A recent bottleneck of Y chromosome diversity coincides with a global change in culture

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

Halloysite/Keratin Nanocomposite for Human Hair Photoprotection Coating

We propose a novel keratin treatment of human hair by its aqueous mixtures with natural halloysite clay nanotubes. The loaded clay nanotubes together with free keratin produce micrometer-thick protective coating on hair. First, colloidal and structural properties of halloysite/keratin dispersions and the nanotube loaded with this protein were investigated. Above the keratin isoelectric point (pH = 4), the protein adsorption into the positive halloysite lumen is favored because of the electrostatic attractions. The ζ-potential magnitude of these core-shell particles increased from -35 (in pristine form) to -43 mV allowing for an enhanced colloidal stability (15 h at pH = 6). This keratin-clay tubule nanocomposite was used for the immersion treatment of hair. Three-dimensional-measuring laser scanning microscopy demonstrated that 50-60% of the hair surface coverage can be achieved with 1 wt % suspension application. Hair samples have been exposed to UV irradiation for times up to 72 h to explore the protection capacity of this coating by monitoring the cysteine oxidation products. The nanocomposites of halloysite and keratin prevent the deterioration of human hair as evident by significant inhibition of cysteic acid. The successful hair structure protection was also visually confirmed by atomic force microscopy and dark-field hyperspectral microscopy. The proposed formulation represents a promising strategy for a sustainable medical coating on the hair, which remediates UV irradiation stress.

Selective Antimicrobial Effects of Curcumin@Halloysite Nanoformulation: A Caenorhabditis elegans Study

Alterations in the normal gastrointestinal microbial community caused by unhealthy diet, environmental factors, and antibiotic overuse may severely affect human health and well-being. Novel antimicrobial drug formulations targeting pathogenic microflora while not affecting or even supporting symbiotic microflora are urgently needed. Here we report fabrication of a novel antimicrobial nanocontainer based on halloysite nanotubes loaded with curcumin and protected with a dextrin outer layer (HNTs+Curc/DX) and its effective use to suppress the overgrowth of pathogenic bacteria in Caenorhabditis elegans nematodes. Nanocontainers have been obtained using vacuum-facilitated loading of hydrophobic curcumin into halloysite lumens. We have applied UV-vis and infrared spectroscopy, thermogravimetry and microscopy to characterize the HNTs+Curc/DX nanocontainers. In experiments in vitro we found that HNTs+Curc/DX effectively suppressed the growth of Serratia marcescens cells, whereas Escherichia coli bacteria were not affected. We applied HNTs+Curc/DX nanocontainers to alleviate the S. marcescens infection in C. elegans nematodes in vivo. The nematodes ingest HNTs+Curc/DX at 4-6 ng per worm, which results in improvement of the nematodes' fertility and life expectancy. Remarkably, treatment of S. marcescens-infected nematodes with HNTs+Curc/DX nanocontainers completely restored the longevity, demonstrating the enhanced bioavailability of hydrophobic curcumin. We believe that our results reported here open new avenues for fabrication of effective antimicrobial nanoformulations based on hydrophobic drugs and clay nanotubes.

Selective Cytotoxic Activity of Prodigiosin@halloysite Nanoformulation

Prodigiosin, a bioactive secondary metabolite produced by Serratia marcescens, is an effective proapoptotic agent against various cancer cell lines, with little or no toxicity toward normal cells. The hydrophobicity of prodigiosin limits its use for medical and biotechnological applications, these limitations, however, can be overcome by using nanoscale drug carriers, resulting in promising formulations for target delivery systems with great potential for anticancer therapy. Here we report on prodigiosin-loaded halloysite-based nanoformulation and its effects on viability of malignant and non-malignant cells. We have found that prodigiosin-loaded halloysite nanotubes inhibit human epithelial colorectal adenocarcinoma (Caco-2) and human colon carcinoma (HCT116) cells proliferative activity. After treatment of Caco-2 cells with prodigiosin-loaded halloysite nanotubes, we have observed a disorganization of the F-actin structure. Comparison of this effects on malignant (Caco-2, HCT116) and non-malignant (MSC, HSF) cells suggests the selective cytotoxic and genotoxic activity of prodigiosin-HNTs nanoformulation.

Surface-Enhanced Raman Scattering to Evaluate Nanomaterial Cytotoxicity on Living Cells

The increasing number of reports about false positive or negative results from conventional cytotoxicity assays of nanomaterials (NMs) suggests that more reliable NM toxicity assessment methods should be developed. Here, we report a novel approach for nanotoxicity evaluation based on surface-enhanced Raman spectroscopy (SERS). Three model NMs were tested on two model cell lines and the results were validated by WST-1 cytotoxicity assay and annexin V-FITC/propidium iodide (PI) staining as apoptosis-necrosis assay. The localization of nanoparticles (NPs) in the cells and the cellular conditions upon NP incubation were visualized by transmission electron microscopy (TEM) and enhanced dark-field (EDF) microscopy. SERS revealed a broader view on the consequences of cell-NM interactions compared to the conventional cytotoxicity assays where only one aspect of toxicity can be measured by one assay type. The results suggest that SERS can significantly contribute to the cytotoxicity evaluation bypassing NM or assay component-related complications with less effort.

DNA/Magnetic Nanoparticles Composite to Attenuate Glass Surface Nanotopography for Enhanced Mesenchymal Stem Cell Differentiation

Mesenchymal stem cells (MSCs) have extensive pluripotent potential to differentiate into various cell types, and thus they are an important tool for regenerative medicine and biomedical research. In this work, the differentiation of hTERT-transduced adipose-derived MSCs (hMSCs) into chondrocytes, adipocytes and osteoblasts on substrates with nanotopography generated by magnetic iron oxide nanoparticles (MNPs) and DNA was investigated. Citrate-stabilized MNPs were synthesized by the chemical co-precipitation method and sized around 10 nm according to microscopy studies. It was shown that MNPs@DNA coatings induced chondrogenesis and osteogenesis in hTERT-transduced MSCs. The cells had normal morphology and distribution of actin filaments. An increase in the concentration of magnetic nanoparticles resulted in a higher surface roughness and reduced the adhesion of cells to the substrate. A glass substrate modified with magnetic nanoparticles and DNA induced active chondrogenesis of hTERT-transduced MSC in a twice-diluted differentiation-inducing growth medium, suggesting the possible use of nanostructured MNPs@DNA coatings to obtain differentiated cells at a reduced level of growth factors.

Kaolin alleviates the toxicity of graphene oxide for mammalian cells

The development of novel nanoscale vehicles for drug delivery promotes the growth of interest in investigations of interaction between nanomaterials. In this paper, we report the in vitro studies of eukaryotic cell physiological response to incubation with graphene oxide and planar kaolin nanoclay. Graphene family materials, including graphene oxide (GO), hold promise for numerous applications due to their unique electronic properties. However, graphene oxide reveals toxicity to some cell lines through an unidentified mechanism. Thus, methods and agents reducing the toxicity of graphene oxide can widen its practical application. We used a colorimetric test, flow cytometry and cell index assay methods to evaluate the effects of separate and combined application of graphene oxide and kaolin on mammalian cells. We have shown that the joint application of graphene oxide and kaolin reduced the negative effects of graphene by almost 20%, most likely because of coagulation of the nanoparticles with each other, which was detected by atomic force microscopy.

Revisiting the Cytotoxicity of Cationic Polyelectrolytes as a Principal Component in Layer-by-Layer Assembly Fabrication

Polycations are an essential part of layer-by-layer (LbL)-assembled drug delivery systems, especially for gene delivery. In addition, they are used for other related applications, such as cell surface engineering. As a result, an assessment of the cytotoxicity of polycations and elucidation of the mechanisms of polycation toxicity is of paramount importance. In this study, we examined in detail the effects of a variety of water-soluble, positively charged synthetic polyelectrolytes on in vitro cytotoxicity, cell and nucleus morphology, and monolayer expansion changes. We have ranked the most popular cationic polyelectrolytes from the safest to the most toxic in relation to cell cultures. 3D cellular cluster formation was disturbed by addition of polyelectrolytes in most cases in a dose-dependent manner. Atomic force microscopy allowed us to visualize in detail the structures of the polyelectrolyte–DNA complexes formed due to electrostatic interactions. Our results indicate a relationship between the structure of the polyelectrolytes and their toxicity, which is necessary for optimization of drug and gene delivery systems.

Nanoarchitectonics meets cell surface engineering: shape recognition of human cells by halloysite-doped silica cell imprints

Cell surface engineering, as a practical manifestation of nanoarchitectonics, is a powerful tool to modify and enhance properties of live cells. In turn, cells may serve as sacrificial templates to fabricate cell-mimicking materials. Herein we report a facile method to produce cell-recognising silica imprints capable of the selective detection of human cells. We used HeLa cells to template silica inorganic shells doped with halloysite clay nanotubes. The shells were destroyed by sonication resulting in the formation of polydisperse hybrid imprints that were used to recognise HeLa cells in liquid media supplemented with yeast. We believe that methodology reported here will find applications in biomedical and clinical research.

East Eurasian ancestry in the middle of Europe: genetic footprints of Steppe nomads in the genomes of Belarusian Lipka Tatars

Medieval era encounters of nomadic groups of the Eurasian Steppe and largely sedentary East Europeans had a variety of demographic and cultural consequences. Amongst these outcomes was the emergence of the Lipka Tatars—a Slavic-speaking Sunni-Muslim minority residing in modern Belarus, Lithuania and Poland, whose ancestors arrived in these territories via several migration waves, mainly from the Golden Horde. Our results show that Belarusian Lipka Tatars share a substantial part of their gene pool with Europeans as indicated by their Y-chromosomal, mitochondrial and autosomal DNA variation. Nevertheless, Belarusian Lipkas still retain a strong genetic signal of their nomadic ancestry, witnessed by the presence of common Y-chromosomal and mitochondrial DNA variants as well as autosomal segments identical by descent between Lipkas and East Eurasians from temperate and northern regions. Hence, we document Lipka Tatars as a unique example of former Medieval migrants into Central Europe, who became sedentary, changed language to Slavic, yet preserved their faith and retained, both uni- and bi-parentally, a clear genetic echo of a complex population interplay throughout the Eurasian Steppe Belt, extending from Central Europe to northern China.

Comparative Toxicity of Fly Ash: An In Vitro Study

Fly ash produced during coal combustion is one of the major sources of air and water pollution, but the data on the impact of micrometer-size fly ash particles on human cells is still incomplete. Fly ash samples were collected from several electric power stations in the United States (Rockdale, TX; Dolet Hill, Mansfield, LA; Rockport, IN; Muskogee, OK) and from a metallurgic plant located in the Russian Federation (Chelyabinsk Electro-Metallurgical Works OJSC). The particles were characterized using dynamic light scattering, atomic force, and hyperspectral microscopy. According to chemical composition, the fly ash studied was ferro-alumino-silicate mineral containing substantial quantities of Ca, Mg, and a negligible concentration of K, Na, Mn, and Sr. The toxicity of the fly ash microparticles was assessed in vitro using HeLa cells (human cervical cancer cells) and Jurkat cells (immortalized human T lymphocytes). Incubation of cells with different concentrations of fly ash resulted in a dose-dependent decrease in cell viability for all fly ash variants. The most prominent cytotoxic effect in HeLa cells was produced by the ash particles from Rockdale, while the least was produced by the fly ash from Chelyabinsk. In Jurkat cells, the lowest toxicity was observed for fly ash collected from Rockport, Dolet Hill and Muscogee plants. The fly ash from Rockdale and Chelyabinsk induced DNA damage in HeLa cells, as revealed by the single cell electrophoresis, and disrupted the normal nuclear morphology. The interaction of fly ash microparticles of different origins with cells was visualized using dark-field microscopy and hyperspectral imaging. The size of ash particles appeared to be an important determinant of their toxicity, and the smallest fly ash particles from Chelyabinsk turned out to be the most cytotoxic to Jukart cells and the most genotoxic to HeLa cells.

Worms eat oil: Alcanivorax borkumensis hydrocarbonoclastic bacteria colonise Caenorhabditis elegans nematodes intestines as a first step towards oil spills zooremediation

The environmental hazards of oil spills cannot be underestimated. Bioremediation holds promise among various approaches to tackle oil spills in soils and sediments. In particular, using oil-degrading bacteria is an efficient and self-regulating way to remove oil spills. Using animals for oil spills remediation is in its infancy, mostly due to the lack of efficient oil-degrading capabilities in eukaryotes. Here we show that Caenorhabditis elegans nematodes survive for extended periods (up to 22 days) on pure crude oil diet. Moreover, we report for the first time the use of Alcanivorax borkumensis hydrocarbonoclastic bacteria for colonisation of C. elegans intestines, which allows for effective digestion of crude oil by the nematodes. The worms fed and colonised by A. borkumensis demonstrated the similar or even better longevity, resistance against oxidative and thermal stress and reproductivity as those animals fed with Escherichia coli bacteria (normal food). Importantly, A. borkumensis-carrying nematodes were able to accumulate oil droplet from oil-contaminated soils. Artificial colonisation of soil invertebrates with oil-degrading bacteria will be an efficient way to distribute microorganisms in polluted soil, thus opening new avenues for oil spills zooremediation.

Nematode Epicuticle Visualisation by PeakForce Tapping Atomic Force Microscopy

The free-living soil nematode Caenorhabditis elegans has become an iconic experimental model animal in biology. This transparent animal can be easily imaged using optical microscopy to visualise its organs, tissues, single cells and subcellular events. The epicuticle of C. elegans nematodes has been studied at nanoscale using transmission and scanning (SEM) electron microscopies. As a result, imaging artefacts can appear due to embedding the worms into resins or coating the worms with a conductive gold layer. In addition, fixation and contrasting may also damage the cuticle. Conventional tapping mode atomic force microscopy (AFM) can be applied to image the cuticle of the dried nematodes in air, however this approach also suffers from imaging defects. Ideally, the nematodes should be imaged under conditions resembling their natural environment. Recently, we reported the use of PeakForce Tapping AFM mode for the successful visualisation and numerical characterisation of C. elegans nematode cuticle both in air and in liquid ( Fakhrullina et al., 2017 ). We imaged the principal nematode surface structures and characterised mechanical properties of the cuticle. This protocol provides the detailed description of AFM imaging of liquid-immersed C. elegans nematodes using PeakForce Tapping atomic force microscopy.

Probing nanoplastics derived from polypropylene face masks with hyperspectral dark-field microscopy

The high worldwide consumption of cheap plastic goods has already resulted in a serious environmental plastic pollution, exacerbated by piling of disposed personal protective equipment because of the recent outbreak of COVID-19. The aim of this study was to assess the feasibility of dark-field hyperspectral microscopy in the 400-1000 wavelength range for detection of nanoplastics derived from weathered polypropylene masks. A surgical mask was separated to layers and exposed to UV radiation (254 nm) for 192 h. Oxidative degradation of the polypropylene was evidenced by ATR FT-IR analysis. UV treatment for 192 h resulted in generation of differently shaped micro- and nano-sized particles, visualized by dark-field microscopy. The presence of nanoparticles was confirmed by AFM studies. The hyperspectral profiles (400-1000 nm) were collected after every 48 h of the UV treatment. The distinct hyperspectral features faded after prolonged UV exposure, but the assignment of some particles to either blue or white layers of mask could still be made based on spectral characteristics.

Comparative Characterization of Iron and Silver Nanoparticles: Extract-Stabilized and Classical Synthesis Methods

Synthesis of silver nanoparticles using extracts from plants is an advantageous technological alternative to the traditional colloidal synthesis due to its simplicity, low cost, and the inclusion of environmentally friendly processes to obtain a new generation of antimicrobial compounds. The work describes the production of silver and iron nanoparticles using sphagnum extract as well as traditional synthesis. Dynamic light scattering (DLS) and laser doppler velocimetry methods, UV-visible spectroscopy, transmission electron microscopy (TEM) combined with energy dispersive X-ray spectroscopy (EDS), atomic force microscopy (AFM), dark-field hyperspectral microscopy, and Fourier-transform infrared spectroscopy (FT-IR) were used to study the structure and properties of synthesized nanoparticles. Our studies demonstrated a high antibacterial activity of the obtained nanoparticles, including the formation of biofilms. Nanoparticles synthesized using sphagnum moss extracts likely have high potential for further research.

Advances in the Toxicity Assessment of Silver Nanoparticles Derived from a Sphagnum fallax Extract for Monolayers and Spheroids

The production of nanomaterials through environmentally friendly methods is a top priority in the sustainable development of nanotechnology. This paper presents data on the synthesis of silver nanoparticles using an aqueous extract of Sphagnum fallax moss at room temperature. The morphology, stability, and size of the nanoparticles were analyzed using various techniques, including transmission electron microscopy, Doppler laser velocimetry, and UV-vis spectroscopy. In addition, Fourier transform infrared spectroscopy was used to analyze the presence of moss metabolites on the surface of nanomaterials. The effects of different concentrations of citrate-stabilized and moss extract-stabilized silver nanoparticles on cell viability, necrosis induction, and cell impedance were compared. The internalization of silver nanoparticles into both monolayers and three-dimensional cells spheroids was evaluated using dark-field microscopy and hyperspectral imaging. An eco-friendly method for the synthesis of silver nanoparticles at room temperature is proposed, which makes it possible to obtain spherical nanoparticles of 20-30 nm in size with high bioavailability and that have potential applications in various areas of human life.

Whole Genome Sequencing of the Novel Probiotic Strain Lactiplantibacillus plantarum FCa3L

Lactiplantibacillus plantarum is best known for its significant adaptive potential and ability to colonize different ecological niches. Different strains of L. plantarum are widely used as probiotics. To characterize the probiotic potential of the novel L. plantarum FCa3L strain isolated from fermented cabbage, we sequenced its whole genome using the Illumina MiSeq platform. This bacterial isolate had a circular chromosome of 3,365,929 bp with 44.3% GC content and a cyclic phage phiX174 of 5386 bp with 44.7% GC content. The results of in vitro studies showed that FCa3L was comparable with the reference probiotic strain L. plantarum 8PA3 in terms of acid and bile tolerance, adhesiveness, H₂O₂ production, and acidification rate. The strain 8PA3 possessed higher antioxidant activity, while FCa3L demonstrated superior antibacterial properties. The antibiotic resistance of FCa3L was more relevant to the probiotic strain than that of 8PA3, although a number of silent antibiotic resistance genes were identified in its genome. Genomic evidence to support adhesive and antibacterial properties, biosynthesis of bioactive metabolites, and safety of FCa3L was also presented. Thus, this study confirmed the safety and probiotic properties of L. plantarum FCa3L via complete genome and phenotype analysis, suggesting its potential as a probiotic, although further in vivo investigations are still necessary.