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1.
Int J Biol Macromol ; 275(Pt 1): 133633, 2024 Jul 02.
Article in English | MEDLINE | ID: mdl-38964695

ABSTRACT

Conversion of toxic nitroarenes into less toxic aryl amines, which are the most suitable precursors for different types of compounds, is done with various materials which are costly or take more time for this conversion. In this regards, a silica@poly(chitosan-N-isopropylacrylamide-methacrylic acid) Si@P(CS-NIPAM-MAA) Si@P(CNM) core-shell microgel system was synthesized through free radical precipitation polymerization (FRPP) and then fabricated with palladium nanoparticles (Pd NPs) by in situ-reduction method to form Si@Pd-P(CNM) and characterized with XRD, TEM, FTIR, SEM, and EDX. The catalytic efficiency of Si@Pd-P(CNM) hybrid microgels was studied for reduction of 4-nitroaniline (4NiA) under diverse conditions. Different nitroarenes were successfully transformed into their corresponding aryl amines with high yields using the Si@Pd-P(CNM) system as catalyst and NaBH4 as reductant. The Si@Pd-P(CNM) catalyst exhibited remarkable catalytic efficiency and recyclability as well as maintaining its catalytic effectiveness over multiple cycles.

3.
Int J Biol Macromol ; 274(Pt 1): 133250, 2024 Jun 20.
Article in English | MEDLINE | ID: mdl-38908628

ABSTRACT

In recent years, the synergistic crosslinked networks formed by zinc oxide (ZnO) particles and organic polymers have gained significant attention. This importance is ascribed due to the valuable combination of low band gap containing ZnO particles with responsive behavior containing organic polymers. These properties of both ZnO and organic polymers make a suitable system of crosslinked ZnO-organic polymer composite (CZOPC) for various applications in the fields of biomedicine, catalysis, and environmental perspectives. The literature extensively provided the diverse morphologies and structures of CZOPC, and these architectural structures play a crucial role in determining their efficiency across various applications. Consequently, the careful design of CZOPC shapes tailored to specific purposes has become a focal point. This comprehensive review provides insights into the classifications, synthetic approaches, characterizations, and applications of ZnO particles decorated in organic polymers with crosslinked network. The exploration extends to the adsorption, environmental, catalytic, and biomedical applications of ZnO-organic polymer composites. Adopting a tutorial approach, the review systematically investigates and elucidates the applications of CZOPC with a comprehensive understanding of their diverse capabilities and uses.

4.
Ecol Evol ; 14(6): e11533, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38911496

ABSTRACT

Dams worldwide have significantly altered the composition of riparian forests. However, research on the functional traits of dominant herbs experiencing flooding stress due to dam impoundment remains limited. Given the high plasticity of leaf traits and their susceptibility to environmental influences, this study focuses on riparian herbs along the Three Gorges Hydro-Fluctuation Zone (TGHFZ). Specifically, it investigates how six leaf physiological traits of leading herbs-carbon, nitrogen, phosphorus, and their stoichiometric ratios-adapt to periodic flooding in the TGHFZ using cluster analysis, one-way analysis of variance (ANOVA), multiple comparisons, Pearson correlation analysis, and principal component analysis (PCA). We categorized 25 dominant herb species into three plant functional types (PFTs), noting that species from the same family tended to fall into the same PFT. Notably, leaf carbon content (LCC) exhibited no significant differences across various PFTs or altitudes. Within riparian forests, different PFTs employ distinct adaptation strategies: PFT-I herbs invest in structural components to enhance stress resistance; PFT-II, mostly comprising gramineous plants, responds to prolonged flooding by rapid growth above the water; and PFT-III, encompassing nearly all Compositae and annual plants, responds to prolonged flooding with vigorous rhizome growth and seed production. Soil water content (SWC) emerges as the primary environmental factor influencing dominant herb growth in the TGHFZ. By studying the response of leaf physiological traits in dominant plants to artificial flooding, we intend to reveal the survival mechanisms of plants under adverse conditions and lay the foundation for vegetation restoration in the TGHFZ.

5.
Sci Total Environ ; 943: 173836, 2024 Sep 15.
Article in English | MEDLINE | ID: mdl-38866157

ABSTRACT

To mitigate anthropogenic CO2 emissions and address the climate change effects, carbon capture and storage by mineralization (CCSM) and industrial mineral carbonation are gaining attraction. Specifically, in-situ carbon mineralization in the subsurface geological formations occurs due to the transformation of silicate minerals into carbonates (e.g., CaCO3, MgCO3) while ex-situ carbon mineralization at the surface undergoes chemical reactions with metal cations - thus leading to permanent storage. However, both processes are complex and require a rigorous investigation to enable large-scale mineralization. This paper, therefore, aims to provide an overreaching review of the in-situ and ex-situ methods for carbon mineralization for different rock types, various engineered processes, and associated mechanisms pertinent to mineralization. Furthermore, the factors influencing in-situ and ex-situ processes, e.g., suitable minerals, optimal operating conditions, and technical challenges, have also been inclusively reviewed. Our findings suggest that in-situ carbon mineralization, i.e., subsurface permanent storage of CO2 by mineralization, arguably is more promising than ex-situ mineralization due to energy efficiency and large-scale storage potential. Furthermore, the effect of rock type can be ranked as igneous (basalt) > carbonates (sedimentary) > sandstone (sedimentary) to consider for rapid and large-scale CCSM. The findings of this review will, therefore, help towards a better understanding of carbon mineralization, which contributes towards large-scale CO2 storage to meet the global net-zero targets.

6.
RSC Adv ; 14(27): 19381-19399, 2024 Jun 12.
Article in English | MEDLINE | ID: mdl-38887640

ABSTRACT

In recent years, there has been growing interest in the composites of multi-responsive microgels and silver nanoparticles. This innovative hybrid system harnesses the responsive qualities of microgels while capitalizing on the optical and electronic attributes of silver nanoparticles. This combined system demonstrates a rapid response to minor changes in pH, temperature, ionic strength of the medium, and the concentration of specific biological substances. This review article presents an overview of the recent advancements in the synthesis, classification, characterization methods, and properties of microgels loaded with silver nanoparticles. Furthermore, it explores the diverse applications of these responsive microgels containing silver nanoparticles in catalysis, the biomedical field, nanotechnology, and the mitigation of harmful environmental pollutants.

7.
Int J Nanomedicine ; 19: 5879-5893, 2024.
Article in English | MEDLINE | ID: mdl-38895145

ABSTRACT

Introduction: Persistent endodontic infections (PEIs) mediated by bacterial biofilm mainly cause persistent periapical inflammation, resulting in recurrent periapical abscesses and progressive bone destruction. However, conventional root canal disinfectants are highly damaging to the tooth and periodontal tissue and ineffective in treating persistent root canal infections. Antimicrobial materials that are biocompatible with apical tissues and can eliminate PEIs-associated bacteria are urgently needed. Methods: Here, ε-poly (L-lysine) derived carbon quantum dots (PL-CQDs) are fabricated using pyrolysis to remove PEIs-associated bacterial biofilms. Results: Due to their ultra-small size, high positive charge, and active reactive oxygen species (ROS) generation capacity, PL-CQDs exhibit highly effective antibacterial activity against Enterococcus faecalis (E. faecalis), which is greatly dependent on PL-CQDs concentrations. 100 µg/mL PL-CQDs could kill E. faecalis in 5 min. Importantly, PL-CQDs effectively achieved a reduction of biofilms in the isolated teeth model, disrupting the dense structure of biofilms. PL-CQDs have acceptable cytocompatibility and hemocompatibility in vitro and good biosafety in vivo. Discussion: Thus, PL-CQDs provide a new strategy for treating E. faecalis-associated PEIs.


Subject(s)
Biofilms , Carbon , Enterococcus faecalis , Gram-Positive Bacterial Infections , Polylysine , Quantum Dots , Enterococcus faecalis/drug effects , Enterococcus faecalis/physiology , Quantum Dots/chemistry , Biofilms/drug effects , Polylysine/chemistry , Polylysine/pharmacology , Carbon/chemistry , Carbon/pharmacology , Animals , Gram-Positive Bacterial Infections/drug therapy , Gram-Positive Bacterial Infections/microbiology , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Humans , Reactive Oxygen Species/metabolism , Mice
8.
Environ Pollut ; 356: 124365, 2024 Jun 11.
Article in English | MEDLINE | ID: mdl-38871166

ABSTRACT

Biochar, a carbon-rich material with a unique surface chemistry (high abundance of surface functional groups, large surface area, and well-distributed), has shown great potential as a sustainable solution for industrial wastewater treatment as compared to conventional industrial wastewater treatment techniques demand substantial energy consumption and generate detrimental byproducts. This critical review emphasizes the surface functionalities formation and development in biochar to enhance its physiochemical properties, for utilization in antibiotics removal. Factors affecting the formation of functionalities, including carbonization processes, feedstock materials, operating parameters, and the influence of pre-post treatments, are thoroughly highlighted to understand the crucial role of factors influencing biochar properties for optimal antibiotics removal. Furthermore, the research explores the removal mechanisms and interactions of biochar-based surface functionalities, hydrogen bonding, encompassing electrostatic interactions, hydrophobic interactions, π-π interactions, and electron donor and acceptor interactions, to provide insights into the adsorption/removal behavior of antibiotics on biochar surfaces. The review also explains the mechanism of factors influencing the removal of antibiotics in industrial wastewater treatment, including particle size and pore structure, nature and types of surface functional groups, pH and surface charge, temperature, surface modification strategies, hydrophobicity/hydrophilicity, biochar dose, pollutant concentration, contact time, and the presence of coexisting ions and other substances. Finally, the study offers reusability and regeneration, challenges and future perspectives on the development of biochar-based adsorbents and their applications in addressing antibiotics. It concludes by summarizing the key findings and emphasizing the significance of biochar as a sustainable and effective solution for mitigating antibiotics contamination in industrial wastewater.

9.
medRxiv ; 2024 May 17.
Article in English | MEDLINE | ID: mdl-38798603

ABSTRACT

Hermansky-Pudlak syndrome (HPS) is a group of rare genetic disorders, with several subtypes leading to fatal adult-onset pulmonary fibrosis (PF) and no effective treatment. Circulating biomarkers detecting early PF have not been identified. We investigated whether endocannabinoids could serve as blood biomarkers of PF in HPS. We measured endocannabinoids in the serum of HPS, IPF, and healthy human subjects and in a mouse model of HPSPF. Pulmonary function tests (PFT) were correlated with endocannabinoid measurements. In a pale ear mouse model of bleomycin-induced HPSPF, serum endocannabinoid levels were measured with and without treatment with zevaquenabant (MRI-1867), a peripheral CB1R and iNOS antagonist. In three separate cohorts, circulating anandamide levels were increased in HPS-1 patients with or without PF, compared to healthy volunteers. This increase was not observed in IPF patients or in HPS-3 patients, who do not have PF. Circulating anandamide (AEA) levels were negatively correlated with PFT. Furthermore, a longitudinal study over the course of 5-14 years with HPS-1 patients indicated that circulating AEA levels begin to increase with the fibrotic lung process even at the subclinical stages of HPSPF. In pale ear mice with bleomycin-induced HpsPF, serum AEA levels were significantly increased in the earliest stages of PF and remained elevated at a later fibrotic stage. Zevaquenabant treatment reduced the increased AEA levels and attenuated progression in bleomycin-induced HpsPF. Circulating AEA may be a prognostic blood biomarker for PF in HPS-1 patients. Further studies are indicated to evaluate endocannabinoids as potential surrogate biomarkers in progressive fibrotic lung diseases.

11.
Int J Biol Macromol ; 270(Pt 1): 132331, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38750843

ABSTRACT

Most of the transition metal ions and organic dyes are toxic in nature. Therefore, their removal from water is imperative for human health. For this purpose, various types of systems have been developed to tackle either transition metal ions or organic dyes individually. A core-shell microgel system is introduced which is capable of effectively removing both types (toxic organic dyes and transition metal ions) of pollutants. A long-rod-shaped silica@poly(chitosan-N-isopropylacrylamide-methacrylic acid) S@P(CS-NIPAM-MAA) S@P(CNM) core-shell microgel system was developed by free radical precipitation polymerization method (FRPPM). S@P(CNM) was utilized as an adsorbent for extracting palladium (II) (Pd (II)) ions from water under different concentrations of S@P(CNM), several agitation times, palladium (II) ion content, and pH levels. The adsorption data of Pd (II) ions on S@P(CNM) was evaluated by various adsorption isotherms. The kinetic study was investigated by employing pseudo-2nd order (Ps2O), Elovich model (ElM), intra-particle diffusion (IPDM), and pseudo-1st order (Ps1O). Additionally, palladium nanoparticles (Pd NPs) were generated via in-situ reduction of adsorbed Pd (II) ions within the P(CNM) shell region of S@P(CNM). The resulting Pd NPs loaded S@P(CNM) exhibited the capability to reduce organic pollutants like methyl orange (MeO), 4-nitrophenol (4NiP), methylene blue (MeB), and Rhodamine B (RhB) from aqueous medium. 0.766 min-1, 0.433 min-1, 0.682 min-1, and 1.140 min-1 were the values of pseudo 1st order rate constant (kobs) for catalytic reduction of MeB, 4NiP, MeO, and RhB respectively. The S@Pd-P(CNM) system exhibits significant catalytic potential for various organic transformations.


Subject(s)
Chitosan , Metal Nanoparticles , Palladium , Silicon Dioxide , Water Pollutants, Chemical , Palladium/chemistry , Chitosan/chemistry , Silicon Dioxide/chemistry , Water Pollutants, Chemical/chemistry , Water Pollutants, Chemical/isolation & purification , Adsorption , Metal Nanoparticles/chemistry , Kinetics , Acrylamides/chemistry , Gels/chemistry , Water Purification/methods , Hydrogen-Ion Concentration , Methacrylates/chemistry , Ions/chemistry
12.
J Environ Manage ; 360: 121188, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38759556

ABSTRACT

Afforestation is an acknowledged method for rehabilitating deteriorated riparian ecosystems, presenting multiple functions to alleviate the repercussions of river damming and climate change. However, how ecosystem multifunctionality (EMF) responds to inundation in riparian afforestation ecosystems remains relatively unexplored. Thus, this article aimed to disclose how EMF alters with varying inundation intensities and to elucidate the key drivers of this variation based on riparian reforestation experiments in the Three Gorges Reservoir Region in China. Our EMF analysis encompassed wood production, carbon storage, nutrient cycling, decomposition, and water regulation under different inundation intensities. We examined their correlation with soil properties and microbial diversity. The results indicated a substantial reduction in EMF with heightened inundation intensity, which was primarily due to the decline in most individual functions. Notably, soil bacterial diversity (23.02%), soil properties such as oxidation-reduction potential (ORP, 11.75%), and temperature (5.85%) emerged as pivotal variables elucidating EMF changes under varying inundation intensities. Soil bacterial diversity and ORP declined as inundation intensified but were positively associated with EMF. In contrast, soil temperature rose with increased inundation intensity and exhibited a negative correlation with EMF. Further insights gleaned from structural equation modeling revealed that inundation reduced EMF directly and indirectly by reducing soil ORP and bacterial diversity and increasing soil temperature. This work underscores the adverse effects of dam inundation on riparian EMF and the crucial role soil characteristics and microbial diversity play in mediating EMF in response to inundation. These insights are pivotal for the conservation of biodiversity and functioning following afforestation in dam-induced riparian habitats.


Subject(s)
Ecosystem , Rivers , China , Soil/chemistry , Climate Change , Soil Microbiology , Conservation of Natural Resources
14.
Sci Total Environ ; 933: 173125, 2024 Jul 10.
Article in English | MEDLINE | ID: mdl-38734095

ABSTRACT

The abuse of antibiotics has caused the accumulation of antibiotic residues in environmental media, threatening the ecosystem and human health. Many studies on the distribution of aqueous antibiotics have been reported. However, the pollution status of antibiotics in the environment in Chinese herbal medicine planting areas is rarely comprehensively clarified, resulting in the lack of updated pollution data and conducive suggestions for ecological cultivation and sustainable development of Chinese herbal medicine. Thus, we comprehensively investigated the distribution, profiles, sources, and risks of the antibiotics in the surface water of an important tributary of the Huaihe River Basin, located in Bozhou City, a significant Chinese herbal medicine planting region. Solid-phase extraction coupled with an ultra-performance liquid chromatography-tandem mass spectrometer (SPE-UPLC-MS) was utilized to detect the antibiotics in the water. 27 kinds of antibiotics were identified with total concentrations ranging from 75.01 to 1737.99 ng·L-1, with doxycycline (DC) and doxycycline hydrochloride (DCH) possessed the highest concentration. And DC, DCH, oxilinic acid (OA), sulfamethoxazole (SMZ), clarithromycin (CLA), and roxithromycinum (ROX) were the main antibiotics detected in this basin. Correlation analysis and principal component analysis (PCA) indicated that animal husbandry was the primary source of antibiotics. Furthermore, the ecological risk assessment revealed that certain antibiotics could seriously threaten the survival of aquatic organisms, implying that local Chinese herbal medicines might be at similar growth risk. The drinking risk assessment showed that antibiotics in the water posed low risks for human, and children faced a greater drinking risk than adults. The study can help to facilitate the management of aqueous antibiotic pollution for the ecological cultivation and safe production of Chinese herbal medicine.


Subject(s)
Anti-Bacterial Agents , Environmental Monitoring , Rivers , Water Pollutants, Chemical , Water Pollutants, Chemical/analysis , Anti-Bacterial Agents/analysis , Rivers/chemistry , China , Drugs, Chinese Herbal
15.
Heliyon ; 10(10): e30927, 2024 May 30.
Article in English | MEDLINE | ID: mdl-38779003

ABSTRACT

The purpose of this study was to synthesize ecofriendly nano-composite in which agricultural waste (seeds of Tamarindus indica) was used to synthesize tamarind seed polysaccharides (TSP) and its composite with copper nanoparticles (Cu-NPs) for the purpose of green and clean environment as well as reduction of green-house gases. Confirmation of extracted TSP, synthesized nanocomposite was carried out using FTIR, SEM, PXRD and EDX techniques. In FTIR analysis TSP gives a strong broad peak at 3331 cm-1 due to -OH group and in case of composite its intensity is reduced which might be due to the interactions between -OH and Cu+2 ions. SEM analysis gives that TSP have irregular and rough surface while Cu-NPs exhibited spherical morphology and composite showed clustering of spherical shape to rough surface. EDX analysis quantitatively represented copper having atomic ratio 0.57 % which confirms the synthesis of composite. Furthermore, synthesized composite demonstrated excellent antibacterial activity against gram-positive (S.aureus) and gram-negative bacteria (E.coli) even greater than standard medicine (ciprofloxacin). From this study it was revealed that agriculture waste can be utilized to make environment green as well as synthesized composite from agricultural waste seed also displayed excellent antimicrobial activities which directs that they can be utilized in medical field. This study aims to assess the antimicrobial properties of the nanocomposite, aiming to contribute to the development of effective antimicrobial agents. Through these objectives, the research seeks to bridge the gap between green technology and antimicrobial efficacy, offering a promising avenue for both environmental conservation and healthcare advancements.

16.
Environ Sci Technol ; 58(19): 8464-8479, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38701232

ABSTRACT

Microplastics threaten soil ecosystems, strongly influencing carbon (C) and nitrogen (N) contents. Interactions between microplastic properties and climatic and edaphic factors are poorly understood. We conducted a meta-analysis to assess the interactive effects of microplastic properties (type, shape, size, and content), native soil properties (texture, pH, and dissolved organic carbon (DOC)) and climatic factors (precipitation and temperature) on C and N contents in soil. We found that low-density polyethylene reduced total nitrogen (TN) content, whereas biodegradable polylactic acid led to a decrease in soil organic carbon (SOC). Microplastic fragments especially depleted TN, reducing aggregate stability, increasing N-mineralization and leaching, and consequently increasing the soil C/N ratio. Microplastic size affected outcomes; those <200 µm reduced both TN and SOC contents. Mineralization-induced nutrient losses were greatest at microplastic contents between 1 and 2.5% of soil weight. Sandy soils suffered the highest microplastic contamination-induced nutrient depletion. Alkaline soils showed the greatest SOC depletion, suggesting high SOC degradability. In low-DOC soils, microplastic contamination caused 2-fold greater TN depletion than in soils with high DOC. Sites with high precipitation and temperature had greatest decrease in TN and SOC contents. In conclusion, there are complex interactions determining microplastic impacts on soil health. Microplastic contamination always risks soil C and N depletion, but the severity depends on microplastic characteristics, native soil properties, and climatic conditions, with potential exacerbation by greenhouse emission-induced climate change.


Subject(s)
Carbon , Climate , Microplastics , Nitrogen , Soil , Nitrogen/analysis , Soil/chemistry , Carbon/analysis , Soil Pollutants/analysis
17.
Arch Microbiol ; 206(4): 198, 2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38558101

ABSTRACT

Micro- plastics (MPs) pose significant global threats, requiring an environment-friendly mode of decomposition. Microbial-mediated biodegradation and biodeterioration of micro-plastics (MPs) have been widely known for their cost-effectiveness, and environment-friendly techniques for removing MPs. MPs resistance to various biocidal microbes has also been reported by various studies. The biocidal resistance degree of biodegradability and/or microbiological susceptibility of MPs can be determined by defacement, structural deformation, erosion, degree of plasticizer degradation, metabolization, and/or solubilization of MPs. The degradation of microplastics involves microbial organisms like bacteria, mold, yeast, algae, and associated enzymes. Analytical and microbiological techniques monitor microplastic biodegradation, but no microbial organism can eliminate microplastics. MPs can pose environmental risks to aquatic and human life. Micro-plastic biodegradation involves fragmentation, assimilation, and mineralization, influenced by abiotic and biotic factors. Environmental factors and pre-treatment agents can naturally degrade large polymers or induce bio-fragmentation, which may impact their efficiency. A clear understanding of MPs pollution and the microbial degradation process is crucial for mitigating its effects. The study aimed to identify deteriogenic microorganism species that contribute to the biodegradation of micro-plastics (MPs). This knowledge is crucial for designing novel biodeterioration and biodegradation formulations, both lab-scale and industrial, that exhibit MPs-cidal actions, potentially predicting MPs-free aquatic and atmospheric environments. The study emphasizes the urgent need for global cooperation, research advancements, and public involvement to reduce micro-plastic contamination through policy proposals and improved waste management practices.


Subject(s)
Microplastics , Water Pollutants, Chemical , Humans , Plastics , Biodegradation, Environmental , Industry , Microbiological Techniques
18.
BMC Bioinformatics ; 25(1): 145, 2024 Apr 05.
Article in English | MEDLINE | ID: mdl-38580921

ABSTRACT

BACKGROUND: Drug targets in living beings perform pivotal roles in the discovery of potential drugs. Conventional wet-lab characterization of drug targets is although accurate but generally expensive, slow, and resource intensive. Therefore, computational methods are highly desirable as an alternative to expedite the large-scale identification of druggable proteins (DPs); however, the existing in silico predictor's performance is still not satisfactory. METHODS: In this study, we developed a novel deep learning-based model DPI_CDF for predicting DPs based on protein sequence only. DPI_CDF utilizes evolutionary-based (i.e., histograms of oriented gradients for position-specific scoring matrix), physiochemical-based (i.e., component protein sequence representation), and compositional-based (i.e., normalized qualitative characteristic) properties of protein sequence to generate features. Then a hierarchical deep forest model fuses these three encoding schemes to build the proposed model DPI_CDF. RESULTS: The empirical outcomes on 10-fold cross-validation demonstrate that the proposed model achieved 99.13 % accuracy and 0.982 of Matthew's-correlation-coefficient (MCC) on the training dataset. The generalization power of the trained model is further examined on an independent dataset and achieved 95.01% of maximum accuracy and 0.900 MCC. When compared to current state-of-the-art methods, DPI_CDF improves in terms of accuracy by 4.27% and 4.31% on training and testing datasets, respectively. We believe, DPI_CDF will support the research community to identify druggable proteins and escalate the drug discovery process. AVAILABILITY: The benchmark datasets and source codes are available in GitHub: http://github.com/Muhammad-Arif-NUST/DPI_CDF .


Subject(s)
Proteins , Software , Amino Acid Sequence , Position-Specific Scoring Matrices , Biological Evolution , Computational Biology/methods
19.
Anal Biochem ; 693: 115550, 2024 Apr 26.
Article in English | MEDLINE | ID: mdl-38679191

ABSTRACT

Interactions between proteins are ubiquitous in a wide variety of biological processes. Accurately identifying the protein-protein interaction (PPI) is of significant importance for understanding the mechanisms of protein functions and facilitating drug discovery. Although the wet-lab technological methods are the best way to identify PPI, their major constraints are their time-consuming nature, high cost, and labor-intensiveness. Hence, lots of efforts have been made towards developing computational methods to improve the performance of PPI prediction. In this study, we propose a novel hybrid computational method (called KSGPPI) that aims at improving the prediction performance of PPI via extracting the discriminative information from protein sequences and interaction networks. The KSGPPI model comprises two feature extraction modules. In the first feature extraction module, a large protein language model, ESM-2, is employed to exploit the global complex patterns concealed within protein sequences. Subsequently, feature representations are further extracted through CKSAAP, and a two-dimensional convolutional neural network (CNN) is utilized to capture local information. In the second feature extraction module, the query protein acquires its similar protein from the STRING database via the sequence alignment tool NW-align and then captures the graph embedding feature for the query protein in the protein interaction network of the similar protein using the algorithm of Node2vec. Finally, the features of these two feature extraction modules are efficiently fused; the fused features are then fed into the multilayer perceptron to predict PPI. The results of five-fold cross-validation on the used benchmarked datasets demonstrate that KSGPPI achieves an average prediction accuracy of 88.96 %. Additionally, the average Matthews correlation coefficient value (0.781) of KSGPPI is significantly higher than that of those state-of-the-art PPI prediction methods. The standalone package of KSGPPI is freely downloaded at https://github.com/rickleezhe/KSGPPI.

20.
Environ Res ; 252(Pt 2): 118945, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38631466

ABSTRACT

Microplastics pollution and climate change are primarily investigated in isolation, despite their joint threat to the environment. Greenhouse gases (GHGs) are emitted during: the production of plastic and rubber, the use and degradation of plastic, and after contamination of environment. This is the first meta-analysis to assess underlying causal relationships and the influence of likely mediators. We included 60 peer-reviewed empirical studies; estimating GHGs emissions effect size and global warming potential (GWP), according to key microplastics properties and soil conditions. We investigated interrelationships with microbe functional gene expression. Overall, microplastics contamination was associated with increased GHGs emissions, with the strongest effect (60%) on CH4 emissions. Polylactic-acid caused 32% higher CO2 emissions, but only 1% of total GWP. Phenol-formaldehyde had the greatest (175%) GWP via 182% increased N2O emissions. Only polystyrene resulted in reduced GWP by 50%, due to N2O mitigation. Polyethylene caused the maximum (60%) CH4 emissions. Shapes of microplastics differed in GWP: fiber had the greatest GWP (66%) whereas beads reduced GWP by 53%. Films substantially increased emissions of all GHGs: 14% CO2, 10% N2O and 60% CH4. Larger-sized microplastics had higher GWP (125%) due to their 9% CO2 and 63% N2O emissions. GWP rose sharply if soil microplastics content exceeded 0.5%. Higher CO2 emissions, ranging from 4% to 20%, arose from soil which was either fine, saturated or had high-carbon content. Higher N2O emissions, ranging from 10% to 95%, arose from soils that had either medium texture, saturated water content or low-carbon content. Both CO2 and N2O emissions were 43%-56% higher from soils with neutral pH. We conclude that microplastics contamination can cause raised GHGs emissions, posing a risk of exacerbating climate-change. We show clear links between GHGs emissions, microplastics properties, soil characteristics and soil microbe functional gene expression. Further research is needed regarding underlying mechanisms and processes.


Subject(s)
Global Warming , Greenhouse Gases , Microplastics , Soil Pollutants , Microplastics/analysis , Greenhouse Gases/analysis , Soil Pollutants/analysis , Climate Change , Soil/chemistry , Air Pollutants/analysis
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