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Sugarcane (Saccharum officinarum, Poaceae) is cultivated on a large scale in (sub)tropical regions such as Brazil and has considerable economic value for sugar and biofuel production. The plant is a rich substrate for endo- and epiphytic fungi. Black yeasts in the family Herpotrichiellaceae (Chaetothyriales) are colonizers of human-dominated habitats, particularly those rich in toxins and hydrocarbon pollutants, and may cause severe infections in susceptible human hosts. The present study assessed the diversity of Herpotrichiellaceae associated with sugarcane, using in silico identification and selective isolation. Using metagenomics, we identified 5833 fungal sequences, while 639 black yeast-like isolates were recovered in vitro. In both strategies, the latter fungi were identified as members of the genera Cladophialophora, Exophiala, and Rhinocladiella (Herpotrichiellaceae), Cyphellophora (Cyphellophoraceae), and Knufia (Trichomeriaceae). In addition, we discovered new species of Cladophialophora and Exophiala from sugarcane and its rhizosphere. The first environmental isolation of Cladophialophora bantiana is particularly noteworthy, because this species up to now is exclusively known from the human host where it mostly causes fatal brain disease in otherwise healthy patients.

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River water is an essential human resource that may be contaminated with hazardous microorganisms. However, the risk of yeast infection through river water exposure is unclear because it is highly dependant on individual susceptibility and has therefore not been well-studied, to date. To evaluate this undefined risk, we analysed the fungal communities in less polluted (LP) and highly polluted (HP) river water, as determined using principal coordinate analysis of pollution indicators. We enumerated culturable yeasts using a thermally selective isolation procedure (37 °C) and thus promoted the growth of potentially opportunistic species. Yeast species identified as clinically relevant were then tested for antifungal resistance. In addition, we propose a quantitative microbial risk assessment (QMRA) framework to quantitatively assess the potential risk of yeast infection. Our results indicated that pollution levels significantly altered fungal communities (p = 0.007) and that genera representing opportunistic and pathogenic members were significantly more abundant in HP waters (p = 0.038). Additionally, the yeast species Candida glabrata and Clavispora lusitaniae positively correlated with other pollution indicators, demonstrating the species' indicator potential. Our QMRA results further indicate that higher risk of infection is associated with increased water pollution levels (considering both physicochemical and bacterial indicators). Furthermore, yeast species with higher pathogenic potential present an increased risk of infection despite lower observed concentrations in the river water. Interestingly, the bloom of Meyerozyma guilliermondii during the wet season suggests that other environmental factors, such as dissolved oxygen levels and water turbulence, might affect growth characteristics of yeasts in river water, which consequently affects the distribution of annual infection risks. The presence of antifungal resistant yeasts, observed in this study, could further contribute to variation in risk distribution. Research on the ecophysiology of yeasts in these environments is therefore necessary to ameliorate the uncertainty and sensitivity of the proposed QMRA model. In addition to the vital knowledge on opportunistic and pathogenic yeast occurrence in river water and their observed association with pollution, this study provides valuable methods and insights to initiate future QMRAs of yeast infections.

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Anaerobic fungi (AF), belonging to the phylum Neocallimastigomycota, are a pivotal component of the digestive tract microbiome of various herbivorous animals. In the last decade, the diversity of AF has rapidly expanded due to the exploration of numerous (novel) habitats. Studies aiming at understanding the role of AF require robust and reliable isolation and cultivation techniques, many of which remained unchanged for decades. Using amplicon sequencing, we compared three different media: medium with rumen fluid (RF), depleted rumen fluid (DRF), and no rumen fluid (NRF) to enrich the AF from the feces of yak, as a rumen control; and Przewalski's horse, llama, guanaco, and elephant, as a non-rumen habitats. The results revealed the selective enrichment of Piromyces and Neocallimastix from the feces of elephant and llama, respectively, in the RF medium. Similarly, the enrichment culture in DRF medium explicitly manifested Piromyces-related sequences from elephant feces. Five new clades (MM1-5) were defined from llama, guanaco, yak, and elephant feces that could as well be enriched from llama and elephant samples using non-conventional DRF and NRF media. This study presents evidence for the selective enrichment of certain genera in medium with RF and DRF from rumen as well as from non-rumen samples. NRF medium is suggested for the isolation of AF from non-rumen environments.

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The type strains of all 33 species in the genus Kribbella were tested for growth on oxalate (-OOC-COO-) as sole carbon source. Media were initially formulated to contain sodium oxalate, but even a concentration as low as 7.5 mM oxalate prevented growth. A modified medium based on calcium oxalate was very successful in characterising oxalate utilisation by Kribbella strains (metabolism of oxalate by oxalotrophic bacteria results in visible zones of clearing around the growth streaks on the opaque plates). To assess the variability of oxalate utilisation in Kribbella species, we also tested eight non-type strains for their ability to use oxalate. Thirty of 33 type strains (90.9%) and six of eight non-type strains (75%) were able to use oxalate as a sole carbon source. Based on these results, we propose that oxalate would be an excellent carbon source for the selective isolation of Kribbella strains. Based on the oxalate-utilisation phenotype and analyses of the 19 publicly available Kribbella type-strain genome sequences, we propose a pathway for oxalate metabolism in Kribbella. This pathway is significantly different from those previously proposed for oxalate metabolism in other bacteria, involving the indirect catabolism of oxalate to formate. Formate production is proposed to be involved in energy generation and to be crucial for oxalate import via an oxalate:formate antiporter. To our knowledge, this is the first report of an oxalate:formate antiporter in an aerobic, Gram-positive bacterium.

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Pseudomonas strains are a promising host cell in metabolic engineering for bioconversion, environmental remediation, and most recently for bioelectrochemical applications. This study isolated an electrochemically active Pseudomonas sp. from an anaerobic sludge using a colorimetric and electrochromic WO3 nanorod (WO3-NR) probe. A strategy was developed to determine the presence of electroactive species from enriched cultures. A mixed consortium was enriched using Pseudomonas isolation media containing betaine and triclosan as the carbon source and antibacterial reagent, respectively. A single blue colony was isolated using WO3-NR sandwiched agar plates. The isolate was sequenced by 16 s rRNA and designated Pseudomonas aeruginosa PBH03, producing phenazines and pyocyanin aerobically. The isolate exhibited clear electrochemical characteristics from cyclic voltammetry and linear sweep voltammetry and produced a current density of 9.01 µA cm-2 in a microbial fuel cell.

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Bacteria are well known producers of bioactive secondary metabolites, including some of the most effective antibiotics in use today. While the caves of Oceania are still largely under-explored, they form oligotrophic and extreme environments that are a promising source for identifying novel species of bacteria with biologically active compounds. By using selective media that mimicked a cave environment, and pretreatments that suppressed the growth of fast-growing bacteria, we have cultured genetically diverse bacteria from a limestone cave in Fiji. Partial 16S rRNA gene sequences from isolates were determined and compared with 16S rRNA gene sequences in EzBioCloud and SILVA data bases. Fifty-five isolates purified from culture had Actinomycete-like morphologies and these were investigated for antibacterial activity. Initial screening using a cross streak test with pathogenic bacteria indicated that 34 of the isolates had antibacterial properties. The best matches for the isolates are bacteria with potential uses in the manufacture of antibiotics and pesticides, in bioremediation of toxic waste, in biomining, in producing bioplastics, and in plant growth promotion. Nineteen bacteria were confirmed as Actinomycetes. Thirteen were from the genus Streptomyces and six from genera considered to be rare Actinomycetes from Pseudonocardia, Kocuria, Micromonospora, Nonomuraea. Ten isolates were Firmicutes from the genera Bacillus, Lysinbacillus, Psychrobacillus and Fontibacillus. Two were Proteobacteria from the genera Mesorhizobium and Cupriavidus. Our findings identify a potentially rich source of microbes for applications in biotechnologies.

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In this study, a series of the functionalized mesoporous polystyrene-based microspheres (FMPMs) with different functional comonomers (acrylamide, AM; ethyleneglycol dimethacrylate, EGDMA; hydroxyethyl methacrylate, HEMA) and ratios of styrene (St) to divinylbenzene (DVB) were designed and synthesized by a double emulsion interface polymerization method. Among them, St and DVB existed in the oil phase, forming the skeleton structure of FMPMs. AM, EGDMA or HEMA in the water phase formed functional layers on the inner and outer surfaces of FMPMs. The experimental results indicated that the optimal functional comonomers and the ratio of St to DVB were AM (provided the hydrophilic -CONH2 groups) and 1:1, respectively. Thus, A-FMPMs-2 exhibited the highest adsorption capacity of 108.95 ± 8.13 mg/g and the selectivity of 5.14 ± 0.17. These results were attributed to the hydrophilic -CONH2 groups on A-FMPMs-2, and these groups were beneficial to ACT molecules diffusion driven by concentration gradient, improving the adsorption performance. Furthermore, hydrophilic -CONH2 groups on the inner and outer surfaces of A-FMPMs-2 acted as hydrophilic sites that had a high-affinity interaction with ACT molecules, thus increasing the adsorption selectivity. In addition, A-FMPMs-2 had the highest specific surface area and largest pore volume, resulting in the highest adsorption capacity and adsorption selectivity. Therefore, the development of adsorbents with adjustable pore structure and a large number of hydrophilic sites will provide a new strategy for selective separation of bioactive components from natural products.

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AIMS: The current study aimed to evaluate the occurrence of actinomycetes in the Coast of Bejaia City using selective isolation, as well as their bioactivity and phylogenitic diversity. METHODS AND RESULTS: Different selective media and methods were used, leading to the isolation of 103 actinomycete strains. The number of strains was influenced by isolation procedures and their interactions based on a three-way ANOVA and a post hoc Tukey test, which revealed that using M2 medium, dilution of samples followed by moderate heat treatment, and sampling at 10-20 m yielded the highest numbers of actinomycetes. The isolates were screened for their antimicrobial activity against human pathogenic microorganisms using agar and well diffusion methods. Of all the isolates, ten displayed activity against at least one Gram-positive bacterium, of which P21 showed the highest activity against Staphylococcus aureus, Methicillin-resistant S. aureus and Bacillus subtilis, with a diameter of 32, 28 and 25 mm respectively. Subsequently, active isolates were assigned to Streptomyces spp. and Nocardiopsis spp. based on 16S rRNA gene sequencing, including a putative new Streptomyces species (S3). The phenotypic characteristics of the P21 strain were determined, and interesting enzymatic capacities were shown. CONCLUSION: The recovery of actinomycetes along the Coast of Bejaia City was influenced by the isolation procedure. Ten strains displayed interesting antibacterial activity against Gram-positive bacteria, of which the P21 strain was selected as the most active strain. SIGNIFICANCE AND IMPACT OF THE STUDY: This work provides a new insight into the occurrence of actinobacteria in the Coast of Bejaia. It suggests also that polluted environments such as Bejaia Bay could provide access to interesting actinomycetes as sources of antibiotic leads.

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Studies of unculturable microbes often combine methods, such as 16S rRNA sequencing, metagenomics, and metaproteomics. To apply these techniques to the microbial community inhabiting the surfaces of marine macrophytes, it is advisable to perform a selective DNA and protein isolation prior to the analysis to avoid biases due to the host material being present in high quantities. Two protocols for DNA and protein isolation were adapted for selective extractions of DNA and proteins from epiphytic communities inhabiting the surfaces of two marine macrophytes, the seagrass Cymodocea nodosa and the macroalga Caulerpa cylindracea. Protocols showed an almost complete removal of the epiphytic community regardless of the sampling season, station, settlement, or host species. The obtained DNA was suitable for metagenomic and 16S rRNA sequencing, while isolated proteins could be identified by mass spectrometry. Low presence of host DNA and proteins in the samples indicated a high specificity of the protocols. The procedures are based on universally available laboratory chemicals making the protocols widely applicable. Taken together, the adapted protocols ensure an almost complete removal of the macrophyte epiphytic community. The procedures are selective for microbes inhabiting macrophyte surfaces and provide DNA and proteins applicable in 16S rRNA sequencing, metagenomics, and metaproteomics.

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Twenty-eight multidrug-resistant bacterial strains closely related or identical to Pedobacter cryoconitis, Pedobacter lusitanus and Pedobacter steynii were isolated from soil samples by selection for multidrug-resistance. Approximately 3-30% of the selected isolates were identified as Pedobacter, whereas isolation without antibiotics did not yield any isolates of this genus. Next generation sequencing data showed Pedobacter to be on 69th place among the bacterial genera (0.32% of bacterial sequences). The Pedobacter isolates produced a wide array of novel compounds when screened by UHPLC-MS/MSMS, and hierarchical cluster analysis resulted in several distinct clusters of compounds produced by specific isolates of Pedobacter, and most of these compounds were found to be peptides. The Pedobacter strain UP508 produced isopedopeptins, whereas another set of strains produced pedopeptins, which both are known cyclic lipodepsipeptides produced by Pedobacter sp. Other Pedobacter strains produced analogous peptides with a sequence variation. Further strains of Pedobacter produced additional novel antibacterial cyclic lipopeptides (ca 800 or 1400 Da in size) and/or linear lipopeptides (ca 700-960 Da in size). A 16S rRNA phylogenetic tree for the Pedobacter isolates revealed several distinct clades and subclades of isolates. One of the subclades comprised isolates producing isopedopeptin analogs, but the isopedopeptin producing isolate UP508 was clearly placed on a separate branch. We suggest that the non-ribosomal peptide synthases producing pedopeptins, isopedopeptins, and the analogous peptides, may derive from a common ancestral non-ribosomal peptide synthase gene cluster, which may have been subjected to a mutation leading to changed specificity in one of the modules and then to a modular rearrangement leading to the changed sequence found in the isopedopeptins produced by isolate UP508.

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Actinobacteria are a group of ecologically important bacteria capable of producing diverse bioactive compounds. However, much remains unknown about the taxonomic and metabolic diversities of actinobacteria from many geographic regions and ecological niches. In this study, we report the isolation of actinobacteria from moss and moss-associated rhizosphere soils in Thailand. Among the 89 isolates analyzed for their bioactivities, 86 strains produced indole-3-acetic acid (IAA, ranging from 0.04 to 59.12 mg/L); 42 strains produced hydroxamate type of siderophore; 35 strains produced catecholate type of siderophore; 21 strains solubilized tricalcium phosphate; and many strains exhibited antagonistic activities against one to several of the seven selected plant, animal, and human pathogens. Overall, actinobacteria from the rhizosphere soil of mosses showed greater abilities to produce IAA and siderophores and to solubilize tricalcium phosphate than those from mosses. Among these 89 isolates, 37 were analyzed for their 16S rRNA gene sequences, which revealed their diverse phylogenetic distributions among seven genera, Streptomyces, Micromonospora, Nocardia, Actinoplanes, Saccharothrix, Streptosporangium, and Cryptosporangium. Furthermore, gas chromatography-mass spectrometry analyses of ethyl acetate crude extracts of three selected isolates with inhibitory effects against a methicillin-resistant Staphylococcus aureus strain revealed diverse metabolites with known antimicrobial activities. Together, our results demonstrate that actinobacteria from mosses in Thailand are taxonomically diverse and capable of producing a range of metabolites with plant-growth-promoting and microbial pathogen-inhibiting potentials.

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The genus Streptomyces constitutes approximately 50% of all soil actinomycetes, playing a significant role in the soil microbial community through vital functions including nutrient cycling, production of bioactive metabolites, disease-suppression and plant growth promotion. Streptomyces produce many bioactive compounds and are prime targets for industrial and biotechnological applications. In addition to their agrobiological roles, some Streptomyces spp. can, however, be phytopathogenic, examples include, common scab of potato that causes economic losses worldwide. Currently used chemical control measures can have detrimental effect to environmental and human health as a result alternative methods to chemical disease control are being investigated. One alternative is the use of streptomycete specific phages to remove this pathogenic bacterium before it can cause the disease on potatoes. However, due to co-existence of non-common scab-causing species belonging to the genus Streptomyces, phage treatment is likely to affect a wide range of non-target streptomycete species including the beneficial ones in the soil. Therefore, before such treatment starts the host range of the phages within the targeted family of bacteria should be determined. In a study conducted using soil samples from a Tasmanian potato farm, streptomycetes were isolated and tested against streptomycete-specific phages. Their antifungal activity was also determined using multiple assays against selected phytopathogens. The four strongest antifungal activity-displaying isolates were further tested for their persistent antifungal activity using wheat and Fusarium solani in a pot trial. A second pot trial was also conducted to evaluate whether the beneficial streptomycetes were affected by streptophage treatment and whether their removal via the phage battery would cause opportunistic fungal infections to plants in soil. The streptomycetes prevented the reduction in wheat shoot weight caused by F. solani indicating their disease suppressive effect. However, when phages were added into the pots, the growth of wheat was detrimentally impacted. This finding might suggest that the reduced presence of antifungal streptomycetes via phage-induced lysis might encourage opportunistic fungal infections in plants.

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The diagnosis of tumor metastasis using circulating tumor cells (CTCs) has been considered an important developmental target for several decades but remains a formidable challenge because of the rarity and heterogeneity of CTCs. Additional downstream analysis is required after isolating CTCs on-chip for subtype verification. To solve those problems, we have developed microfluidic based integrated system which uses magnetic field gradient and immune-fluorescence differences to on-chip isolation and discrimination of CTCs simultaneously. The system presented in the present study can isolate CTCs with an efficiency of >99% by utilizing magnetic nanoparticles conjugated to CTC membranes. Furthermore, the statuses of three biomarkers can be determined on-chip simultaneously. The devised microfluidic system can differentiate eight different subtypes of heterogenic CTCs by on-chip isolation and based on the statuses of three biomarkers (HER2, ER, and PR) which are critical variables to five-year overall survivals for breast cancer patients.

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Novel flower-type and three-dimensional porous nanoparticles are prepared for the isolation of low density lipoprotein (LDL). The amino-terminated dendritic mesoporous silica nanoparticles (A-DMSNs) show highly accessible central-radial pore (0.655 cm3 g-1) and surface area (362.263 m2 g-1), which play an important role in the superior adsorption capacity of 816.7 µg mg-1. The A-DMSNs is anchored with chondroitin sulfate (CS), shortly termed as ADC, for ensuring the selectivity of the adsorption. The adsorbed LDL is thereafter readily recovered at pH 9.0 by using 4 mmol L-1 Britton-Robinson buffer as stripping reagent, providing a recovery of 79.1%. ADC nanoparticles are further applied as sorbent for the selective isolation of LDL from simulated serum of hypercholesterolemia patient. High-purity LDL is achieved as demonstrated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) assays.

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The prevalence of black fungi in the order Chaetothyriales has often been underestimated due to the difficulty of their isolation. In this study, three methods which are often used to isolate black fungi are compared. Enrichment on aromatic hydrocarbon appears effective in inhibiting growth of cosmopolitan microbial species and allows appearance of black fungi. We miniaturized the method for high-throughput purposes. The new procedure saves time, consumes less space and can process multiple samples simultaneously.

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A metal affinity-carboxymethyl cellulose functionalized magnetic graphene, namely MGCI-Cu composite, was prepared by successive modifications of graphene oxide nanosheets with magnetic nanoparticles, carboxymethyl cellulose (CMC), iminodiacetic acid (IDA) and then chelated with copper ions. The successful modifications of the graphene surface were demonstrated by various characterizations, and a high density of 6.17 µmol m-2 for metal affinity groups was obtained. The composite exhibited high adsorption selectivity toward histidine-rich proteins. The adsorption was governed by strong metal affinity binding force between hisitidine residues of proteins and immobilized Cu2+ ions of MGCI-Cu composite. In particular, highly selective isolation of hemoglobin (Hb) was achieved in 0.2 mol L-1 phosphate buffer at pH 8. The adsorption capacity of Hb significantly increased to 769 mg g-1 in comparison to that of 435 mg g-1 on metal affinity modified magnetic graphene composite (MGI-Cu) without CMC modification. The adsorbed Hb molecules were recovered with a carbonate buffer (0.2 mol L-1 pH 10) containing 0.5 mol L-1 imidazole. MGCI-Cu composite displayed favorable reusability for at least four times after regeneration of the composite by edetic acid (EDTA) and Cu2+ solution. The practical applications demonstrated that MGCI-Cu composite could highly selectively isolate Hb from human whole blood and polyhistidine-tagged recombinant protein from Escherichia coli (E. coli) lysate.

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The genus Burkholderia is an emerging source of novel natural products chemistry, yet to date few methods exist for the selective isolation of strains of this genus from the environment. More broadly, tools to efficiently design selection media for any given genus would be of significant value to the natural products and microbiology communities. Using a modification of the recently published SMART protocol, we have developed a two-stage isolation protocol for strains from the genus Burkholderia. This method uses a combination of selective agar isolation media and multiplexed PCR profiling to derive Burkholderia strains from environmental samples with 95% efficiency. Creation of this new method paves the way for the systematic exploration of natural products chemistry from this important genus and offers new insight into potential methods for selective isolation method development for other priority genera.

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Lipids are gaining relevance over the last 20 years, as our knowledge about their role has changed from merely energy/structural molecules to compounds also involved in several biological processes. This led to the creation in 2003 of a new emerging research field: lipidomics. In particular the phospholipids have pharmacological/food applications, participate in cell signalling/homeostatic pathways while their analysis faces some challenges. Their fractionation/purification is, in fact, especially difficult, as they are amphiphilic compounds. Moreover, it usually involves SPE or TLC procedures requiring specific materials hampering their suitableness for routine analysis. Finally, they can interfere with the ionization of other molecules during mass spectrometry analysis. Thus, simple high-throughput reliable methods to selectively isolate these compounds based on the difference between chemical characteristics of lipids would represent valuable tools for their study besides that of other compounds. The current review work aims to describe the state-of-the-art related to the extraction of phospholipids using liquid-liquid methods for their targeted isolation. The technological and biological importance of these compounds and ion suppression phenomena are also reviewed. Methods by precipitation with acetone or isolation using methanol seem to be suitable for selective isolation of phospholipids in both biological and food samples.

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Polymeric ionic liquids (PILs) with 1-vinyl-3-ethylimidazolium cations and two different anions of Br- and PF6- were assembled onto the surface of graphene (G) nanosheets. The derived two composites, i.e., PIL(Br)-G and PIL(PF6)-G, were further efficiently immobilized onto the surface of silica nanoparticles via self-assembly technique. The obtained two PIL-G/SiO2 nanocomposites exhibited diverse adsorption performances toward proteins through adjusting the anions of PILs. Electrostatic attractions between proteins and the nanocomposites dominated protein adsorption, while the presence of PF6- anions weakened electrostatic interactions and deteriorated the selective adsorption of target protein, i.e., bovine serum albumin (BSA) in this case. Specifically, PIL(Br)-G/SiO2 nanocomposite displayed high selectivity toward BSA and a high adsorption efficiency of ca. 98% was achieved for 100 mg L-1 BSA in a Britton-Robinson (B-R) buffer at pH 5. HPLC analysis demonstrated the selectivity of PIL(Br)-G/SiO2 nanocomposite toward BSA in the presence of abundant hemoglobin and cytochrome c. The practical applicability was verified by performing selective isolation of human serum albumin (HSA) from human whole blood. Graphical abstract Selective isolation of human serum albumin from blood by polymeric ionic liquid assembled graphene immobilized silica nanocomposite with tunable anions.

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Novel unilamellar and homogeneous titanate nanosheets were prepared by anchoring (3-aminopropyl)triethoxysilane (APTES) and chelating copper ions, also know by the short form Cu-APTES-TiNSs. The nanosheets were uniform two-dimensional lamellas/monolayers with a thickness of 1.9 nm, and they were further characterized by atomic force microscopy, scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectra, X-ray diffraction, X-ray photoelectron spectroscopy, inductively coupled plasma mass spectrometry, and N2 adsorption-desorption. The copper-decorated titanate nanosheets possess a copper content of 4.28 ± 0.14% and exhibit a favorable selectivity to the adsorption of hemoglobin, with a considerable capacity of 5314.2 mg g-1. The adsorbed hemoglobin is easily collected with a recovery rate of 91.3% by using 0.5% w/v sodium dodecyl sulfate as an eluent. Circular dichroism spectra confirmed that virtually no conformational alteration is observed for hemoglobin. Cu-APTES-TiNSs are further applied for the selective adsorption of hemoglobin from the human whole blood.

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