PCA Analysis Research Articles

Synergic effect of thermo-chemical pretreatment of waste-activated sludge on bio-methane enhancement

Sustainable and environmentally friendly energy production is feasible via anaerobic digestion (AD) of organic wastes, such as waste-activated sludge (WAS). However, due to its limited degradation, a pretreatment strategy is applied to WAS to enhance its bio-degradation and, thus, biogas yield. Alkaline (0.5%–9% g NaOH/gTS, 30 min), microwave (MW) (90°C–175°C), and hybrid (0.5% g NaOH/gTS +125°C) pretreatments were applied to WAS. The characterization of untreated and pretreated WAS revealed that with higher alkaline and MW pretreatment, the soluble chemical oxygen demand (sCOD), carbohydrate, and protein increased; however, the readily biodegradable COD (rbCOD) rate was unlike the sCOD. The sCOD was 7%–18%, 8%–23%, and 37% for alkaline, MW, and hybrid pretreatments, respectively. Stronger alkaline and MW pretreatment induced higher turbidity, capillary suction time, and lower average particle size. AD of alkaline-, MW-, and hybrid-pretreated WAS produced 94% (0.5% NaOH), 125% (MW at 125°C), and 199% (0.5% NaOH and MW at 125°C) increased biogas, respectively, compared to the AD of untreated sludge. The AD data on the alkaline-, MW-, and hybrid-pretreated BMP assays fitted well with the modified Gompertz model with a coefficient of determination above 0.95. The PCA analysis showed that biogas production is closely correlated with pretreatment temperature, VFA production, rbCOD, sCOD, and soluble carbohydrates and protein. Microbial genome sequencing analysis showed an improvement in microbial abundance and diversity. Acetoclastic methanogen (Methanothrix) growth was improved by 37% (MW pretreatment). Abundances of Methanosarcina, using all three metabolic pathways for methanogenesis, were 17, 21, 11, and 48% in the control, alkaline-, MW-, and hybrid-pretreated digestate, respectively, corresponding to 186% improvement in hybrid pretreatment when compared to the control.

Anthropogenic Influence and Climate Change on Water and Nutrient Dynamics in the Kebir-Rhumel Basin, (Northeastern Algeria)

<p>This study investigates the Anthropogenic Influence and Climate Change: Water and Nutrient Dynamics in the Kebir-Rhumel Basin in Northeastern Algeria. Utilizing an advanced methodology and integrating 10 physicochemical variables, this research provides a novel insight into the environmental factors shaping the basin's ecosystem. By employing a PCA analysis, it highlights two distinct factors accounting for 80.90% of the total variance and identifies a strong positive correlation between various variables, particularly NH4+ and PO43-. Two contrasting river areas were noted: Oued Radjas and Oued Rhumel rivers, displaying evidence of anthropogenic activities, and Oued Kebir and Oued El-Kotone rivers, indicative of pristine conditions. Seasonal fluctuations were noted in atmospheric temperature, precipitation, humidity, and wind speed, as well as in physical parameters and nutrient concentrations of surface water, revealing new details about the potential impact of human activities on water quality and ecosystem health. The findings here are not only significant in understanding the dynamics of water quality but also crucial in devising effective management strategies. High EC and TDS values in the Oued Radjas River point to anthropogenic pollution, and high nitrogen nutrient concentrations in the Oued El-Kotonne River hint at potential eutrophication. The study underscores the importance of understanding the interplay between human activities and natural processes in managing water resources and ecosystems. This research contributes to the existing body of knowledge by shedding light on specific aspects of water quality in the region, paving the way for more focused investigations and policy interventions for sustainable development.</p>

HOFE: an interactive forensic entomological database.

The significance of entomological evidence in inferring the time, location and cause of death has been demonstrated both theoretically and practically. With the advancement of sequencing technologies, reports have emerged on necrophagous insects' nuclear genomes, transcriptomes, proteomes and mitochondrial genomes. However, within the field of forensic entomology, there is currently no available database that can integrate, store and share the resources of necrophagous insects. The absence of a database poses an inconvenience to the application of entomological evidence in judicial practice and hampers the development of the forensic entomology discipline. Given this, we have developed the Home Of Forensic Entomology database, encompassing 10 core functional modules: Home, Browse, Mitochondria, Proteome, JBrowse, Search, BLAST, Tools, Case base and Maps. Notably, the 'Tools' module enables multiple sequence alignment analysis (Muscle), homologous protein prediction (Genewise), primer design (Primer), large-scale genomic analysis (Lastz), Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, as well as expression profiling (PCA Analysis, Hcluster and Correlation Heatmap). In addition, the present database also works as an interactive platform for researchers by sharing forensic entomological case reports and uploading data and material. This database provides potential visitors with a comprehensive function for multi-omics data analysis, offers substantial references to researchers and criminal scene investigators and facilitates the utilization of entomological evidence in court. Database URL: http://ihofe.com/.

Comparison of the Bactericidal Effect of Ultrasonic and Heat Combined with Ultrasonic Treatments on Egg Liquids and Additional Analysis of Their Effect by NIR Spectral Analysis.

Eggs are a valuable source of nutrients, but they represent a food safety risk due to the presence of microbes. In this work, three types of egg liquids (albumen, yolk and whole egg) previously contaminated with E. coli were treated with ultrasound (US) and a combination of ultrasound and low (55 °C) temperature (US+H). The US treatment parameters were 20 and 40 kHz and 180 and 300 W power and a 30, 45 or 60 min treatment time. The ultrasonic treatment alone resulted in a reduction in the microbial count of less than 1 log CFU, while the US+H treatment resulted in a reduction in CFU counts to below detectable levels in all three egg liquids. Heat treatment and ultrasound treatment had a synergistic effect on E. coli reduction. For all measurements, except for the whole egg samples treated with US, the 20 kHz treated samples showed a significantly (>90% probability level) lower bactericidal effect than the 40 kHz treated samples. PCA and aquaphotometric analysis of NIR spectra showed significant differences between the heat-treated groups' (H and US+H) and the non-heat-treated groups' (US and control) NIR spectra. LDA results show that heat-treated groups are distinguishable from non-heat-treated groups (for albumen 91% and for egg yolk and whole egg 100%).

A tiny-sized Herpetotheriidae (Mammalia, Metatheria) from the Itaboraí basin (early Eocene), Brazil: Paleobiogeographic and systematic implications for Herpetotheriidae

The Itaboraí Basin, located in Itaboraí, Rio de Janeiro, Brazil, has preserved one of the most important early Eocene vertebrate assemblages of the Southern Hemisphere. Among its representatives, Metatheria comprises its most diverse group, with a minimum of 29 genera and 43 species. Considering this diversity, tiny and very small taxa are represented by Jaskhadelphyidae and closely related taxa, “Peradectoidea”, Sternbergiidae, Derorhynchidae, and an undescribed taxon with uncertain affinities, previously referred to as “cf. Armintodelphys”. Here, this last taxon is named Thylacopygmaeus oliveirai gen. et sp. nov.; it is distinguished by its extremely small size (inferred body mass less than 15 g) and in that its lower molars show the metaconid placed distally to the protoconid and a developed postentocristid. Two PCA analyses of T. oliveirai and other tiny-sized taxa from Itaboraí indicate that the new taxon exhibits distinctive morphometric and morphofunctional patterns compared to other sympatric tiny-sized taxa. The inclusion of T. oliveirai gen. et sp. nov. in a phylogenetic analysis recovered it as the sister taxon of Rumiodon, an early Oligocene herpetotheriid from Peru, based on the presence of a labiolingually compressed metaconid on m3 and a labiolingually compressed protoconid on m4. We group these two taxa within the Herpetotheriidae in a new clade, the Rumiodontinae nov. Contrary to a previous hypothesis, Thylacopygmaeus is not closely related to Armintodelphys. The results confirm the Paleogene occurrence of Herpetotheriidae in South America.

Exploring the antiviral inhibitory activity of Niloticin against the NS2B/NS3 protease of Dengue virus (DENV2)

Dengue virus (DENV2) is the cause of dengue disease and a worldwide health problem. DENV2 replicates in the host cell using polyproteins such as NS3 protease in conjugation with NS2B cofactor, making NS3 protease a promising antiviral drug-target. This study investigated the efficacy of ‘Niloticin’ against NS2B/NS3-protease. In silico and in vitro analyses were performed which included interaction of niloticin with NS2B/NS3-protease, protein stability and flexibility, mutation effect, betweenness centrality of residues and analysis of cytotoxicity, protein expression and WNV NS3-protease activity. Similar like acyclovir, niloticin forms strong H-bonds and hydrophobic interactions with residues LEU149, ASN152, LYS74, GLY148 and ALA164. The stability of the niloticin-NS2B/NS3-protease complex was found to be stable compared to the apo NS2B/NS3-protease in structural deviation, PCA, compactness and FEL analysis. The IC50 value of niloticin was 0.14 μM in BHK cells based on in vitro cytotoxicity analysis and showed significant activity at 2.5 μM in a concentration-dependent manner. Western blotting and qRT-PCR analyses showed that niloticin reduced DENV2 protein transcription in a dose-dependent manner. Besides, niloticin confirmed the inhibition of NS3-protease by the SensoLyte 440 WNV protease detection kit. These promising results suggest that niloticin could be an effective antiviral drug against DENV2 and other flaviviruses.

Dynamics of Noctiluca scintillans blooms: A 20-year study in Jangmok Bay, Korea

This 20-year study (2001–2020) conducted in Jangmok Bay, Korea, assessed the intricate relationships between environmental factors and Noctiluca scintillans blooms. Granger causality tests and PCA analysis were used to assess the impact of sea surface temperature (SST), salinity, dissolved oxygen (DO) concentration, wind patterns, rainfall, and chlorophyll-a (Chl-a) concentration on bloom dynamics. The results revealed significant, albeit delayed, influences of these variables on bloom occurrence, with SST exhibiting a notable 2-month lag and salinity a 1-month lag in their impact. Additionally, the analysis highlighted the significant roles of phosphate, ammonium, and silicate, which influenced N. scintillans blooms with lags of 1 to 3 months. The PCA demonstrates how SST and wind speed during spring and summer, along with wind direction and salinity in winter, significantly impact N. scintillans blooms. We noted not only an increase in large-scale N. scintillans blooms but also a cyclical pattern of occurrence every 3 years. These findings underscore the synergistic effects of environmental factors, highlighting the complex interplay between SST, salinity, DO concentration, and weather conditions to influence bloom patterns. This research enhances our understanding of harmful algal blooms (HABs), emphasizing the importance of a comprehensive approach that considers multiple interconnected environmental variables for predicting and managing N. scintillans blooms.

Study of Volatile Organic Compounds in Emission from Bottom Sediments of Three Lakes with Impact of Anthropopression Using the Proton Transfer Reaction Mass Spectrometry

Studies of volatile organic compounds (VOCs) emitted from the bottom sediments of three Pomeranian lakes in Poland: Łazienkowskie, Rychnowskie, and Jeleń were conducted. All three lakes are subject to anthropogenic pressure but to varying degrees. In 2021, bottom sediment samples were taken from the lakes studied and an analysis of the emission of 20 volatile organic compounds was carried out using a proton transfer reaction mass spectrophotometer (PTR-MS). Concentrations in emissions from the bottom sediments of VOCs with the following mass–charge ratio (m/z) were analyzed: 57, 61, 63, 69, 75, 81, 83, 85, 87, 95, 97, 99, 101, 109, 111, 127, 129, 137, 149, and 157. The obtained data were analyzed by performing statistical tests and multivariate cluster and PCA analysis. The analysis shows that the lowest concentrations of VOCs were observed from bottom sediments in Lake Jeleń, which is subject to the lowest anthropopressure among the studied lakes. The analysis shows that the lowest concentrations of VOCs were observed from bottom sediments in Lake Jeleń, which is subject to lower anthropopressure among the studied lakes. With the help of cluster analysis, it was possible to collect data on the VOC concentrations into clusters, which resulted in demonstrating similarities between Łazienkowskie and Rychnowskie lakes—lakes connected by an isthmus, and the different characteristics of Lake Jeleń. PCA analysis leads to similar observations. The tested m/z VOCs can be identified using additional analytical methods.

Optimal harvest period and quality control markers of cultivated Flos Chrysanthemi Indici using untargeted/targeted metabolomics, chemometric analysis and in vivo study

Ethnopharmacological relevanceFlos Chrysanthemi Indici (FCI), the flower of Chrysanthemum Indicum L., is a popular traditional Chinese medicine (TCM) for treatment of inflammatory diseases in China. FCI is also a functional food, and is widely used as herbal tea for clearing heat and detoxicating. Aim of the studyTo explore quality control markers of FCI based on the optimal harvest period. Materials and methodsFirst, UPLC-Q-TOF/MS based untargeted metabolomics was applied to explore the chemical profiles of FCIs collected at bud stages (BS), initial stages (IS), full bloom stages (FS) and eventual stages (ES) from eight cultivated regions in China. Subsequently, lipopolysaccharide (LPS)-induced RAW264.7 cell inflammatory model and carrageenan-induced rat paw edema model were used to confirm the anti-inflammatory effect of FCIs collected at IS/FS. Then, UPLC-PDA targeted metabolomics was used to quantitatively analyze 9 constituents with anti-inflammatory activity (7 flavonoids and 2 phenolic acids) changed significantly (VIP > 4) during flowering stages. Finally, ROC curves combined with PCA analysis based on the variation of 9 active constituents in FCIs from different flowering stages were applied to screen the quality markers of FCI. ResultsFCIs at IS/FS had almost same chemical characteristics, but quite different from those at BS and ES. A total of 32 constituents in FCIs including flavonoids and phenolic acids were changed during flowering development. Most of the varied constituents had the highest or higher contents at IS/FS compared with those at ES, indicating that the optimal harvest period of FCI should be at IS/FS. FCI extract could effectively suppress nitric oxide (NO) production in LPS-induced RAW264.7 cells and regulate the abnormal levels of cytokines and PGE2 in carrageenan-induced paw edema model rat. The results of quantitatively analysis revealed that the variation trends of phenolic acids and flavonoids in FCIs were different during flowering development, but most of them had higher contents at IS/FS than those at ES in all FCIs collected from eight cultivated regions, except one sample from Anhui. Finally, linarin, luteolin, apigenin and 3,5-dicaffeoylquinic acid were selected as the Q-markers based on the contribution of their AUC values in ROC and clustering of PCA analysis. ConclusionsOur study demonstrates the optimal harvest period of FCI and specifies the multi-constituents Q-markers of FCI based on the influence of growth progression on the active constituents using untargeted/targeted metabolomics. The findings not only greatly increase the utilization rate of FCI resources and improve quality control of FCI products, but also offer new strategy to identify the Q-markers of FCI.

Research on the Use of Organic Fertilizer Instead of Chemical Fertilizer and Its Effect on the Morphological and Yield in Fennel Plant

Objective: Organic manures can be used as an alternative method to replace chemical fertilizers for sustainable agricultural production. Sheep manure and vermicompost are the most important alternative applications. These manures can increase soil fertility, plant productivity, and quality. Fennel (Foeniculum vulgare L.) has been used as a medicinal and aromatic plant throughout human history, and it is widely used as a food additive, pharmacological substance, and medicinal application. Materials and Methods: This study was conducted to determine the effect of different organic applications (sheep manure (SM) and vermicompost manure (VM)-10, 15, and 20 t/ha) and chemical fertilizer (Ammonium sulfate (AS)-40, 80, and 120 kg/ha) with a control (no fertilizer or manure) on the morphology, yield, and essential oil, and fixed oil yield of fennel. Results: The results of the study showed that significant statistical differences were found only in plant height and the fixed oil yield of fennel. The fruit yield ranged from 90.14 kg/da to 122.72 kg/da, and the 80 kg/ha ammonium sulfate (AS-2) and 10 t/ha sheep manure (SM-1) applications had the highest values. Essential oil yield and fixed oil yield changed between 2.57-3.85 L/da and 16.18-36.90 L/da, respectively. The result of the study suggested that applications of SM-1 had the highest thousand fruit weight, fruit yield, essential oil yield, and fixed oil yield compared to other applications. PCA analysis showed the relationships among the examined properties, and component 1 and component 2 revealed 61.50% of the total variation of the valuables. Conclusion: Sheep manure application (SM-1) can be used for the high fruit, essential oil, and fixed oil yield of fennel for sustainable agriculture.

Optimising microbial processes with nano-carbon/selenite materials: An eco-friendly approach for antibiotic resistance mitigation in broiler manure

The presence of antibiotic resistance genes (ARGs) in animal excrement has been a significant threat to global public health, necessitating sustainable animal husbandry practices to mitigate agriculture’s environmental impact. This study introduces two innovative nano-carbon/selenite materials: carbon-based selenite (Cse) and graphene-based selenite (Gse), synthesized using nano-carbon powder and graphene as carriers. These materials, with their high specific surface area, stability, and adsorption capabilities, were hypothesized to modulate microbial structure in broiler manure, potentially reducing ARGs pollution risk through effects on nitrogen metabolism and DNA replication. The order of ARGs abundance in broiler manure was as follows: control (CON) group > Cse group > Gse group, supporting the hypothesis. The top five antibiotic classes made up over 80 % of total gene abundances, with the multidrug class being the most prevalent, reaching 40.69 % and 40.48 % in Cse and Gse groups, respectively. PCA and LEfSe analyses revealed different ARG subtypes and biomarkers in the groups, showing the impact of these materials on ARG subtypes. Notably, the study demonstrated that Gse, utilizing graphene, exhibited greater efficacy in inhibiting essential microbial DNA replication genes compared to Cse. Additionally, the research identified associations between microbial DNA replication genes and ARGs, indicating a potential relationship between DNA replication and cellular reactions to antibiotics. Furthermore, both Cse and Gse were found to significantly impact nitrogen cycling pathways, possibly through their distinct characteristics that could alter key gene abundance. The findings expand our understanding of the genetic mechanisms underlying biogeochemical processes at a microscopic level. The study also reveals new ideas for mitigating potential hazards of ARGs in livestock waste to human well-being and ecological stability arising.

Impact of PAHs compounds on air quality in Maragheh city: Probabilistic risk assessment and source apportionment

This study explores the concentrations and spatial distribution of polycyclic aromatic hydrocarbons (PAHs) in the ambient air of Maragheh city, Iran, while evaluating their potential health implications. PAHs levels were examined in PAHs-bound to particulate matter samples collected from diverse locations across the city. The results showed that in all sampling points, there was contamination by PAHs. The mean total PAHs concentration was 11.5 ng.m−3, with Benzo[a]pyrene (BaP) emerging as the predominant compound. Comparative analysis with other cities revealed relatively lower BaP levels in Maragheh, yet surpassing WHO guidelines in 92 % of samples. Spatial assessment heightened pollution in areas characterized by heavy traffic and industrial operations. Based on PCA analysis, it appears that 74 % of PAHs compounds originate from vehicle emissions, 13 % from the combustion of petroleum, and 6 % from a possible petroleum source. Health risk appraisal uncovered escalated carcinogenic and mutagenic hazards, especially among children. While risks remained below USEPA thresholds, ongoing monitoring and targeted interventions are advised to mitigate PAHs pollution in Maragheh and similar urban locales. Future endeavors should prioritize source elucidation, health impact assessments, and public awareness initiatives to safeguard community well-being.

Candida albicans in the oral cavities of pets: biofilm formation, putative virulence, antifungal resistance profiles and classification of the isolates.

The study aimed to investigate Candida albicans presence, antifungal resistance, biofilm formation, putative virulence genes, and molecular characterization in oral samples of dogs and cats. A total of 239 oral samples were collected from cats and dogs of various breeds and ages at Erciyes University, Faculty of Veterinary Medicine Clinics, between May 2017 and April 2018. Among 216 isolates obtained, 15 (6.95%) were identified as C. albicans, while 8 (3.7%) were non-albicans Candida species. Antifungal susceptibility testing revealed sensitivities to caspofungin, fluconazole, and flucytosine in varying proportions. Molecular analysis indicated the presence of fluconazole and caspofungin resistance genes in all C. albicans isolates. Additionally, virulence genes ALS1, HWP1, and HSP90 showed variable presence. Biofilm formation varied among isolates, with 46.7% strong, 33.3% moderate, and 20% weak producers. PCA analysis categorized isolates into two main clusters, with some dog isolates grouped separately. The findings underscore the significance of oral care and protective measures in pets due to C. albicans prevalence, biofilm formation, virulence factors, and antifungal resistance in their oral cavity, thereby aiding clinical diagnosis and treatment in veterinary medicine.

Morphological and genetic diversity of Eichwald Toad, Bufo eichwaldi in marginal populations of the east and west Caspian Sea lowland

The Eichwald Toad, Bufo eichwaldi is one of the endemic amphibians distributed throughout Hyrcanian forests, marshes, wetlands, and streams in the north of Iran and the south of Azerbaijan. Populations of B. eichwaldi have previously been studied based on a few molecular and morphological data. Here, we undertake taxonomic and phylogenetic analyses based on morphological and morphometric features for 56 specimens of B. eichwaldi from Iran, and mitochondrial cyt b marker for 20 specimens from the whole species range in the west and east Caspian Sea lowland. Molecular analyses based on 794 bp of cyt b gene demonstrated two clusters: the east Caspian Sea lowland (A1) and the west Caspian Sea lowland (A2) clusters. Univariate analyses indicated six out of 25 morphometric variables in male B. eichwaldi specimens from the east (A1) are significantly different from male specimens of B. eichwaldi from the west Caspian Sea (A2; P≤0.05). Females have been also significantly different between two clusters in one character (distance between lids; P≤0.05). Sexual size dimorphism was also significantly different within and between populations in some variables. However, the PCA analyses show no differentiation among B. eichwaldi populations in the east and west Caspian Sea lowland. Based on p-distance parameter, the east and west groups showed a low level of genetic differentiation (0.2%).

Weighted gene coexpression network analysis and machine learning for the determination of tfh cell and B cell infiltrating biomarkers in thymoma-associated myasthenia gravis

Patients with thymoma (THYM)-associated myasthenia gravis (MG) typically have a poor prognosis and recurring illness. This study aimed to discover important biomarkers associated with immune cell infiltration and THYM-associated MG (THYM-MG) development. Gene expression microarray data were downloaded from The Cancer Genome Atlas website (TCGA) and Gene Expression Omnibus (GEO). A total of 102 differentially expressed genes were investigated. According to the immune infiltration data, the distribution of Tfh cells, B cells, and CD4 T cells differed significantly between the THYM-MG and THYM-NMG groups. WGCNA derived 25 coexpression modules; one hub module (the blue module) strongly correlated with Tfh cells. Combining differential genes revealed 21 intersecting genes. LASSO analysis subsequently revealed 16 hub genes as potential THYM-MG biomarkers. ROC curve analysis of the predictive model revealed moderate diagnostic value. The association between the 16 hub genes and infiltrating immune cells was further evaluated in TIMER2.0 and the validation dataset. Draggability analysis identified the therapeutic target genes PTGS2 and ALB, along with significant drugs including Firocoxib, Alclofenac, Pyridostigmine, and Stavudine. This was validated through MD simulation, PCA, and MM-GBSA analyses. The interaction between numerous activated B cells and follicular helper T cells is closely associated with THYM-MG pathogenesis from a bioinformatics perspective. Hub genes (including SP6, SCUBE3, B3GNT7, and MAGEL2) may be downregulated in immune cells in THYM-MG and associated with progression.

Bioavailable fractions of heavy metals in the road dust during infrastructure construction at urban Coimbatore and its potential health implications, India.

Over the past two decades the Global South is witnessing unprecedented economic transformation and Asian Cities in particular have a remarkable upsurge. Coimbatore, an industrial city in Southern India with an estimated population of 2 million (in 2022) is witnessing a rapid transition in terms of infrastructure development. In this context, the present study attempts to assess the particulate matter (PM10 and PM2.5) emissions at road network construction sites and the heavy metal fractionation in the road dust/sediment samples with a core focus to quantify the bioavailable fraction of metals (Fe, Cu, Cr, Cd, Pb and Ni) and its source apportionment in the road side dust/sediment samples. About 60 composite road dust/sediment samples were collected for heavy metal fractionation analysis in the six arterial roads that undergo core developments like construction of road over bridges, additional road incorporation and street expansions. PM monitoring revealed that 24h average PM2.5 (47µg/m3) and PM10 (69µg/m3) concentrations at many construction sites exceeded 24h average recommended by WHO guidelines [PM2.5 (15µg/m3) and PM10 (45µg/m3), respectively]. The bioavailable fractions of Fe, Cu, Cr and Cd are notably higher in the roadside sediment samples at road construction sites. Health Risk assessment, such as carcinogenic risks (Children-4.41 × 10-2, Adult-3.598 × 10-6) and non-carcinogenic risks, inferred substantial risks at high intensity construction sites with statistical analyses, including PCA and cluster analysis, indicating considerable anthropogenic influences in the heavy metal fractions.

Hubungan komunitas moluska dengan parameter lingkungan di kawasan mangrove Pulau Penyu, Tanjung Benoa, Bali

Mangroves are plants in coastal and estuary areas that are influenced by tides. Mangroves provide essential habitats as spawning, nursery and food sources for various biota, including mollusks. Mollusks have a reciprocal relationship with mangrove plants, play an important role in maintaining the balance of the food chain in mangrove ecosystems. The objective of the research is to establish the structure of the mollusk community and its correlation with environmental conditions in the Pulau Penyu mangroves. The study was carried out in September 2023. The method employed the 1x1m quadrat transect with 15 points per station. Salinity, pH, temperature and substrate type are all measurements of environmental conditions. The research revealed 24 species, including 20 gastropod species and 4 bivalvia species from 12 mollusk families. Families found include Potamididae, Cerithiidae, Batillariidae, Ellobiidae, Mitridae, Neritidae, Littorinidae, Naticidae, Muricidae, Veneridae, Cyrenidae and Corbulidae. Mollusk abundance ranged from 0,07 to 13,07 ind/m2 at the research site, with Cerithium coralium being the most abundant species and Corbula macgillivrayi being the least abundant. The results of diversity index is 1,90 to 2,25; evenness index is 0,68 to 0,78; dominance index is 0,18 to 0,25; indicating moderate species diversity, high individual numbers each species, and no dominant species. The range of environmental parameter values obtained were; temperature ranges from 34,1 to 35,37 oC; pH ranges from 6,43 to 6,68; and salinity ranges from 35,2 to 36,3 ppt. The substrate type at the research site was sandy clay and clayey sand. PCA analysis results indicate a strong relationship between mollusk abundance and pH, salinity and sand fraction, but very weak relationship with temperature, dust and clay fraction.

The Geochemistry of Unalloyed Copper Metallurgical Group Indicates Copper Ore Sources in the Late Bronze and Early Iron Ages of the Urals

Trace elements in copper artifacts from Late Bronze and Early Iron Age sites in the Urals, formerly attributed to the metallurgical group of “chemically pure” copper, were analyzed using the method of laser ablation inductively coupled plasma mass spectrometry. The metal of which artifacts included in this group are made reveals geochemical markers suggesting that “pure” copper actually falls into several subgroups. The PCA analysis of the results identifies 11 clusters corresponding to various sources of copper ores and their mixtures. At least seven principal associations can be linked to copper deposits of different geological types and origin: Au-Te-Bi, Au-Se-Te-Sb, Fe-Co-Ni-As-Sb, Fe-Co-Ni -Zn, Se-Co-Fe, Ag-Pb-Ni, and Sb-Pb-Zn-As. Also, several mixed associations reflect the fusion of copper items and metal scrap initially obtained from different sources: Sn-Pb, Fe-Co-Ni-Zn + Sn, Fe-Co-Ni + Au-Te-Bi-Ag, Fe-Co-Ni + Au-Te-Bi + Sn. A separate association, for which the ore source remains unknown, consists of artifacts characterized by a low content of trace elements, jointly making up less than 0.01 wt%. The largest sample in the Late Bronze Age “pure copper” group falls within the Sn-Pb cluster representing a mixture of local copper and imported Sn-containing copper scrap. Judging by trace elements, the main sources of ore in the “pure copper” group of the Itkul and Sarmatian cultures were the Gumeshki mine and another unidentified source. Both could have been used already in the Final Bronze Age.

Molecular Dynamics Simulations and Binding Free Energy Calculations to Discover New Insights into NLRP3 Inhibitors

Background: Inflammation is an immunological reaction against an aggressor agent. NLRP3 inflammasome is a component of the immune system, which, when excessively activated, results in several inflammatory diseases, making it an attractive target for discovering antiinflammatory drugs. Computer-Aided Drug Design (CADD) techniques are powerful tools used to search for new drugs in less time and financial cost. Recently, studies demonstrated the CADD methods to discover information about NLRP3 inhibitors MCC950 and NP3-146. In addition, the discovery of GDC-2394 and its evaluation in clinical trials instigate new studies to find binding modes and structural attributes that can used in drug design works against this target. Objectives: Here, molecular modeling methods were used to discover the significant interactions of GDC-2394, MCC950, and NP3-146 with NLRP3 to obtain helpful information in drug design compared to other inhibitors. Methods: Molecular docking was performed using GOLD software. The best complexes were submitted into molecular dynamics simulations using GROMACS software, and the MM-PBSA was used to provide the free binding energy, which was performed using the tool g_mmpbsa compiled in GROMACS. Results: The RMSD, RMSF, Rg, SASA, and H-bond plots showed that the compound was stable during MD simulation time (100 ns) for GDC-2394. The PCA analysis for all compounds verified similar variance of the complex with the inhibitors to the apo-NLRP3, indicative of stability. DCCM analysis showed the best correlation in residues 134 - 371 region, which contains critical amino acids from the binding site (Ala227, Ala228, and Arg578), besides the newly identified residues. Using MMPBSA to provide the binding free energy, it was observed that the high affinity of the drugs against NLRP3 is related to the lower rigidity of the structure. Furthermore, we identified the critical residues Phe575, Pro352, Tyr632, and Met661 related to the coupling process. result: Then, RMSD, RMSF, Rg, SASA, and H-bond plots showed that the compound was stable during MD simulation time (100 ns) for GDC-2394. The PCA analysis for all compounds verified similar variance of the complex with the inhibitors to the apo-NLRP3, indicative of stability. Through DCCM analysis, the best correlation was observed in residues 134 - 371 region, which contains critical amino acids from the binding site (Ala227, Ala228, and Arg578), besides the newly identified residues. Using MM-PBSA to provide the binding free energy, it was observed that the high affinity of the drugs against NLRP3 is related to the lower rigidity of the structure. Furthermore, we identified the critical residues Phe575, Pro352, Tyr632, and Met661 related to the coupling process. Conclusion: Thus, these discoveries may contribute to the development of new anti-inflammatory drugs, such as NLRP3 inhibitors.

Varying the ratio of Lys: Met through enhancing methionine supplementation improved milk secretion ability through regulating the mRNA expression in bovine mammary epithelial cells under heat stress.

The ratio of lysine (Lys) to methionine (Met) with 3.0: 1 is confirmed as the "ideal" profile for milk protein synthesis, but whether this ratio is suitable for milk protein synthesis under HS needs to be further studied. To evaluate the molecular mechanism by which HS and Lys to Met ratios affect mammary cell functional capacity, an immortalized bovine mammary epithelial cell line (MAC-T) is incubated with 5 doses of Met while maintaining a constant concentration of Lys. The MAC-T cells was treated for 6 h as follow: Lys: Met 3.0: 1 (control 37°C and IPAA 42°C) or treatments under HS (42°C) with different ratios of Lys: Met at 2.0: 1 (LM20), 2.5: 1 (LM25), 3.5: 1 (LM35) and 4.0: 1 (LM40). RNA sequencing was used to assess transcriptome-wide alterations in mRNA abundance. The significant difference between control and other groups was observed base on PCA analysis. A total of 2048 differentially expressed genes (DEGs) were identified in the IPAA group relative to the control group. Similarly, 226, 306, 148, 157 DEGs were detected in the LM20, LM25, LM35 and LM40 groups, respectively, relative to the IPAA group. The relative mRNA abundance of HSPA1A was upregulated and anti-apoptotic genes (BCL2L1 and BCL2) was down-regulated in the IPAA group, compared to the control group (p < 0.05). Compared with the IPAA group, the relative mRNA abundance of anti-apoptotic genes and casein genes (CSN1S2 and CSN2) was up-regulated in the LM25 group (p < 0.05). The DEGs between LM25 and IPAA groups were associated with the negative regulation of transcription RNA polymerase II promoter in response to stress (GO: 0051085, DEGs of BAG3, DNAJB1, HSPA1A) as well as the mTOR signaling pathway (ko04150, DEGs of ATP6V1C2, WNT11, WNT3A, and WNT9A). Several DEGs involved in amino acids metabolism (AFMID, HYKK, NOS3, RIMKLB) and glycolysis/gluconeogenesis (AFMID and MGAT5B) were up-regulated while DEGs involved in lipolysis and beta-oxidation catabolic processes (ALOX12 and ALOX12B) were down-regulated. These results suggested that increasing Met supply (Lys: Met at 2.5: 1) may help mammary gland cells resist HS-induced cell damage, while possibly maintaining lactation capacity through regulation of gene expression.