The 2004 tsunami and coastal subsidence resulted in 97% mangrove loss in the Nicobar Islands (India), leading to major social-ecological change. We assessed how the Nicobar mangrove social-ecological system (SES) responded to the 2004 event using the adaptive cycle (AC) framework. We describe the changes across AC phases (collapse-Ω, reorganisation-α, growth-r, and conservation-K) concerning various capital types (natural, built, human, social), connectedness and resilience. The subsidence and tsunami triggered a rapid collapse (Ω) in the mangrove SES, particularly depleting natural and built capitals. Despite declines in social and human capital, some knowledge and skills were retained within Nicobari communities. We suggest that locally managed interventions involving mangrove restoration are critical to escape the poverty trap caused by resource insufficiency hindering growth. The AC model helps visualise and describe temporal changes, preparing for recovery challenges. This approach is relevant to SESs beyond Nicobar, offering insights for sites confronting similar social-ecological dynamics and challenges.
{"title":"Shifted baselines: Using the adaptive cycle to assess the post-tsunami mangrove social-ecological system recovery in the Nicobar Islands.","authors":"Nehru Prabakaran, Meenakshi Poti, Jean Hugé, Nico Koedam, Kartik Shanker, Farid Dahdouh-Guebas","doi":"10.1007/s13280-024-02088-3","DOIUrl":"10.1007/s13280-024-02088-3","url":null,"abstract":"<p><p>The 2004 tsunami and coastal subsidence resulted in 97% mangrove loss in the Nicobar Islands (India), leading to major social-ecological change. We assessed how the Nicobar mangrove social-ecological system (SES) responded to the 2004 event using the adaptive cycle (AC) framework. We describe the changes across AC phases (collapse-Ω, reorganisation-α, growth-r, and conservation-K) concerning various capital types (natural, built, human, social), connectedness and resilience. The subsidence and tsunami triggered a rapid collapse (Ω) in the mangrove SES, particularly depleting natural and built capitals. Despite declines in social and human capital, some knowledge and skills were retained within Nicobari communities. We suggest that locally managed interventions involving mangrove restoration are critical to escape the poverty trap caused by resource insufficiency hindering growth. The AC model helps visualise and describe temporal changes, preparing for recovery challenges. This approach is relevant to SESs beyond Nicobar, offering insights for sites confronting similar social-ecological dynamics and challenges.</p>","PeriodicalId":461,"journal":{"name":"Ambio","volume":" ","pages":"536-551"},"PeriodicalIF":5.8,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780072/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142589306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-01Epub Date: 2024-05-25DOI: 10.1007/s13280-024-02015-6
Freya Olsson, Eleanor B Mackay, Bryan M Spears, Philip Barker, Ian D Jones
Globally, climate warming is increasing air temperatures and changing river flows, but few studies have explicitly considered the consequences for lake temperatures of these dual effects, or the potential to manage lake inflows to mitigate climate warming impacts. Using a one-dimensional model, we tested the sensitivity of lake temperatures to the separate and interacting effects of changes in air temperature and inflow on a small, short-residence time (annual average ≈ 20 days), temperate lake. Reducing inflow by 70% increased summer lake surface temperatures 1.0-1.2 °C and water column stability by 11-19%, equivalent to the effect of 1.2 °C air temperature warming. Conversely, similar increases in inflow could result in lake summer cooling, sufficient to mitigate 0.75 °C air temperature rise, increasing to more than 1.1 °C if inflow temperature does not rise. We discuss how altering lake inflow volume and temperature could be added to the suite of adaptation measures for lakes.
{"title":"Interacting impacts of hydrological changes and air temperature warming on lake temperatures highlight the potential for adaptive management.","authors":"Freya Olsson, Eleanor B Mackay, Bryan M Spears, Philip Barker, Ian D Jones","doi":"10.1007/s13280-024-02015-6","DOIUrl":"10.1007/s13280-024-02015-6","url":null,"abstract":"<p><p>Globally, climate warming is increasing air temperatures and changing river flows, but few studies have explicitly considered the consequences for lake temperatures of these dual effects, or the potential to manage lake inflows to mitigate climate warming impacts. Using a one-dimensional model, we tested the sensitivity of lake temperatures to the separate and interacting effects of changes in air temperature and inflow on a small, short-residence time (annual average ≈ 20 days), temperate lake. Reducing inflow by 70% increased summer lake surface temperatures 1.0-1.2 °C and water column stability by 11-19%, equivalent to the effect of 1.2 °C air temperature warming. Conversely, similar increases in inflow could result in lake summer cooling, sufficient to mitigate 0.75 °C air temperature rise, increasing to more than 1.1 °C if inflow temperature does not rise. We discuss how altering lake inflow volume and temperature could be added to the suite of adaptation measures for lakes.</p>","PeriodicalId":461,"journal":{"name":"Ambio","volume":" ","pages":"402-415"},"PeriodicalIF":5.8,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780241/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141097182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-03DOI: 10.1007/s11356-024-35756-8
Poushali Biswas, Amit Kumar, Manjari Upreti, Gajendra Kumar, Purabi Saikia
In the present study, the impact of urban growth on green spaces in Kolkata Metropolitan City (KMC) was evaluated using the multi-temporal satellite observations spanning the last four decades (1990-2022). The study exhibited a rapid rise in urban areas (178.38% growth; net increase 498 sq.km), leading to a significant conversion of areas into moderate to very high built-up density zones. This urbanization has markedly altered the green-blue infrastructure, notably causing a 27% decline in urban green space (UGS) resulting a net loss of 254 sq.km. Fragmentation analysis exhibited a trend of compact, infill development in urban regions, contrasting with outgrowth, which has influenced both the cluster size and quality of UGS over the decades. The multi-indices and biophysical characterization of UGS concluded a deteriorating trend in terms of quantity (- 27.9%) and quality as well with reference. However, the existing UGS are primarily scattered and having less dense. Spatial estimation of above ground biomass (AGB) of UGS using regression analysis of field-derived AGB and L-band SAR backscatter depicted a dominance of low AGB (< 30 t/ha-1) across KMC, while the certain zones with improved UGS exhibited moderate AGB levels (50-100 t/ha-1). The fuzzy AHP-based multi-criteria analysis of urban ecological quality exhibited severe ecological deterioration in the central urban areas, moderate to high in peri-urban regions, and comparatively improved ecological conditions in the peripheral rural parts of KMC. The study also identified major native tree species for plantation strategies comprising urban afforestation, rooftop gardens, and the development of green corridors in ecologically deficient hotspot zones to improve the ecological quality within the urban landscape.
{"title":"Kolkata's green oasis: a comprehensive analysis of urban green spaces for ecosystem sustainability.","authors":"Poushali Biswas, Amit Kumar, Manjari Upreti, Gajendra Kumar, Purabi Saikia","doi":"10.1007/s11356-024-35756-8","DOIUrl":"https://doi.org/10.1007/s11356-024-35756-8","url":null,"abstract":"<p><p>In the present study, the impact of urban growth on green spaces in Kolkata Metropolitan City (KMC) was evaluated using the multi-temporal satellite observations spanning the last four decades (1990-2022). The study exhibited a rapid rise in urban areas (178.38% growth; net increase 498 sq.km), leading to a significant conversion of areas into moderate to very high built-up density zones. This urbanization has markedly altered the green-blue infrastructure, notably causing a 27% decline in urban green space (UGS) resulting a net loss of 254 sq.km. Fragmentation analysis exhibited a trend of compact, infill development in urban regions, contrasting with outgrowth, which has influenced both the cluster size and quality of UGS over the decades. The multi-indices and biophysical characterization of UGS concluded a deteriorating trend in terms of quantity (- 27.9%) and quality as well with reference. However, the existing UGS are primarily scattered and having less dense. Spatial estimation of above ground biomass (AGB) of UGS using regression analysis of field-derived AGB and L-band SAR backscatter depicted a dominance of low AGB (< 30 t/ha<sup>-1</sup>) across KMC, while the certain zones with improved UGS exhibited moderate AGB levels (50-100 t/ha<sup>-1</sup>). The fuzzy AHP-based multi-criteria analysis of urban ecological quality exhibited severe ecological deterioration in the central urban areas, moderate to high in peri-urban regions, and comparatively improved ecological conditions in the peripheral rural parts of KMC. The study also identified major native tree species for plantation strategies comprising urban afforestation, rooftop gardens, and the development of green corridors in ecologically deficient hotspot zones to improve the ecological quality within the urban landscape.</p>","PeriodicalId":545,"journal":{"name":"Environmental Science and Pollution Research","volume":" ","pages":""},"PeriodicalIF":5.8,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-03DOI: 10.1007/s12010-025-05180-w
Uma Kumari, Pratibha Gupta
{"title":"Correction to: Evaluation and Optimization of the Different Process Parameters of Mild Acid Pretreatment of Waste Lignocellulosic Biomass for Enhanced Energy Procreation.","authors":"Uma Kumari, Pratibha Gupta","doi":"10.1007/s12010-025-05180-w","DOIUrl":"https://doi.org/10.1007/s12010-025-05180-w","url":null,"abstract":"","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-03DOI: 10.1007/s11030-025-11122-9
Urvashi Tiwari, Salman Akhtar, Snober S Mir, Mohammad Kalim Ahmad Khan
In this study, we conducted an extensive analysis of 252 bioactive compounds derived from native spices and herbs for their potential anti-breast cancer activity against sterol regulatory element-binding protein (SREBP), using in silico techniques. To evaluate the oral bioavailability, overall pharmacokinetics, and safety profiles of these compounds, we employed Lipinski's rule of five and ADME descriptors, which depicted 66 lead molecules. These molecules were then docked with the SREBP using molecular docking tools, which revealed that diosgenin and smilagenin were the most promising hits compared to the reference inhibitor betulin, with average binding affinities of - 7.42 and - 7.37 kcal/mol and - 6.27 kcal/mol, respectively. To further assess the stability of these complexes along with betulin, we conducted molecular dynamics simulations over a 100 ns simulation period. We employed various parameters, including the root-mean-square deviation, root-mean-square fluctuation, solvent-accessible surface area, free energy of solvation, and radius of gyration, followed by principal component analysis. Furthermore, we evaluated the toxicity of the selected compounds against various anticancer cell lines, as well as their metabolic activity related to CYP450 metabolism and biological activity spectrum. Based on these results, both molecules exhibited promising drug candidate potential and could be utilized for further experimental analysis to elucidate their anticancer potential.
{"title":"Evaluation of selected indigenous spices- and herbs-derived small molecules as potential inhibitors of SREBP and its implications for breast cancer using MD simulations and MMPBSA calculations.","authors":"Urvashi Tiwari, Salman Akhtar, Snober S Mir, Mohammad Kalim Ahmad Khan","doi":"10.1007/s11030-025-11122-9","DOIUrl":"https://doi.org/10.1007/s11030-025-11122-9","url":null,"abstract":"<p><p>In this study, we conducted an extensive analysis of 252 bioactive compounds derived from native spices and herbs for their potential anti-breast cancer activity against sterol regulatory element-binding protein (SREBP), using in silico techniques. To evaluate the oral bioavailability, overall pharmacokinetics, and safety profiles of these compounds, we employed Lipinski's rule of five and ADME descriptors, which depicted 66 lead molecules. These molecules were then docked with the SREBP using molecular docking tools, which revealed that diosgenin and smilagenin were the most promising hits compared to the reference inhibitor betulin, with average binding affinities of - 7.42 and - 7.37 kcal/mol and - 6.27 kcal/mol, respectively. To further assess the stability of these complexes along with betulin, we conducted molecular dynamics simulations over a 100 ns simulation period. We employed various parameters, including the root-mean-square deviation, root-mean-square fluctuation, solvent-accessible surface area, free energy of solvation, and radius of gyration, followed by principal component analysis. Furthermore, we evaluated the toxicity of the selected compounds against various anticancer cell lines, as well as their metabolic activity related to CYP450 metabolism and biological activity spectrum. Based on these results, both molecules exhibited promising drug candidate potential and could be utilized for further experimental analysis to elucidate their anticancer potential.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Since the coronavirus disease 2019 (COVID-19) outbreak, research has been conducted on treatment and countermeasures against the causative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the development of new seeds is urgently needed because viruses have the characteristic of becoming resistant through mutation. We hypothesize that endophytes produce antiviral substances to combat foreign viruses in host plants. According to this hypothesis, the seeds of therapeutic agents for infectious diseases could be obtained from endophytes by culture experiments. This report found that Aspergillus sp. endophyte isolated from Catharanthus roseus produced ( +)-eupenoxide and its 3-ketone form with anti-SARS-CoV-2 activity. In addition, ( +)-eupenoxide-3,6-diketon was discovered as a new compound with potent 3C-like protease inhibitory activity (IC50: 0.048 μM) by synthesis based on ( +)-eupenoxide. This finding could be an important evidence that endophytic fungi symbiosis with medicinal plants is useful as antiviral producers.
{"title":"Potent SARS-CoV-2 3C-like protease inhibitor ( +)-eupenoxide-3,6-diketone (IC<sub>50</sub>: 0.048 μM) was synthesized based on ( +)-eupenoxide; lead from ( +)-eupenoxide analogs study by endophytic fermentation.","authors":"Shoji Maehara, Moeka Kumamoto, Shogo Nakajima, Yuhzo Hieda, Koichi Watashi, Toshiyuki Hata","doi":"10.1007/s11418-024-01874-3","DOIUrl":"https://doi.org/10.1007/s11418-024-01874-3","url":null,"abstract":"<p><p>Since the coronavirus disease 2019 (COVID-19) outbreak, research has been conducted on treatment and countermeasures against the causative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the development of new seeds is urgently needed because viruses have the characteristic of becoming resistant through mutation. We hypothesize that endophytes produce antiviral substances to combat foreign viruses in host plants. According to this hypothesis, the seeds of therapeutic agents for infectious diseases could be obtained from endophytes by culture experiments. This report found that Aspergillus sp. endophyte isolated from Catharanthus roseus produced ( +)-eupenoxide and its 3-ketone form with anti-SARS-CoV-2 activity. In addition, ( +)-eupenoxide-3,6-diketon was discovered as a new compound with potent 3C-like protease inhibitory activity (IC<sub>50</sub>: 0.048 μM) by synthesis based on ( +)-eupenoxide. This finding could be an important evidence that endophytic fungi symbiosis with medicinal plants is useful as antiviral producers.</p>","PeriodicalId":654,"journal":{"name":"Journal of Natural Medicines","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder which is caused by abrupt degeneration of dopaminergic neuronal cells in the substantia nigra pars compacta (SNPc) area of the midbrain. Adenosine A2A receptors have become promising therapeutic targets for PD; however, many A2A receptor antagonists face challenges, such as limited accessibility or failure in clinical trials due to poor selectivity and bioavailability. To identify novel A2A receptor antagonists, a 3D-QSAR-pharmacophore modeling approach was employed, involving virtual screening of ZINC, NCI, and MayBridge databases. The virtual hits were filtered via ADMET criteria to select compounds with favorable bioavailability and solubility profiles. From the MayBridge database, a potent monocyclic A2A receptor antagonist, AW00032 (N-(furan-2-ylmethyl)-5-methylthiazole-4-yl) thiophene-2-sulfonamide, was identified. AW00032 possessed key pharmacophoric features: two lipophilic hydrogen bond acceptors, one hydrophobic aliphatic/aromatic group, and one aromatic ring. Docking analysis revealed AW00032 had a strong binding affinity for A2A receptors (1.23 nM, ∆G - 10.49 kcal/mol), and its ADMET profile indicated good bioavailability. In 6-OHDA induced SH-SY5Y cells, AW00032 increased dopamine levels and tyrosine hydroxylase (TH) expression, demonstrating its potential as an A2A receptor antagonist. AW00032, discovered through 3D-QSAR pharmacophore modeling, also reduced reactive oxygen species (ROS) levels and showed depletion in mitochondrial dysfunction in 6-OHDA-induced SH-SY5Y cells. It exhibited A2A receptor antagonist activity comparable to the standard antagonist ZM241385, partially restoring dopamine and TH levels. Furthermore, AW00032 improved behavioral symptoms in haloperidol-induced C-57 bl/6 mice.
{"title":"Discovery of novel A<sub>2A</sub>R antagonist via 3D-QSAR pharmacophore modeling: neuroprotective effects in 6-OHDA-induced SH-SY5Y cells and haloperidol-induced Parkinsonism in C57 bl/6 mice.","authors":"Ankit Singh, Amresh Prakash, Jyoti Mishra, Pratibha Mehta Luthra","doi":"10.1007/s11030-025-11120-x","DOIUrl":"https://doi.org/10.1007/s11030-025-11120-x","url":null,"abstract":"<p><p>Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder which is caused by abrupt degeneration of dopaminergic neuronal cells in the substantia nigra pars compacta (SNPc) area of the midbrain. Adenosine A<sub>2A</sub> receptors have become promising therapeutic targets for PD; however, many A<sub>2A</sub> receptor antagonists face challenges, such as limited accessibility or failure in clinical trials due to poor selectivity and bioavailability. To identify novel A<sub>2A</sub> receptor antagonists, a 3D-QSAR-pharmacophore modeling approach was employed, involving virtual screening of ZINC, NCI, and MayBridge databases. The virtual hits were filtered via ADMET criteria to select compounds with favorable bioavailability and solubility profiles. From the MayBridge database, a potent monocyclic A<sub>2A</sub> receptor antagonist, AW00032 (N-(furan-2-ylmethyl)-5-methylthiazole-4-yl) thiophene-2-sulfonamide, was identified. AW00032 possessed key pharmacophoric features: two lipophilic hydrogen bond acceptors, one hydrophobic aliphatic/aromatic group, and one aromatic ring. Docking analysis revealed AW00032 had a strong binding affinity for A<sub>2A</sub> receptors (1.23 nM, ∆G - 10.49 kcal/mol), and its ADMET profile indicated good bioavailability. In 6-OHDA induced SH-SY5Y cells, AW00032 increased dopamine levels and tyrosine hydroxylase (TH) expression, demonstrating its potential as an A<sub>2A</sub> receptor antagonist. AW00032, discovered through 3D-QSAR pharmacophore modeling, also reduced reactive oxygen species (ROS) levels and showed depletion in mitochondrial dysfunction in 6-OHDA-induced SH-SY5Y cells. It exhibited A<sub>2A</sub> receptor antagonist activity comparable to the standard antagonist ZM241385, partially restoring dopamine and TH levels. Furthermore, AW00032 improved behavioral symptoms in haloperidol-induced C-57 bl/6 mice.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-03DOI: 10.1007/s00775-025-02096-y
Wai Chung Dorothy Cheng, Yuxin Li, Maileen Nakashima, Pierre Moënne-Loccoz, Katherine W Rush, Arthur Glasfeld
NiaR is a regulatory protein that represses the expression of proteins involved in the de novo biosynthesis and uptake of nicotinic acid (NA), with NA acting as a co-repressor. The previously published structure of NiaR from Thermotoga maritima (TmNiaR) identified it as a functional homodimer containing a transition metal ion in a suspected NA-binding pocket. Here, we present the crystal structure of NA bound to the iron-metalated form of TmNiaR. Supported by spectroscopic and solution studies, this structure shows that NA binds to a protein-bound ferrous ion via its ring nitrogen. In addition, the carboxylate group on NA interacts with Tyr108 from the dyad-related subunit, repositioning the likely DNA-binding domains of the dimer to promote high-affinity interactions with DNA operators. The specificity of TmNiaR for NA can be explained by the hydrogen bonding scheme within the NA-binding pocket.
{"title":"The activation of the metal-containing regulatory protein NiaR from Thermotoga maritima by its effector, nicotinic acid.","authors":"Wai Chung Dorothy Cheng, Yuxin Li, Maileen Nakashima, Pierre Moënne-Loccoz, Katherine W Rush, Arthur Glasfeld","doi":"10.1007/s00775-025-02096-y","DOIUrl":"https://doi.org/10.1007/s00775-025-02096-y","url":null,"abstract":"<p><p>NiaR is a regulatory protein that represses the expression of proteins involved in the de novo biosynthesis and uptake of nicotinic acid (NA), with NA acting as a co-repressor. The previously published structure of NiaR from Thermotoga maritima (TmNiaR) identified it as a functional homodimer containing a transition metal ion in a suspected NA-binding pocket. Here, we present the crystal structure of NA bound to the iron-metalated form of TmNiaR. Supported by spectroscopic and solution studies, this structure shows that NA binds to a protein-bound ferrous ion via its ring nitrogen. In addition, the carboxylate group on NA interacts with Tyr108 from the dyad-related subunit, repositioning the likely DNA-binding domains of the dimer to promote high-affinity interactions with DNA operators. The specificity of TmNiaR for NA can be explained by the hydrogen bonding scheme within the NA-binding pocket.</p>","PeriodicalId":603,"journal":{"name":"Journal of Biological Inorganic Chemistry","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-03DOI: 10.1007/s00894-025-06294-y
Hicham Mahdjoub-Araibi, Mourad Zouaoui-Rabah, Madani Hedidi, Abdelkader M Elhorri, Assia Laib, Mohammed Zenati
<p><strong>Context: </strong>This research is based on the theoretical study of seven push-pull molecules composed of conjugated bridges based on two different organometallic rings, these bridges are linked at their ends by acceptor groups (-NO<sub>2</sub>) and donor groups (-N(CH<sub>3</sub>)<sub>2</sub>) on the α position of the rings mentioned above. The location of the donor and acceptor groups revealed that the addition of the acceptor groups near the rings (Titanol, Ferrol and Nickelol) improves the NLO response in comparison with the grafting of these groups on the Zinkol ring and also influences the positioning of the π electrons at the level of the chromophores studied. The molecule 2B gave the highest values of static first hyperpolarisabilitiy (β<sub>tot</sub>) and static second hyperpolarisabilitiy (γ<sub>av</sub>), knowing that: β<sub>tot</sub> (2B) = 135.79 * 10<sup>-30</sup> esu and γ<sub>av</sub> (2B) = 135.79 * 10<sup>-35</sup> esu. The highest values of dynamic first <math> <mrow><msubsup><mi>β</mi> <mo>‖</mo> <mi>λ</mi></msubsup> <mfenced><mo>-</mo> <mn>2</mn> <mi>ω</mi> <mo>;</mo> <mi>ω</mi> <mo>,</mo> <mspace></mspace> <mi>ω</mi></mfenced> </mrow> </math> and second <math> <mrow><msubsup><mi>γ</mi> <mo>‖</mo> <mi>λ</mi></msubsup> <mfenced><mo>-</mo> <mn>2</mn> <mi>ω</mi> <mo>;</mo> <mi>ω</mi> <mo>,</mo> <mspace></mspace> <mi>ω</mi> <mo>,</mo> <mspace></mspace> <mn>0</mn></mfenced> </mrow> </math> hyperpolarisabilities are assigned to the molecule 1C with the following values: <math> <mrow><msubsup><mi>γ</mi> <mo>‖</mo> <mi>λ</mi></msubsup> <mfenced><mo>-</mo> <mn>2</mn> <mi>ω</mi> <mo>;</mo> <mi>ω</mi> <mo>,</mo> <mspace></mspace> <mi>ω</mi> <mo>,</mo> <mspace></mspace> <mn>0</mn></mfenced> </mrow> </math> =1,218,310.00 * 10<sup>-30</sup> esu and <math> <mrow><msubsup><mi>γ</mi> <mo>‖</mo> <mi>λ</mi></msubsup> <mfenced><mo>-</mo> <mn>2</mn> <mi>ω</mi> <mo>;</mo> <mi>ω</mi> <mo>,</mo> <mspace></mspace> <mi>ω</mi> <mo>,</mo> <mspace></mspace> <mn>0</mn></mfenced> </mrow> </math> =1,324,520,000 * 10<sup>-35</sup> esu. The metal Zn is considered as an acceptor group and the remaining metals (Ti, Fe and Ni) are considered as donor groups. The specific solvents for the seven molecules are water, ethanol and acetonitrile. The maximum wavelengths recorded for all molecules in combination with all solvents are in the range of 421.39 to 765.28 nm. λ METHOD: The calculations were performed using Gaussian 16 software to perform DFT calculations with B3LYP functional. The LanL2DZ basis-set was used for transition metals, while the 6-31 + + G(d,p) basis-set was used for nonmetal atoms. The functionals used are: CAM-B3LYP, LC-wPBE, LC-BLYP, M11, wB97X, M08-HX, M06-2X, MN12SX, MN15, and M06HF. The basis-sets used are: 6-31G(d,p), 6-31 + + G(d,p), cc-pVDZ, aug-cc-pVDZ, 6-311G(d,p), 6-311 + + G(d,p), cc-pVTZ, and aug-cc-pVTZ. The Natural Bond Orbital (NBO) calculations are performed by the NBO program incorporated by default in the Gaus
{"title":"Theoretical study by DFT and TD-DFT of NLO-active push-pull molecules composed of conjugated bridges based on cyclic rings: Titanol, Ferrol, Nickelol and Zinkol.","authors":"Hicham Mahdjoub-Araibi, Mourad Zouaoui-Rabah, Madani Hedidi, Abdelkader M Elhorri, Assia Laib, Mohammed Zenati","doi":"10.1007/s00894-025-06294-y","DOIUrl":"https://doi.org/10.1007/s00894-025-06294-y","url":null,"abstract":"<p><strong>Context: </strong>This research is based on the theoretical study of seven push-pull molecules composed of conjugated bridges based on two different organometallic rings, these bridges are linked at their ends by acceptor groups (-NO<sub>2</sub>) and donor groups (-N(CH<sub>3</sub>)<sub>2</sub>) on the α position of the rings mentioned above. The location of the donor and acceptor groups revealed that the addition of the acceptor groups near the rings (Titanol, Ferrol and Nickelol) improves the NLO response in comparison with the grafting of these groups on the Zinkol ring and also influences the positioning of the π electrons at the level of the chromophores studied. The molecule 2B gave the highest values of static first hyperpolarisabilitiy (β<sub>tot</sub>) and static second hyperpolarisabilitiy (γ<sub>av</sub>), knowing that: β<sub>tot</sub> (2B) = 135.79 * 10<sup>-30</sup> esu and γ<sub>av</sub> (2B) = 135.79 * 10<sup>-35</sup> esu. The highest values of dynamic first <math> <mrow><msubsup><mi>β</mi> <mo>‖</mo> <mi>λ</mi></msubsup> <mfenced><mo>-</mo> <mn>2</mn> <mi>ω</mi> <mo>;</mo> <mi>ω</mi> <mo>,</mo> <mspace></mspace> <mi>ω</mi></mfenced> </mrow> </math> and second <math> <mrow><msubsup><mi>γ</mi> <mo>‖</mo> <mi>λ</mi></msubsup> <mfenced><mo>-</mo> <mn>2</mn> <mi>ω</mi> <mo>;</mo> <mi>ω</mi> <mo>,</mo> <mspace></mspace> <mi>ω</mi> <mo>,</mo> <mspace></mspace> <mn>0</mn></mfenced> </mrow> </math> hyperpolarisabilities are assigned to the molecule 1C with the following values: <math> <mrow><msubsup><mi>γ</mi> <mo>‖</mo> <mi>λ</mi></msubsup> <mfenced><mo>-</mo> <mn>2</mn> <mi>ω</mi> <mo>;</mo> <mi>ω</mi> <mo>,</mo> <mspace></mspace> <mi>ω</mi> <mo>,</mo> <mspace></mspace> <mn>0</mn></mfenced> </mrow> </math> =1,218,310.00 * 10<sup>-30</sup> esu and <math> <mrow><msubsup><mi>γ</mi> <mo>‖</mo> <mi>λ</mi></msubsup> <mfenced><mo>-</mo> <mn>2</mn> <mi>ω</mi> <mo>;</mo> <mi>ω</mi> <mo>,</mo> <mspace></mspace> <mi>ω</mi> <mo>,</mo> <mspace></mspace> <mn>0</mn></mfenced> </mrow> </math> =1,324,520,000 * 10<sup>-35</sup> esu. The metal Zn is considered as an acceptor group and the remaining metals (Ti, Fe and Ni) are considered as donor groups. The specific solvents for the seven molecules are water, ethanol and acetonitrile. The maximum wavelengths recorded for all molecules in combination with all solvents are in the range of 421.39 to 765.28 nm. λ METHOD: The calculations were performed using Gaussian 16 software to perform DFT calculations with B3LYP functional. The LanL2DZ basis-set was used for transition metals, while the 6-31 + + G(d,p) basis-set was used for nonmetal atoms. The functionals used are: CAM-B3LYP, LC-wPBE, LC-BLYP, M11, wB97X, M08-HX, M06-2X, MN12SX, MN15, and M06HF. The basis-sets used are: 6-31G(d,p), 6-31 + + G(d,p), cc-pVDZ, aug-cc-pVDZ, 6-311G(d,p), 6-311 + + G(d,p), cc-pVTZ, and aug-cc-pVTZ. The Natural Bond Orbital (NBO) calculations are performed by the NBO program incorporated by default in the Gaus","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":"73"},"PeriodicalIF":2.1,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-03DOI: 10.1007/s10661-025-13696-1
José Abel Espinoza-Guillen, Marleni Beatriz Alderete-Malpartida, Franchesco David Roncal-Romero, Joycy Claudia Vilcanqui-Sarmiento
The identification of different air pollution sources is essential to effectively control atmospheric pollution, particularly in megacities of emerging countries with rapid economic development, such as the Metropolitan Area of Lima-Callao (MALC). The objective of this research was to identify the main sources of particulate matter pollution by applying bivariate polar plots and the k-means clustering algorithm. These statistical techniques were applied to hourly in situ data of four variables collected over a 5-year period (2015-2019) by the Automatic Air Quality Monitoring Network of the MALC: wind direction, wind speed, PM10, and PM2.5 concentrations. Average PM10 concentrations ranged from 34 μg m-3 (CDM station) to 126.7 μg m-3 (VMT station), while average PM2.5 concentrations ranged from 16.8 μg m-3 (CDM station) to 41.2 μg m-3 (ATE station). The diurnal variation of PM presented two peaks, one in the morning (from 0800 to 1000 h) and the other at night (from 1900 to 2300 h), with the highest concentrations of PM10 recorded at the ATE (0800 h: 155.8 μg m-3) and VMT (2100 h: 154.6 μg m-3) stations, and PM2.5 at the ATE station (0800 h: 60.3 μg m-3 and 2300 h: 37.5 μg m-3). The results showed that the contributions of PM10 are directly related to emissions from industrial activities, automotive fleet, construction, demolition, wind erosion, and the suspension and resuspension of particulates from unpaved roads. Meanwhile, high concentrations of PM2.5 are mainly attributed to vehicle exhaust emissions, industrial emissions, secondary particulate formation, and drag by the action of the winds. The major source of particulate matter contamination is the vehicle fleet, and within this, automobiles, station wagons, combi vans, and 2 and 3-wheel motorcycles are those that have the greatest contribution. These results were supported by non-parametric statistical tests such as Kruskal-Wallis and Mann-Whitney U and validated by the conditional bivariate probability function. The findings of this work may help to implement pollution prevention and control strategies in the future within this South American megacity.
{"title":"Identification of particulate matter (PM<sub>10</sub> and PM<sub>2.5</sub>) sources using bivariate polar plots and k-means clustering in a South American megacity: Metropolitan Area of Lima-Callao, Peru.","authors":"José Abel Espinoza-Guillen, Marleni Beatriz Alderete-Malpartida, Franchesco David Roncal-Romero, Joycy Claudia Vilcanqui-Sarmiento","doi":"10.1007/s10661-025-13696-1","DOIUrl":"https://doi.org/10.1007/s10661-025-13696-1","url":null,"abstract":"<p><p>The identification of different air pollution sources is essential to effectively control atmospheric pollution, particularly in megacities of emerging countries with rapid economic development, such as the Metropolitan Area of Lima-Callao (MALC). The objective of this research was to identify the main sources of particulate matter pollution by applying bivariate polar plots and the k-means clustering algorithm. These statistical techniques were applied to hourly in situ data of four variables collected over a 5-year period (2015-2019) by the Automatic Air Quality Monitoring Network of the MALC: wind direction, wind speed, PM<sub>10</sub>, and PM<sub>2.5</sub> concentrations. Average PM<sub>10</sub> concentrations ranged from 34 μg m<sup>-3</sup> (CDM station) to 126.7 μg m<sup>-3</sup> (VMT station), while average PM<sub>2.5</sub> concentrations ranged from 16.8 μg m<sup>-3</sup> (CDM station) to 41.2 μg m<sup>-3</sup> (ATE station). The diurnal variation of PM presented two peaks, one in the morning (from 0800 to 1000 h) and the other at night (from 1900 to 2300 h), with the highest concentrations of PM<sub>10</sub> recorded at the ATE (0800 h: 155.8 μg m<sup>-3</sup>) and VMT (2100 h: 154.6 μg m<sup>-3</sup>) stations, and PM<sub>2.5</sub> at the ATE station (0800 h: 60.3 μg m<sup>-3</sup> and 2300 h: 37.5 μg m<sup>-3</sup>). The results showed that the contributions of PM<sub>10</sub> are directly related to emissions from industrial activities, automotive fleet, construction, demolition, wind erosion, and the suspension and resuspension of particulates from unpaved roads. Meanwhile, high concentrations of PM<sub>2.5</sub> are mainly attributed to vehicle exhaust emissions, industrial emissions, secondary particulate formation, and drag by the action of the winds. The major source of particulate matter contamination is the vehicle fleet, and within this, automobiles, station wagons, combi vans, and 2 and 3-wheel motorcycles are those that have the greatest contribution. These results were supported by non-parametric statistical tests such as Kruskal-Wallis and Mann-Whitney U and validated by the conditional bivariate probability function. The findings of this work may help to implement pollution prevention and control strategies in the future within this South American megacity.</p>","PeriodicalId":544,"journal":{"name":"Environmental Monitoring and Assessment","volume":"197 3","pages":"226"},"PeriodicalIF":2.9,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}