gram-negative bacteria are developing resistance to them, which compromises their therapeutic efficacy. Thus, it is vital to identify novel compounds that can efficiently inhibit DNA gyrase. A recent experimental study shows that the R-enantiomer of compound 1 was likely to be a more favourable stereoisomer than the R-enantiomer in inhibiting the function of DNA gyrase. However, the molecular mechanisms of its selectivity and inhibition remain elusive. To gain insight into the observed inhibitory effect, molecular dynamics simulations have been employed to investigate the inhibitory mechanism as well as selectivity effect. MD simulation revealed that R-enantiomer selectively targeted the ATP-binding pocket residues, with the 2,4 di chloro carbazole ring’s group interacting into the small hydrophobic pocket provided by Asp 25, arg 26, Ile 182, Val 233, Arg 284, and Ala 286 in DNA gyrase. Finding the residues in the catalytic-binding site may pave the way for the development of a new structure-based inhibitor of highly selective DNA gyrase for the treatment of Enterococcus faecalis infection.
... The generated trajectories of each system were analysed using the PTRAJ and CPPTRAJ modules [48]. The generated data and subsequent complexes were visualized using Microcal Origin analytical software [49,50], UCSF Chimera [36]. ...
Phytochemicals are now increasingly exploited as remedial agents
for the management of diabetes due to side effects attributable to
commercial antidiabetic agents. This study investigated the struc
tural and molecular mechanisms by which betulinic acid exhibits its
antidiabetic effect via in vitro and computational techniques. In
vitro antidiabetic potential was analysed via on α-amylase, α-
glucosidase, pancreatic lipase and α-chymotrypsin inhibitory
assays. Its structural and molecular inhibitory mechanisms were
investigated using Density Functional Theory (DFT) analysis, mole
cular docking and molecular dynamics (MD) simulation. Betulinic
acid significantly (p < 0.05) inhibited α-amylase, α-glucosidase, pan
creatic lipase and α-chymotrypsin enzymes with IC
50
of 70.02 μg/
mL, 0.27 μg/mL, 1.70 μg/mL and 8.44 μg/mL, respectively.
According to DFT studies, betulinic acid possesses similar reaction
in gaseous phase and water due to close values observed for high
est occupied molecular orbital (HOMO) and lowest occupied mole
cular orbital (LUMO) and the chemical descriptors. The dipole
moment indicates that betulinic acid has high polarity. Molecular
electrostatic potential surface revealed the electrophilic and
nucleophilic attack-prone atoms of the molecule. Molecular
dynamic studies revealed a stable complex between betulinic acid
and α-amylase, α-glucosidase, pancreatic lipase and α-
chymotrypsin. The study elucidated the potent antidiabetic proper
ties of betulinic acid by revealing its conformational inhibitory
mode of action on enzymes involved in the onset of diabetes
... If specific M and SD are not provided in the article, the corresponding author of the article should be contacted via email for the data or the data can be extracted from the graphs using OriginPro 2022 software [26]. In accordance with the data transformation method provided by the Cochrane Handbook [27], when only standard error of mean (SEM) is reported in the article, the SD can be calculated as SD = SEM* √ n. ...
Photobiomodulation therapy (PBMT) was introduced as an ergogenic aid for sport performance in healthy individuals is still controversial. The main aim of this study is to assess the potential enhancements in muscle endurance and recovery from muscle strength and injuries mediated by PBMT among individuals exhibiting diverse activity levels. Randomized controlled trials (RCT) of PBMT interventions for healthy people (both trained and untrained individuals) exercising were searched (up to January 16, 2024) in four electronic databases: Web of Science, PubMed, Scopus and Embase. Primary outcome measures included muscle endurance, muscle strength and creatine kinase (CK) levels; secondary outcome measure included Lactate dehydrogenase (LDH) levels. Subgroup analyses based on physical activity levels were conducted for each outcome measure. Thirty-four RCTs were included based on the article inclusion and exclusion criteria. Statistical results showed that PBMT significantly improved muscle endurance (standardized mean difference [SMD] = 0.31, 95%CI 0.11, 0.51, p < 0.01), indicating a moderate effect size. It also facilitated the recovery of muscle strength (SMD = 0.24, 95%CI 0.10, 0.39, p < 0.01) and CK (mean difference [MD] = -77.56, 95%CI -112.67, -42.44, p < 0.01), indicating moderate and large effect sizes, respectively. Furthermore, pre-application of PBMT significantly improved muscle endurance, recovery of muscle strength and injuries in physically inactive individuals and athletes (p < 0.05), while there was no significant benefit for physically active individuals. Pre-application of PBMT improves muscle endurance and promotes recovery from muscle strength and injury (includes CK and LDH) in athletes and sedentary populations, indicating moderate to large effect sizes, but is ineffective in physically active populations. This may be due to the fact that physically active people engage in more resistance training, which leads to a decrease in the proportion of red muscle fibres, thus affecting photobiomodulation.
... The trajectories acquired by MD simulations were evaluated using the AMBER18 suite's CPPTRAJ module after saving them every 1 ps (Roe and Cheatham 2013). All graphs and visualizations were created using the Origin data analysis tool and Chimera (Seifert 2014;Pettersen et al. 2004). ...
Abstract
Sustained inflammatory responses can badly affect several vital organs and lead to chronic inflammation-related disorders, such as atherosclerosis, pneumonia, rheumatoid arthritis, obesity, diabetes, Alzheimer’s disease, and cancers. Salvia multicaulis is one of the widely distributed plants that contains several biologically active phytochemicals and diterpenoids with anti-inflammatory effects. Therefore, finding alternative and safer natural plant-extracted compounds with good curative anti-inflammatory efficiencies is an urgent need for the clinical treatment of inflammation-related diseases. In the current study, S. multicaulis Vahl was used to extract and isolate two compounds identified as salvimulticanol and candesalvone B methyl ester to examine their effects against inflammation in murine macrophage RAW264.7 cells that were induced by lipopolysaccharide (LPS). Accordingly, after culturing RAW264.7 cells and induction of inflammation by LPS (100 ng/ml), cells were exposed to different concentrations (9, 18, 37.5, 75, and 150 µM) of each compound. Then, Griess assay for detection of nitric oxide (NO) levels and western blotting for the determination of inducible nitric oxide synthase (iNOS) expression were performed. Molecular docking and molecular dynamics (MD) simulation studies were employed to investigate the anti-inflammatory mechanism. Our obtained results validated that the level of NO was significantly decreased in the macrophage cell suspensions as a response to salvimulticanol treatment in a dose-dependent manner (IC50: 25.1 ± 1.2 µM) as compared to the methyl ester of candesalvone B which exerted a weaker inhibition (IC50: 69.2 ± 3.0 µM). This decline in NO percentage was comparable with a down-regulation of iNOS expression by western blotting. Salvimulticanol strongly interacted with both the Toll-like receptor 4 (TLR4)/myeloid differentiation factor 2 (MD-2) complex and the inhibitor of nuclear factor kappa-B (NF-κB) kinase subunit beta (IKKβ) to disrupt their inflammatory activation due to the significant hydrogen bonds and effective interactions with amino acid residues present in the target proteins’ active sites. S.multicaulis is a rich natural source of the aromatic abietane diterpenoid, salvimulticanol, which exerted a strong anti-inflammatory effect through targeting iNOS and diminishing NO production in LPS-induced RAW264.7 cells in a mechanism that is dependent on the inhibition of TLR4-MD-2 and IKKβ as activators of the classical NF-κB-mediated inflammatory pathway.
... We analyzed the correlation between shoot phytolith concentrations and MAT (obtained from CHELSA). The linear regressions between the phytolith concentration in rice and wheat and the temperature at the sampling points were completed using Origin 2021 77 . The mapping of China was also done using R 4.3.1. ...
While research on terrestrial silicon (Si) biogeochemistry and its beneficial effects for plants has received significant attention in last decades, the reasons for the emergence of high-Si taxa remain unclear. Although the “arms race” hypothesis (i.e. increased silicification through co-evolution with mammalian grazers) has received some support, other studies have pointed to the role of environmental factors, such as high temperatures and low atmospheric CO2 levels, which could have favored the emergence of silicification. Here, we combine experimentation and analysis of existing databases to test the role of temperature on the expression and emergence of silicification in terrestrial plants. We first show through experimental manipulations of rice that Si is beneficial for growth under high temperature stress, but harmful under low temperature. We then found that, globally, the average temperature of the distribution of high-Si plants was 1.2°C higher than that of low-Si plants. Moreover, within China, a notable positive correlation emerged between the concentrations of phytoliths in wheat and rice and air temperature. From an evolutionary perspective, 65–77% of high-Si families (> 10 mg Si g− 1 DW) originated during warm geological periods, while 57–75% of low-Si families (< 1 mg Si g− 1 DW) originated during cold geological periods. On average, Earth's temperatures during the emergence of high-Si families were 3°C higher than those during the emergence of low-Si families. A correlation was also observed between the divergence of proteins related to Si transport (Lsi1, Lsi2, Lsi3, and Lsi6) and historical climatic variability. Together, cumulative evidence suggests that plant Si variation is closely related to global and long-term climate change, with potential repercussions for global Si and C biogeochemical cycles.
... been calculated for V E , ∆lnη, R-Square values and ANOVA test have been calculated using the OriginPro-2023b software for Graphing and Analysis [33]. The calculated values of the parameters are reported in Table 1. ...
... (https://www.originlab. com/) [59] , NMW is implemented in Visual Molecular Dynamics (https://www.ks.uiuc.edu/Research/vmd/) [60] . ...
Therapeutic activation of G protein-coupled estrogen receptor 1 (GPER-1) shows promise for treating Waldenström's Macroglobulinemia (WM). Recently, the selective small-molecule agonist G-1 or its enantiomer LNS8801 were reported as potent GPER-1 pharmacological activators, however, the molecular events surrounding their chirality towards GPER-1 is still unexplored. This study aimed to explore the molecular events surrounding the chirality of the selective small-molecule agonists G-1 and LNS8801 towards GPER-1. Molecular docking and dynamics simulations revealed strong binding affinities and key amino acid residues involved in the activation process. The results revealed favourable binding affinities of -29.87kcal/mol, and -28.09kcal/mol for G-1 and LNS8801 towards GPER-1, respectively. Per-residue energy decomposition and time-dependent analysis proved that Arg253 and Arg254 are key amino acid residues in binding these activators towards GPER-1. The activators affected stability, flexibility, and structure of GPER-1. G-1 exhibited greater rigidity when bound to GPER-1 compared to LNS880. This study's findings illuminate chirality and the potential for optimizing the enantiomer ratio to enhance inhibitory effects. These results could also reveal the molecular specifics and binding mechanism of the G-1 and its enantiomer LNS8801 with GPER-1, laying the basis for the rational design of enhanced chiral molecules against WM.
... Moreover, the conductor-like polarizable continuum model (CPCM) [88] was utilized for the estimation of solvent effects. Correspondingly, a variety of software such as Origin [89], Chemcraft [90], PyMOlyze 2.0 [91], Multiwfn 3.7 [92] and Avogadro [93] were employed for the interpretation of output files. However, the dipole moment was calculated by following Eq. ...
... Fisher's Least Significant Difference post hoc test and t-test were performed on the datasets, and differences were considered to be statistically significant at p < 0.05. Origin 2021 for nonlinear curve fitting was used to evaluate the accuracy of the diffusion-adsorption model (Seifert, 2014). Figures were also drawn using Origin 2021. ...
... All experiments were performed in triplicate. Statistical analysis was performed using OriginPro2017 (Seifert, 2014) software to plot. For phage adsorption efficiency assays and competitive adsorption assays, a normality test based on independent data was performed using the Shapiro-Wilk method, followed by a Levene test to evaluate the homogeneity of variance of the data. ...
Bacteriophages (phages) represent promising alternative treatments against multidrug-resistant Acinetobacter baumannii (MDRAB) infections. The application of phages as antibacterial agents is limited by their generally narrow host ranges, so changing or expanding the host ranges of phages is beneficial for phage therapy. Multiple studies have identified that phage tail fiber protein mediates the recognition and binding to the host as receptor binding protein in phage infection. However, the tail tubular-dependent host specificity of phages has not been studied well. In this study, we isolated and characterized a novel lytic phage, vB_Ab4_Hep4, specifically infecting MDRAB strains. Meanwhile, we identified a spontaneous mutant of the phage, vB_Ab4_Hep4-M, which revealed an expanded host range compared to the wild-type phage. A single mutation of G to C was detected in the gene encoding the phage tail tubular protein B and thus resulted in an aspartate to histidine change. We further demonstrated that the host range expansion of the phage mutant is driven by the spontaneous mutation of guanine to cytosine using expressed tail tubular protein B. Moreover, we established that the bacterial capsule is the receptor for phage Abp4 and Abp4-M by identifying mutant genes in phage-resistant strains. In conclusion, our study provided a detailed description of phage vB_Ab4_Hep4 and revealed the tail tubular-dependent host specificity in A. baumannii phages, which may provide new insights into extending the host ranges of phages by gene-modifying tail tubular proteins.
... The statistical analysis of all data was obtained based on the least significant difference (LSD) at a 1 % probability level for significant differences using SAS software version 9.4 (SAS Institute, 2018). Correlation analyses and principal component analyses (PCA) were assessed to determine the relationships between the traits using OriginPro 9.1 software (Seifert and Modeling, 2014). ...
... For every system, the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF) were computed. To plot graphs, the Origin data version 6.0 tool [44] was used. ...
... Discovery studio version v19.10.18289 (Biovia, 2017) and UCSF Chimera were used to visualize the trajectories whiles Origin data version 9.1 (Seifert, 2014) tool was used to plot the graphs. ...
The goal of this work is to use a variety of in-silico techniques to identify anti-diabetic agents against DPP-IV enzyme from five main curcumin analogues. To produce the successful molecules, five main curcumin analogues were docked into the active site of DPP-IV enzyme. In comparison to the control molecule (Saxagliptin, −6.9 kcal/mol), all the compounds have the highest binding affinity (-7.6 to −7.7 kcal/mol) for the DPP-IV enzyme. These compounds underwent further testing for studies on drug-likeness, pharmacokinetics, and acute toxicity to see the efficacy and safety of compounds. To assess the stability of the docking complex and the binding posture identified during the docking experiment, our study
got THC as the lead compound, which was then exposed to 200 ns of molecular dynamic simulation and PCA analysis. Additionally, DFT calculations were conducted to determine the thermodynamic, molecular orbital, and electrostatic potential characteristics of lead compound. Overall, the lead chemical has shown strong drug-like properties, is non-toxic, and has a sizable affinity for the DPP-IV enzyme.
... These generated trajectories were further analysed using the CPPTRAJ and PTRAJ modules of AMBER18 [79]. Graphical plots for analysis of the generated trajectories created with the Microcal Origin 6.0 analytical software [80]. ...
Bacterial DNA gyrase remains a prominent and vital target in discovering new antibacterial drugs. In the present research work, we designed and synthesized a series of novel 4,5-dibromo-N-phenyl-1H-pyrrole-2-carboxamide hybrids containing substituted 1,2,3-triazole and isoxazole moieties which could serve as potential E. coli DNA gyrase inhibitors. The title compounds were synthesized with a good to excellent yield, and all the newly synthesized compounds were characterized by physicochemical and spectral analysis (FTIR, 1H NMR, and 13C NMR). The DNA gyrase (E. coli) inhibitory assay was performed for all synthesized compounds. Results showed that four compounds, 11a (IC50 = 0.90 µM), 11b (IC50 = 0.28 µM), 17a (IC50 = 0.72 µM) and 17b (IC50 = 0.43 µM), exhibited good DNA gyrase inhibitory activity. In-silico molecular docking study was performed to understand the mode of interaction of compounds with the target enzyme. A docking study on the E. coli DNA gyrase protein revealed that compounds 11b (-7.011 kcal/mol) and 17b (-6.60 kcal/mol) interact with ARG136 and ASP73, two key amino acid residues, with docking scores of −7.01 and −6.60, respectively. The MD simulation was further employed to elucidate the thermodynamic binding energy, RMSD, and RMSF of compounds 11b and 17b. They exhibited binding energies of -47.598 kcal/mol and -41.682 kcal/mol, respectively. This provides valuable information on the binding mode and structure-activity relationship of these new hybrids of 4,5-dibromo-N-phenyl-1H-pyrrole-2-carboxamides as promising E. coli DNA gyrase B inhibitors. In addition, these hybrid derivatives showed more prominent antibacterial action on Gram-negative rather than Gram-positive organisms. Surprisingly, compounds 11b (MIC = 1.56 µg/mL) and 17b (MIC = 3.125 µg/mL) also displayed promising anti-mycobacterial activity.
... The data standardization method used Z-scores. In addition, we used Origin 2021 to perform linear regression (Seifert, 2014), and the psych package in R 4.3.1 to perform factor analysis (Null et al., 2011). Figures were also constructed using Origin 2021 and R 4.3.1. ...
... The averaging of the scans results in diminished noise providing a clearer observation of XANES oscillations. Further normalization and data processing were conducted using OriginPro Software [12]. ...
This research introduces an alternative approach on materials characterization by developing an in-house X-ray Absorption Spectroscopy (XAS) system utilizing powder X-ray Diffraction (XRD) machine. The performance of the in-house XAS system was investigated by analysing the position of Cu K-edge and the absorption spectrum shape within the X-ray Absorption Near Edge Structure (XANES) region. Copper (Cu) based samples were used to test the performance of the system where Cu and Copper Oxide (CuO) thin film deposited on polyimide tape and silicon wafer (100) prepared through the deposition process carried out using RF Magnetron Sputtering machine. Phase confirmation analysis were conducted by XRD and the deposited films’ thickness were measured by Scanning Electron Microscope (SEM). The laboratory-based XAS measurement was carried out using Rigaku SmartLab X-ray Diffractometer configured for Bragg-Brentano (BB) measurement mode. Molybdenum (Mo) target was used to produce white X-rays by energizing it near 20 keV ±0.01 keV. XRD measurements on XRD and SEM analysis proves successful deposition of pure Cu and CuO thin films and the film thickness measured is 1.432 μm and 0.680 μm respectively. The conclusive findings of the laboratory-based XAS measurements indicate successful acquisition of XAS data with similar spectrum shape of experimental Cu and CuO XANES in comparison with theoretical data. Next, experimental XANES shows clear observation of Cu K-edge peaks for Cu thin film at 8.9737 keV, while Cu K-edge for CuO thin films is not observable. Lastly, there is also presence of significant XANES broadening and which then effect consequent peak shiftings.
... The analysis of Radius of gyration (RoG), Root mean square fluctuation (RMSF) and the Root mean square deviation (RMSD) were done using CPPTRAJ module found in the AMBER 18 suit [49]. The Origin data analysis program was used to generate all average raw data visualizations [50]. ...
Three Schiff bases were synthesised by the condensation reaction between 2-napthaldehyde and aromatic amines to afford (E)-N-mesityl-1-(naphthalen-2-yl)methanimine (L1), (E)-N-(2,6-dimethylphenyl)-1-(naphthalen-2-yl)methanimine (L2) and (E)-N-(2,6-diisopropylphenyl)-1-(naphthalen-2-yl)methanimine (L3). The synthesised compounds were characterised using UV–visible, NMR (¹³C & ¹H), and Fourier transform infrared spectroscopic methods while their purity was ascertained by elemental analysis. Structural analysis revealed that the naphthalene ring is almost coplanar with the imine functional group as evident by C1–C10–C11–N1 torsion angles of 176.4(2)° and 179.4(1)° in L2 and L3, respectively. Of all the various intermolecular contacts, H⋯H interactions contributed mostly towards the Hirshfeld surfaces of both L2 (58.7 %) and L3 (69.7 %). Quantum chemical descriptors of L1 - L3 were determined using Density Functional Theory (DFT) and the results obtained showed that the energy band gap (ΔE) for L1, L2 and L3 are 3.872, 4.023 and 4.004 eV respectively. The antidiabetic potential of the three compounds were studied using α-amylase and α-glucosidase assay. Compound L1 showed very promising antidiabetic activities with IC50 values of 58.85 μg/mL and 57.60 μg/mL while the reference drug (Acarbose) had 405.84 μg/mL and 35.69 μg/mL for α-amylase and α-glucosidase respectively. In-silico studies showed that L1 docking score as well as binding energies are higher than that of acarbose, which are recognized inhibitors of α-amylase together with α-glucosidase. Further insight from the RMSF, RMSD and RoG analysis predicted that, throughout the simulation L1 showcased evident influence on the structural stability of α-amylase. The antioxidant potential of the compounds was carried out using nitric oxide (NO), ferric reducing ability power (FRAP) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays. The compounds exhibited good to fairly antioxidant properties with L1 as well as L3 having IC50 values of 70.91 and 91.21 μg/mL respectively for NO scavenging activities assay, which comparatively outshined acarbose (reference drug) with IC50 value of 109.95 μg/mL. Pharmacology and pharmacokinetics approximations of L1 – L3 showed minimal violation of Lipinski's Ro5 and this projects them to be less toxic and orally bioavailable as potential templates for the design of therapeutics with antioxidant and antidiabetic activities.
... To assess the significance of the differences between the means, a one-way ANOVA analysis was performed using a significance threshold of p-value (typically <0.05). For data representation, graphs were plotted by using OriginPro9.1 software (Seifert 2014). ImageJ tool (Schneider 2005) was used for the measurement of root length. ...
... The trajectories that produced from MD simulations have been assessed by AMBER18 suite's CPPTRAJ [31] model. All graphs and visualisations were made using Chimaera [20] and the Origin data analysis programme [32]. ...
Background
The phytochemical constitution and biological capabilities of Fragaria ananassa 's calyx have not been extensively investigated before. Consequently, the research study pointed for characterization, isolation, and identification of the sterols and flavonoids as the major active constituents in the calyx of F. ananassa and evaluation for their impacts as free radicals scavenger and anti-inflammatory agent.
Results
GC/MS investigation for the lipoidal constitutions of F. ananassa 's calyx was performed to identify twenty-six compounds signifying 83.08%, as well as isolation of campesterol, stigmast-4-en-3-one, and β-sitosterol- d -glucoside by column chromatography technique. Additionally, quantification and identification of the flavonoids in the ethyl acetate extract was carried out by HPLC/DAD technique beside to isolation and structure elucidation of 5-hydroxy-7, 4′-dimethoxy flavone and Chrysin. The free radicals scavenging and anti-inflammatory activities of both non-polar and polar extracts have been tested against (DPPH and ABTS radicals) and (COX-1, COX-2, and 5-LOX enzymes), correspondingly. The results illustrated significant effects of the polar extract of F. ananassa calyx greater than non-polar one. The dynamic natures, binding interactions, and protein–ligand stabilities have also been investigated using the molecular dynamics (MD) simulation research. The MD simulation revealed that Chrysin's chromen ring was extended to catalytic position of COX-1 receptor, producing Pi-Pi T-shaped contact with Tyr 354 and Trp 356. In addition, Chrysin's chromen ring has formed a Pi-alkyl bond with Val 318 and Leu 321. However, due to the huge size of ꞵ-sitosterol- d -glucoside, the glycoside ring can form a hydrogen bond with Tyr 317. The cyclopentyl phenanthrene ring also possesses Pi-alkyl interactions with Ile 58, Leu 62, Val 85, Val 318, Tyr 324, Leu 326, Ala 496, and Leu 500.
Conclusions
The findings of our study are crucial in establishing the molecular bases for Chrysin and ꞵ-sitosterol- d -glucoside action against anti-inflammatory targets and for developing more effective selective inhibitors. The discovery of the binding location for ATP can pave the door for development unique, structure-based approach for natural anti-inflammatory medications.
... To compare fairness, abundance rank curves (log) were constructed (Magurran, 2004). In order to identify the relationships between the sites and bird species; the chord diagram was designed with Origin Pro 10.0.5.157 software (Seifert, 2014). With the iNEXT Online program, the accumulation curves, extrapolation and sampling coverage curves by sites were performed (Chao et al., 2016). ...
The Bacalar Lagoon (BL) in Quintana Roo, Mexico; is an area of high interest due to its tourist potential. However, the changes in landuse patterns, urbanization, extensive cattle ranching and rapidly expanding agriculture, have generated negative impacts on areas of adjacent plan communities and wildlife habitats. The objective of this study has to evaluate the level of vegetation conservation in the southern portion of the BL through the avifauna present in sites with contrasting degrees of conservation. Additionally, change “and their habitat preference(s) in the different communities” to and their habitat use preferences in the different communities. To evaluate the level of conservation of the BL, field visits and botanical collections were carried out to identify species. For the counting and identification of birds, monthly surveys were made through coastal tours along the cenote Xul-ha in 2.5 km transects. Four transects were established: two for sites characterized as semi-conserved and two with disturbed sites. A total richness of 40 taxa was observed, which corresponds to 8.1% of the Quintana Roo avifauna and 32% to wetland birds (125 species). The species accumulation curves indicated that semi-conserved and disturbed sites tend to reach asymptotes and with a coverage percentage greater than 90%. In terms of diversity and community structure, no significant differences were observed. However, the semi-conserved and disturbed sites each have 11 unique species and share 18 species. The LB has an intermediate diversity of bird species compared to studies at the Mexican level, the habitat is important for the conservation of birdlife; as it functions as a reservoir of diversity. Strategies has been suggested that promote sustainable tourism, support the restoration of natural vegetation; and facilitate the economic development of the region.
... P ≤ 0.05 indicated statistical significance. Bar charts were created using OriginPro software (Seifert, 2014). ...
Understanding the diet of threatened wildlife is vital for species-specific conservation and habitat managementmeasures. The Red-crowned Crane (Grus japonensis) is a vulnerable bird distributed in Northeast Asia. Previousdietary studies of this bird focused mainly on its plant food composition based on field observations andmicrohistological identification. Herein, a total of 45 fecal samples were collected in November, December andJanuary (15 fecal samples each month) from wintering cranes, and then subjected to a high throughputsequencing meta-barcoding approach to determine the primary plant (rbcL) and animal (COI) food items in theirdiet. A total of 230 operational taxonomic units (OTUs) of plant foods and 371 OTUs of animal foods wereobtained. The main plant foods in the wintering period were Miscanthus, Zea, and Hordeum genera, which weresimilar to those in the breeding and the migration periods. Both agricultural and natural plants were detected,indicating a relatively broad dietary niche for this crane species. However, the main animal foods were repre-sentatives of Theridiidae, Megascolecidae, and Agelenidae, in sharp contrast to previous studies. The highernumber of small terrestrial arthropods in animal foods might be due to the indirect intake of plants. Thecomposition of both plant and animal foods in the diet showed the highest diversity in December, while it washomogeneous in January. The plant of Zea genus became the main source of nutrition in late winter, as sup-plementary feeding was performed in the reserve, which could help Red-crowned Cranes to get through the coldseason. The results obtained in this work would contribute to the development of effective conservation stra-tegies for the Red-crowned Crane.
... The CPPTRAJ [41] module of the AMBER18 suite was used to analyze the trajectories after they had been saved by MD simulations at intervals of 1 ps. All graphs and visualizations were produced using Chimaera [42] and the Origin [43] data analysis program. ...
... Thermodynamic calculation. The Poisson-Boltzmann or generalized Born surface area continuum solvation (MM/PBSA and MM/GBSA) approach were found to be useful in the estimation of ligand binding affinities [33][34][35]. The protein-ligand complex molecular simulations utilized MM/GBSA and MM/PBSA to compute rigorous statistical-mechanical binding free energy within a defined force field. ...
... The analysis of Radius of gyration (RoG), Root mean square fluctuation (RMSF) and the Root mean square deviation (RMSD) were done using CPPTRAJ module found in the AMBER 18 suit [49]. The Origin data analysis program was used to generate all average raw data visualizations [50]. ...
Rhizopus arrhizus is a saprotrophic, sometimes clinically- and industrially-relevant mold (Mucorales) and distributed worldwide, suggesting it can assimilate a broad spectrum of substrates. Here, 69 strains of R. arrhizus were investigated by using the Biolog FF MicroPlate for the profiles of utilizing 95 carbon and nitrogen substrates. The study showed that most R. arrhizus strains were similar in average well color development (AWCD) and substrate richness (SR). Nevertheless, 13 strains were unique in principal component analyses, heatmap, AWCD, and SR analyses, which may imply a niche differentiation within R. arrhizus. The species R. arrhizus was able to utilize all the 95 carbon and nitrogen substrates, consistent with the hypothesis of a great metabolic diversity. It possessed a substrate preference of alcohols, and seven substrates were most frequently utilized, with N-acetyl-d-galactosamine and l-phenylalanine ranking at the top of the list. Eight substrates, especially l-arabinose and xylitol, were capable of promoting sporulation and being applied for rejuvenating degenerated strains. By phenotyping R. arrhizus strains in carbon and nitrogen assimilation capacity, this study revealed the extent of intra-specific variability and laid a foundation for estimating optimum substrates that may be useful for industrial applications.
Anticancer activity, a novel series of 6-((1 H -1,2,3-triazol-4-yl)methyl)-6 H -indolo[2,3- b ]quinoxalines (22–29) were designed and synthesized via the copper( i )-catalyzed azide–alkyne cycloaddition (CuAAC) reactions.
Background
The most prevalent probiotic bacterium employed in the food industry is Lactobacillus because it can produce metabolites with antibacterial capabilities and exhibits hostility towards infections and microorganisms that cause spoilage.
Aim
This study set out to identify naturally occurring Lactobacillus and plantaricin (pln EF) coding genes in raw cow milk and to assess the antibacterial potency of isolated Lactobacillus isolates.
Methods
Following enrichment in De Man, Rogosa and Sharpe (MRS) broth, single colonies were isolated, and pure colonies were obtained by streaking on MRS agar. The 16S rRNA gene was amplified using polymerase chain reaction (PCR) to confirm the cultural positivity of all isolates. Additionally, the presence of plantaricin was verified by targeting the pln EF gene through PCR.
Outcome
Out of the 166 raw milk specimens acquired from cows, 153 (91.17%; CI: 86.98–95.76) were identified as positive for Lactobacillus through both culture and biochemical screening. Subsequently, 121 (72.89%; CI: 65.46–79.49) of the isolates were affirmed to harbour Lactobacillus through PCR analysis. Within this subset, 6 isolates (4.96%; CI: 1.84–10.48) were found to possess the plnEF gene. When exposed to Lactobacillus isolates, Salmonella Typhimurium and Salmonella enterica displayed an average maximum zone of inhibition with a diameter measuring 24 mm. In contrast, Escherichia coli exhibited an average minimum zone of inhibition, featuring a diameter of 11 mm. Additionally, the Lactobacillus isolates demonstrated inhibitory zones against Staphylococcus aureus, Klebsiella pneumoniae and Klebsiella oxytoca, measuring 14, 22 and 19 mm, respectively.
Clinical significance
Lactic acid bacteria, particularly Lactobacilli, are plentiful in cow milk and possess broad‐spectrum antibacterial properties.
Itaconyl‐CoA hydratase in Pseudomonas aeruginosa ( Pa Ich) converts itaconyl‐CoA to ( S )‐citramalyl‐CoA upon addition of a water molecule, a part of an itaconate catabolic pathway in virulent organisms required for their survival in humans host cells. Crystal structure analysis of Pa Ich showed that a unique N‐terminal hotdog fold containing a 4‐residue short helical segment α3‐, named as an “eaten sausage”, followed by a flexible loop region slipped away from the conserved β‐sheet scaffold, whereas the C‐terminal hotdog fold is similar to all MaoC. A conserved hydratase motif with catalytic residues provides mechanistic insights into catalysis, and existence of a longer substrate binding tunnel may suggest the binding of longer CoA derivatives.
As one of the main projects of facility agriculture promotion, the PV (photovoltaic) greenhouse has the problems of PV power generation competing for light with crop production, strong indoor chiaroscuro, and uneven light distribution. The internal light uniformity is tested by a zigzag greenhouse model to compare the light transmission effects of different light-transmitting materials applied to PV greenhouses. Altogether, 20 line/inch 3 mm and 30 line/inch 3 mm, 40 line/inch 2 mm, 25 line/inch 4 mm grating plates and 2 mm and 3 mm thick ordinary glass were used as light-transmitting components, and the light intensity and light uniformity in the greenhouse were the measurement indicators. The results show that the use of grating plates as covering material can improve the light intensity at the intersection of light and dark, but the overall light transmittance is not as good as glass because it is plastic, which ages easily with low light transmittance. It can also improve the use of land under the shade of PV modules to provide a better growth environment for crops. The test results show that using grating plates can maximize the light intensity of the greenhouse and solve the problem of uneven distribution of light inside the greenhouse caused by obstruction of PV equipment and greenhouse framework. In sunny weather, the light intensity in three rows of the measurement points at the north side in the greenhouse is greater than 20,000 Lx, and the light environment in other areas is between 5000 Lx and 20,000 Lx, which is suitable for planting shade-loving crops.
Cancer remains a major challenge in the field of medicine, necessitating innovative therapeutic strategies. Mitogen-activated protein kinase (MAPK) signaling pathways, particularly Extracellular
Signal-Regulated Kinase 1 and 2 (ERK1/2), play pivotal roles in cancer pathogenesis. Recently, ERK5(also known as MAPK7) has emerged as an attractive target due to its compensatory role in cancer progression upon termination of ERK1 signaling. This study explores the potential of Compound 22ac, a novel small molecule inhibitor, to simultaneously target both ERK1 and ERK5 in cancer cells. Using molecular dynamics simulations, we investigate the binding affinity, conformational dynamics, and stability of Compound 22ac when interacting with ERK1 and ERK5. Our results indicate that Compound 22ac forms strong interactions with key residues in the ATP-binding pocket of both ERK1 and ERK5, effectively inhibiting their catalytic activity. Furthermore, the simulations reveal subtle differences in the binding modes of Compound 22ac within the two kinases, shedding light on the dual inhibitory mechanism. This research not only elucidates a structural mechanism of action of Compound 22ac, but also highlights its potential as a promising therapeutic agent for cancer treatment. The dual inhibition of ERK1 and ERK5 by Compound 22ac offers a novel approach to disrupting the MAPK signaling cascade, thereby hindering cancer progression. These findings may contribute to the development of targeted therapies that could improve the prognosis for cancer patients.
Natural compounds such as curcumin, a polyphenolic compound derived from the rhizome of turmeric, have gathered remarkable scientific interest due to their diverse metabolic benefits including anti-obesity potential. However, curcumin faces challenges stemming from its unfavorable pharmacokinetic profile. To address this issue, synthetic curcumin derivatives aimed at enhancing the biological efficacy of curcumin have previously been developed. In silico modelling techniques have gained significant recognition in screening synthetic compounds as drug candidates. Therefore, the primary objective of this study was to assess the pharmacokinetic and pharmacodynamic characteristics of three synthetic derivatives of curcumin. This evaluation was conducted in comparison to curcumin, with a specific emphasis on examining their impact on adipogenesis, inflammation, and lipid metabolism as potential therapeutic targets of obesity mechanisms. In this study, predictive toxicity screening confirmed the safety of curcumin, with the curcumin derivatives demonstrating a safe profile based on their LD50 values. The synthetic curcumin derivative 1A8 exhibited inactivity across all selected toxicity endpoints. Furthermore, these compounds were deemed viable candidate drugs as they adhered to Lipinski’s rules and exhibited favorable metabolic profiles. Molecular docking studies revealed that both curcumin and its synthetic derivatives exhibited favorable binding scores, whilst molecular dynamic simulations showed stable binding with peroxisome proliferator-activated receptor gamma (PPARγ), csyclooxygenase-2 (COX2), and fatty acid synthase (FAS) proteins. The binding free energy calculations indicated that curcumin displayed potential as a strong regulator of PPARγ (−60.2 ± 0.4 kcal/mol) and FAS (−37.9 ± 0.3 kcal/mol), whereas 1A8 demonstrated robust binding affinity with COX2 (−64.9 ± 0.2 kcal/mol). In conclusion, the results from this study suggest that the three synthetic curcumin derivatives have similar molecular interactions to curcumin with selected biological targets. However, in vitro and in vivo experimental studies are recommended to validate these findings.
As an important input of environmental micropollutants into aquaculture environment, feed is now considered to be a critical factor in shaping gastrointestinal evacuation characteristics of animals. We analyzed the gastrointestinal evacuation characteristics and gut bacteria of Apostichopus japonicus within 30 h after feeding in recirculating aquaculture system (RAS) and explored the evacuation mechanism interacting by bacteria. The Gauss model was the most precise gastrointestinal evacuation curve, and 80% of gastrointestinal evacuation time was 27.81 h after feeding. Linear discriminant analysis effect size analysis revealed that gut microbial abundance associated significantly with time (P < 0.05), and 42 biomarkers that could predict gastrointestinal evacuation were totally detected, such as Lutibacter and Vibrio. Biomarkers at 25 h after feeding were related to harmful bacteria. A dynamic response between gastrointestinal content ratio and gut microbial abundance was detected. Taken together, we could discharge sewage about 25 h after feeding and carry out the next round of feeding activities.
Breast cancer (BC) remains the most common cancer among women worldwide, and estrogen receptor-α expression is a critical diagnostic factor for BC. Estrogen receptor (ER-α36) is a dominant-negative effector of ER-α66-mediated estrogen-responsive gene pathways. ER-α36 is a novel target that mediates the non-genomic estrogen signaling pathway. However, the crystallized structure of ER-α36 remains unavailable for molecular studies. ER-positive and triple-negative BC tumors aggressively resist the FDA-approved drugs; therefore, highly potent structure-based inhibitors with preeminent benefits over toxicity will preferably replace the current BC treatment. Broussoflanol B (BFB), a B. papyrifera bark compound, exhibits potent growth inhibitory activity in ER-negative BC cells by inducing cell cycle arrest. For the first time, we unravel the comparative dynamic events of the enzymes’ structures and the binding mechanisms of BFB when bound to the ER-α36 and ER-α66 ligand-binding domain using an all-atom molecular dynamics simulations approach and MM/PBSA-binding-free energy calculations. The dynamic findings have revealed that ER-α36 and ER-α66 LBD undergo timescale “coiling”, opening and closing conformations favoring the high-affinity BFB-bound ER-α36 (ΔG = −52.57 kcal/mol) compared to the BFB-bound ER-α66 (ΔG = −42.41 kcal/mol). Moreover, the unbound (1.260 Å) and bound ER-α36 (1.182 Å) exhibit the highest flexibilities and atomistic motions relative to the ER-α66 systems. The RMSF (Å) of the unbound ER-α36 and ER-α66 exhibit lesser stabilities than the BFB-bound systems, resulting in higher structural flexibilities and atomistic motions than the bound variants. These findings present a model that describes the mechanisms by which the BFB compound induces downregulation-accompanied cell cycle arrest at the Gap0 and Gap1 phases.
The study has effectively highlighted the significance of B. trispinosa as a promising reservoir of chemopreventive and anti-inflammatory attributes, particularly exemplified through the potent acetyl barlerin (1). This compound exhibited a remarkable ability to stimulate the chemopreventive NQO1 enzyme activity and protein expression. Moreover, its proficiency in curbing LPS-triggered inflammatory responses within a murine inflammation model has been evidenced by the suppression of iNOS protein expression and subsequent NO production in activated RAW264.7 macrophages. These results were supported by computational insights from molecular docking and MD simulations.
The International Agency for Research on Cancer has unequivocally classified inorganic arsenic as a Group 1 carcinogen, definitively establishing its potential to induce cancer in humans. Paradoxically, despite its well-documented toxicity, arsenic finds utility as a chemotherapeutic agent. Notable examples include melarsoprol and arsenic trioxide, both employed in the treatment of acute promyelocytic leukemia. In both therapeutic and hazardous contexts, arsenic can accumulate within cellular environments, where it engages in intricate interactions with protein molecules. Gaining a comprehensive understanding of how arsenic compounds interact with proteins holds immense promise for the development of innovative inhibitors and pharmaceutical agents. These advancements could prove invaluable in addressing a spectrum of arsenic-related diseases. In pursuit of this knowledge, we undertook a systematic exploration of the Protein Data Bank, with a focus on 902 proteins intricately associated with 26 arsenic compounds. Our comprehensive investigation reveals insights into the interactions between these arsenical compounds and amino acids located within a 4.0 Å molecular distance from arsenic-binding sites. Our findings identify that cysteine, glutamic acid, aspartic acid, serine, and arginine frequently engage with arsenic. In complement to our computational analyses, we conducted rigorous Raman spectroscopy studies on the top five amino acids displaying robust interactions with arsenic. The results derived from experimental Raman spectroscopy were meticulously compared with our computational assessments, thereby enhancing the reliability and depth of our investigations. The current study presents a multidimensional exploration into the elaborate interplay between arsenic compounds and proteins. By elucidating the specific amino acids that preferentially interact with arsenic, this study not only contributes to the fundamental understanding of these molecular associations but also lays the foundation for future endeavors in drug design and therapeutic interventions targeting arsenic-related illnesses. Our work at the convergence of toxicology, medicine, and molecular biology carries profound implications for advancing our knowledge of arsenic's dual nature as both a poison and a potential cure.
Blue honeysuckle (Lonicera caerulea L.) is an emerging fruit crop; however, determining its proper harvest time in commercial cultivation remains challenging due to its rapid fruit development characteristics. In this study, we investigated 17 agronomic traits of three blue honeysuckle cultivars harvested on 5 successive dates within their respective harvest windows. ‘Lanjingling’, ‘Wulan’, and ‘Berel’ showed solid–acid ratios (SS:TA) ranging from 10.00 to 16.01, 8.13 to 10.23, and 5.77 to 7.11, respectively; anthocyanin contents ranged from 233.85 to 276.83 mg/100 g, 236.38 to 312.23 mg/100 g, and 235.71 to 334.98 mg/100 g, respectively; vitamin C contents ranged from 88.43 to 99.68 mg/100 g, 108.13 to 191.23 mg/100 g, and 89.71 to 120.40 mg/100 g, respectively; phenolic contents ranged from 25.22 to 37.59 mg/g, 25.40 to 36.52 mg/g, and 37.66 to 50.00 mg/g, respectively. The results revealed the SS:TA value consistently increased with delayed harvesting and were significantly negatively correlated with fruit firmness, total acidity, shelf life, and respiration intensity, suggesting it is an ideal maturity indicator for blue honeysuckle berries. The factor analysis suggests that the suitable harvest date for ‘Lanjingling’ could be either 47 days after flowering (DAF) with an SS:TA value of approximately 10.0, characterized by high firmness, extended shelf life, and elevated levels of anthocyanins and phenolics; or 67 DAF (SS:TA ≈ 16.0), characterized by high vitamin C content and sweetness, and larger size and weight. For ‘Wulan’, it suggests the suitable harvest date is either 54 DAF (SS:TA ≈ 9.0), yielding fruit with high levels of anthocyanins and vitamin C; or 62 DAF (SS:TA > 10.0), yielding fruit with high sweetness and large size and weight. For ‘Berel’, it is suggested to be either 52 DAF (SS:TA ≈ 6.5), resulting in fruit with high levels of anthocyanins and vitamin C; or 62 DAF (SS:TA > 7.0), resulting in balanced levels of the fruit quality traits.
Targeting C-X-C motif chemokine receptor 4 (CXCR4), as an oncogenic factor in Waldenström’s Macroglobulinemia (WM), has been considered a promising treatment strategy, and various CXCR4 antagonists, such as small molecules, peptides, and antibodies, are currently in preclinical and clinical phases. Recently, a 16-mer fragment of human serum albumin, the most abundant protein in plasma, has been identified as a potent inhibitor of CXCR4. Hence, it was given the name Endogenous Peptide Inhibitor of CXCR4 (EPI-X4) and demonstrated a less toxic alternative to the current therapies due to its improved selectivity profile. Further research has led to the discovery of optimized EPI-X4 derivatives, JM#21, and WSC02, as potent CXCR4 antagonists. Despite the ongoing research in this area, the molecular basis of how EPI-X4 and its derivatives bind to CXCR4 is still unexplored. In this study, three aspects were investigated using molecular dynamics (MD) simulations and binding energy calculations: (1) mapping the structure- function of the amino acid sequence composition of the peptides to determine the contribution of each amino acid towards the overall binding to CXCR4, as well as the key interaction peptide motifs; (2) the detailed binding mechanism of EPI-X4, JM#21, and WSC02 against CXCR4 at the molecular level; and (3) the impact of peptide binding on the conformational landscape of CXCR4. Per-residue energy decomposition analysis revealed that the inclusion of arginine residue in the peptide sequence has significantly improved the binding affinity towards CXCR4, particularly at positions Arg3 for EPI-X4 and WSC02 and Arg3 and Arg6 for JM#21. This may explain the finding that JM#21 exhibited the highest binding affinity. Additionally, MD simulations coupled with thermodynamic calculations provided a comprehensive picture of the “dynamic” interaction motif of the peptides with CXCR4. Separate MD simulations in a POPC bilayer were executed to determine its effect on the binding energy. This study provides molecular insights into the binding mechanism of the endogenous peptide EPI-X4 and its optimized derivatives with CXCR4, laying the basis for the rational design of optimized peptide derivatives against WM.
Various features of Origin 7.5, computer software were discussed. Origin 7.5 requires Window XP professional and minimum 128 MB of RAM. Origin 7.5 has a more intuitive plotting interface using a plot setup dialouge and an import wizard to provide visual assistance when importing binary and ASCII data files. The software has an improved day/time support which can utilize a variety of customized formats and the inter-range instrumentation group (IRIG) time format.
The design and blood brain barrier crossing of glycine/NMDA receptor antagonists are of significant interest in pharmaceutical research. The use of these antagonists in stroke or seizure reduction have been considered. Measuring the inhibitory concentrations, however, can be time-consuming and costly. The use of quantitative structure-activity relationships to estimate IC(50) values for these receptor antagonists is an attractive alternative compared to experimental measurement. A data set of 109 compounds with measured log(IC(50)) values ranging from -0.57 to 4.5 is used. Structural information is encoded with numerical descriptors for topological, electronic, geometric, and polar surface properties. A genetic algorithm with a computational neural network fitness evaluator is used to select the best descriptor subsets. Multiple linear regression and computational neural network models are developed. Additionally, a quantitative radial basis function neural network (QRBFNN) was developed with the intent of introducing nonlinearity at a faster speed. A genetic algorithm using the radial basis function network as a fitness evaluator was also developed to search descriptor space for optimum subsets. All models are tested using an external prediction set. The nonlinear computational neural network model has root-mean-square errors of approximately half a log unit.