Smart materials-integrated sensor technologies for COVID-19 diagnosis

After the first case has appeared in China, the COVID-19 pandemic continues to pose an omnipresent threat to global health, affecting more than 70 million patients and leading to around 1.6 million deaths. To implement rapid and effective clinical management, early diagnosis is the mainstay. Today, real-time reverse transcriptase (RT)-PCR test is the major diagnostic practice as a gold standard method for accurate diagnosis of this disease. On the other side, serological assays are easy to be implemented for the disease screening. Considering the limitations of today's tests including lengthy assay time, cost, the need for skilled personnel, and specialized infrastructure, both strategies, however, have impediments to be applied to the resource-scarce settings. Therefore, there is an urgent need to democratize all these practices to be applicable across the globe, specifically to the locations comprising of very limited infrastructure. In this regard, sensor systems have been utilized in clinical diagnostics largely, holding great potential to have pivotal roles as an alternative or complementary options to these current tests, providing crucial fashions such as being suitable for point-of-care settings, cost-effective, and having short turnover time. In particular, the integration of smart materials into sensor technologies leverages their analytical performances, including sensitivity, linear dynamic range, and specificity. Herein, we comprehensively review major smart materials such as nanomaterials, photosensitive materials, electrically sensitive materials, their integration with sensor platforms, and applications as wearable tools within the scope of the COVID-19 diagnosis.

Approaching environmental human thermophysiological thresholds for the case of Ankara, Turkey

The disclosed study undertook a 'human centred-approach' that ascertained and categorised environmental human thermophysiological risk factors by relating them to the human biometeorological system through the use of three widely utilised energy balance model (EBM) indices, the physiologically equivalent temperature (PET), the modified PET, and the universal thermal climate index (UTCI). The disclosed assessment was carried out over the past decade (i.e., 2010-2019) with a 3-h temporal resolution for the case of Ankara through two WMO meteorological stations to compare both local urban and peri-urban environmental conditions. The study recognised extreme annual variability of human physiological stress (PS) during the different seasons as a result of the biometeorological processing of the singular variables, which in the case of average PET for both stations, varied by up to 75 °C between the winter and summer for the same annual dataset (2012). In addition, all EBMs indicated higher heat stress within the city centre that were conducive of both urban extreme heatwaves and very hot days during the summer months, with extreme heat stress levels lasting for longer than a week with PET values reaching a maximum of 48 °C. Similar cold extremes were found for the winter months, with PET values reaching - 30 °C, and average PS levels varying lower in the case of the peri-urban station. Graphical abstract.

Differential anti-proliferative and apoptotic effects of lichen species on human prostate carcinoma cells

Lichens are stable symbiotic associations between fungus and algae and/or cyanobacteria that have different biological activities. Around 60% of anti-cancer drugs are derived from natural resources including plants, fungi, sea creatures, and lichens. This project aims to identify the apoptotic effects and proliferative properties of extracts of Bryoria capillaris (Ach.) Brodo & D.Hawksw, Cladonia fimbriata (L.) Fr., Evernia divaricata (L.) Ach., Hypogymnia tubulosa (Schaer.) Hav., Lobaria pulmonaria (L.) Hoffm., and Usnea florida (L.) Weber ex Wigg. lichen species on prostate cancer cells. Lichen extracts were performed by ethanol, methanol, and acetone separately by using the Soxhlet apparatus and the effects of the extracts on cell viability, proliferation, and apoptosis were measured with the utilization of MTT, LDH assay, Annexin V assay, and Western Blot. Findings of our study revealed a positive correlation between the elevation of cell sensitivity and the increase in the treatment doses of the extract in that higher doses applied reverberate to higher cell sensitivity. A similar correlation was also identified between cell sensitivity elevation and the duration of the treatment. Evidence in our study have shown the existence of an anti-proliferative effect in the extracts of Bryoria capillaris, Evernia divaricata (L.) Ach., Hypogymnia tubulosa (Schaer.) Hav., Lobaria pulmonaria (L.) Hoffm., and Usnea florida (L.) Weber ex Wigg., while a similar effect was not observed in the extracts of Cladonia fimbriata. Evernia divaricata induced anti-proliferative and apoptotic effects in PC-3 cells, which induced apoptotic cell death by both extrinsic and intrinsic pathways. Hypogymnia tubulosa has been shown to have anti-proliferative and apoptotic effects in all extractions methods and our findings identified that both the percentage of the apoptotic cells and apoptotic protein expressions recorded an increase at lower treatment concentrations. Although Lobaria pulmonaria is known to have significant cytotoxic effects, we did not observe a decrease in cell proliferation. Indeed, proliferation marker proliferating cell nuclear antigen (PCNA) protein expression levels have shown an increase in all extracts, while Usnea florida exhibited apoptosis induction and slight proliferation reduction in extract treatments with lower concentrations. We tested 18 extracts of six lichen species during our study. Of these, Evernia divaricata and Hypogymnia tubulosa demonstrated significant apoptotic activity on prostate cancer cells including at low concentrations, which implies that it is worth pursuing the biologically active lead compounds of these extracts on prostate cancer in vitro. Further corroboratory studies are needed to validate the relative potential of these extracts as anti-metastatic and anti-tumorigenic agents.

The EDN2 rs110287192 gene polymorphism is associated with paratuberculosis susceptibility in multibreed cattle population

Paratuberculosis (pTB), also known as Johne's disease (JD), is a contagious, chronic, and granulomatous inflammatory disease of the intestines of ruminants which is caused by Mycobacterium avium subsp. paratuberculosis (MAP) infection, resulting in billions of dollars in economic losses worldwide. Since, currently, no effective cure is available for MAP infection, it is important to explore the genetic variants that affect the host MAP susceptibility. The aim of this study was to analyze a potential association between EDN2 synonymous gene mutations (rs110287192, rs109651404 and rs136707411), that modifies susceptibility to pTB. EDN2 rs110287192, rs109651404 and rs136707411 mutations were genotyped in 68 infected and 753 healthy animals from East Anatolian Red crossbred, Anatolian Black crossbred and Holstein breed cattle by using Custom TaqMan SNP Genotyping Assays. For pTB status, serum antibody levels S/P ≥ 1.0 were assessed in carriers of the different EDN2 genotypes. EDN2 rs110287192 mutation showed a significant association with bovine pTB (adj. p < 0.05). For rs110287192 locus, the odd ratios for GG and TG genotypes versus TT genotypes were 1.73; (95% CI = 0.34–8.59) and 0.53 (95% CI = 0.12–2.37) respectively, which indicated that proportion of TG heterozygotes were significantly higher in control animals as compared to pTB animals. On the other hand, while rs136707411 mutation showed a suggestive association with pTB status in the examined cattle population (nominal p < 0.05); no association was detected between rs109651404 genotypes and pTB status. Selecting animals against rs110287192-GG genotype may decrease the risk of pTB in cattle of the Bos taurus taurus subspecies.

Effects of processing on onion skin powder added extrudates

It is possible to enhance the functional properties of extruded products with the inclusion of fruit and vegetable by-products. Onion skin, a rich source of quercetin and fiber, is considered as waste in the industry and can be used as an alternative ingredient to improve the nutritional value of the extruded products. Three levels (3, 6, and 9%) of onion skin powder (OSP) were added to wheat flour and compared with control (0% OSP). The effect of the extrusion process on accessible quercetin, total phenolic content, and antioxidant activity of the samples were investigated. In addition, carbohydrate digestibility analyses were conducted for the products. Mass spectrometry (LC-MS/MS) results indicated that increasing the OSP level increased the quercetin content. The process caused the release of the entrapped quercetin from OSP, which was revealed by significantly higher quercetin levels for the extrudates. Some of the quercetin was lost during in vitro digestion process. Increasing the OSP level increased antioxidant activity and total phenolic contents of the samples. Total phenolic contents decreased significantly after the processing, yet antioxidant activities were not affected. The extruded products showed high amounts of rapidly available glucose (69.5 g/100 g). The OSP enhancement did not change the carbohydrate digestibility of products. The results indicated that the extrusion process could increase the level of accessible bioactive ingredients, and the level of functional compound addition can be optimized further.

In vitro evaluation of the bioaccessibility of antioxidative properties in commercially baby foods

Fruit-vegetable based products are essential for infants as they widely used the first complementary solid foods. This study aimed to investigate the physicochemical properties, the antioxidant capacities, total phenolic content, and bioaccessibility of 24 different commercially fruit-vegetable based complementary foods. To determination of bioaccessibility, samples were processed by an in vitro digestive enzymatic extraction that mimics the conditions in the gastrointestinal tract. Total polyphenol content was analyzed using Folin-Ciocalteu assay, and antioxidant capacities were assessed by CUPRAC and ABTS methods. The total phenol content of the samples ranges from 892.21 to 1729.13 mg GAE mg/100 g. While the antioxidant capacity of the samples averages 256.26 µmol TE mg/100 g according to the ABTS method, they were found 2417.79 µmol TE mg/100 g for CUPRAC method. Also, the bioaccessibility of total phenol content determined 62.72-98.48% of all samples. As a result, antioxidant properties and bioaccessibility of the samples were changed according to the sample content and chemical composition. The use of fruit or fruit juice in the preparation of commercial baby food has improved antioxidant capacity and bioaccessibility, thus increasing the beneficial health effect and nutraceutical properties of the baby meal.

Equilibrium Formation of Stable All-Silicon Versions of 1,3-Cyclobutanediyl

Main group analogues of cyclobutane-1,3-diyls are fascinating due to their unique reactivity and electronic properties. So far only heteronuclear examples have been isolated. Here we report the isolation and characterization of all-silicon 1,3-cyclobutanediyls as stable closed-shell singlet species from the reversible reactions of cyclotrisilene c-Si3 Tip4 (Tip=2,4,6-triisopropylphenyl) with the N-heterocyclic silylenes c-[(CR2 CH2 )(NtBu)2 ]Si: (R=H or methyl) with saturated backbones. At elevated temperatures, tetrasilacyclobutenes are obtained from these equilibrium mixtures. The corresponding reaction with the unsaturated N-heterocyclic silylene c-(CH)2 (NtBu)2 Si: proceeds directly to the corresponding tetrasilacyclobutene without detection of the assumed 1,3-cyclobutanediyl intermediate.

Effect of sub-chronic exposure to cigarette smoke, electronic cigarette and waterpipe on human lung epithelial barrier function

BACKGROUND

Taking into consideration a recent surge of a lung injury condition associated with electronic cigarette use, we devised an in vitro model of sub-chronic exposure of human bronchial epithelial cells (HBECs) in air-liquid interface, to determine deterioration of epithelial cell barrier from sub-chronic exposure to cigarette smoke (CS), e-cigarette aerosol (EC), and tobacco waterpipe exposures (TW).

METHODS

Products analyzed include commercially available e-liquid, with 0% or 1.2% concentration of nicotine, tobacco blend (shisha), and reference-grade cigarette (3R4F). In one set of experiments, HBECs were exposed to EC (0 and 1.2%), CS or control air for 10 days using 1 cigarette/day. In the second set of experiments, exposure of pseudostratified primary epithelial tissue to TW or control air exposure was performed 1-h/day, every other day, until 3 exposures were performed. After 16-18 h of last exposure, we investigated barrier function/structural integrity of the epithelial monolayer with fluorescein isothiocyanate-dextran flux assay (FITC-Dextran), measurements of trans-electrical epithelial resistance (TEER), assessment of the percentage of moving cilia, cilia beat frequency (CBF), cell motion, and quantification of E-cadherin gene expression by reverse-transcription quantitative polymerase chain reaction (RT-qPCR).

RESULTS

When compared to air control, CS increased fluorescence (FITC-Dextran assay) by 5.6 times, whereby CS and EC (1.2%) reduced TEER to 49 and 60% respectively. CS and EC (1.2%) exposure reduced CBF to 62 and 59%, and cilia moving to 47 and 52%, respectively, when compared to control air. CS and EC (1.2%) increased cell velocity compared to air control by 2.5 and 2.6 times, respectively. The expression of E-cadherin reduced to 39% of control air levels by CS exposure shows an insight into a plausible molecular mechanism. Altogether, EC (0%) and TW exposures resulted in more moderate decreases in epithelial integrity, while EC (1.2%) substantially decreased airway epithelial barrier function comparable with CS exposure.

CONCLUSIONS

The results support a toxic effect of sub-chronic exposure to EC (1.2%) as evident by disruption of the bronchial epithelial cell barrier integrity, whereas further research is needed to address the molecular mechanism of this observation as well as TW and EC (0%) toxicity in chronic exposures.

First characterization of the complete mitochondrial genome of fungal plant-pathogen Monilinia laxa which represents the mobile intron rich structure

Monilinia laxa is an important fungal plant pathogen causing brown rot on many stone and pome fruits worldwide. Mitochondrial genome (mitogenome) plays a critical role in evolutionary biology of the organisms. This study aimed to characterize the complete mitogenome of M. laxa by using next-generation sequencing and approaches of de novo assembly and annotation. The total length of the mitogenome of M. laxa was 178,357 bp, and its structure was circular. GC content of the mitogenome was 30.1%. Annotation of the mitogenome presented 2 ribosomal RNA (rRNA) genes, 32 transfer RNA genes (tRNA), 1 gene encoding mitochondrial ribosomal protein S3, 14 protein-coding genes and 15 open reading frame encoding hypothetical proteins. Moreover, the group I mobile introns encoding homing endonucleases including LAGLIDADG and GIY-YIG families were found both within coding regions (genic) and intergenic regions of the mitogenome, indicating an enlarged size and a dynamic structure of the mitogenome. Furthermore, a comparative mitogenomic analysis was performed between M. laxa and the three closely related fungal phytopathogen species (Botryotinia fuckeliana, Sclerotinia sclerotiorum and, S. borealis). Due to the number and distribution of introns, the large extent of structural rearrangements and diverse mitogenome sizes were detected among the species investigated. Monilinia laxa presented the highest number of homing endonucleases among the fungal species considered in the analyses. This study is the first to report a detailed annotation of the mitogenome of an isolate of M. laxa, providing a solid basis for further investigations of mitogenome variations for the other Monilinia pathogens causing brown rot disease.

Inhibitory potential on key enzymes relevant to type II diabetes mellitus and antioxidant properties of the various extracts and phytochemical constituents from Rumex acetosella L

Type II diabetes mellitus is a common and costly disease worldwide, characterized by hyperglycemia. Alpha (α)-amylase and α-glucosidase are important targets in diabetes therapy. Inhibition of these enzymes may lessen hyperglycemia, preventing diabetic complications. Oxidative stress is another factor involved in the disease's etiology. In the present study, we investigated antidiabetic profiles of the various extracts and phytochemicals of Rumex acetosella. Since the plant has been traditionally used for the antidiabetic purposes. α-amylase and α-glucosidase inhibitory studies in addition to DPPH•, ABTS•+, NO 2 - radical scavenging, and phosphomolybdate antioxidant assays were performed to evaluate the antidiabetic property. Specifically, the ethanol and ethanol-water extracts remarkably inhibited α-glucosidase than that of acarbose, unlike their slight/no inhibition on α-amylase. Convincing α-glucosidase inhibitory and antioxidant potential of alcohol-including extracts verified the ethnobotanical use of R. acetosella as an antidiabetic agent. PRACTICAL APPLICATIONS: The incidence of Type II DM is rising globally. Reducing hyperglycemia holds great importance to prevent devastating outcomes of diabetic complications. Ethnobotanical use of natural sources for medical purposes provides a basis for their potential activity against various diseases. The introduction of herbal agents may lead to the development of new drug candidates with convincing activity. Rumex acetosella L. has been traditionally used for the antidiabetic purposes. The research pointed out various extracts and phytochemical constituents from R. acetosella may act as antihyperglycemic agents. Particularly, alcohol-including extracts of R. acetosella may be considered as promising alternatives in the prevention or treatment of type II DM. The study puts emphasis on the therapeutic value of the plants for antidiabetic medication.

Low magnitude high frequency vibrations expedite the osteogenesis of bone marrow stem cells on paper based 3D scaffolds

Anabolic effects of low magnitude high frequency (LMHF) vibrations on bone tissue were consistently shown in the literature in vivo, however in vitro efforts to elucidate underlying mechanisms are generally limited to 2D cell culture studies. Three dimensional cell culture platforms better mimic the natural microenvironment and biological processes usually differ in 3D compared to 2D culture. In this study, we used laboratory grade filter paper as a scaffold material for studying the effects of LHMF vibrations on osteogenesis of bone marrow mesenchymal stem cells in a 3D system. LMHF vibrations were applied 15 min/day at 0.1 g acceleration and 90 Hz frequency for 21 days to residing cells under quiescent and osteogenic conditions. mRNA expression analysis was performed for alkaline phosphatase (ALP) and osteocalcin (OCN) genes, Alizarin red S staining was performed for mineral nodule formation and infrared spectroscopy was performed for determination of extracellular matrix composition. The highest osteocalcin expression, mineral nodule formation and the phosphate bands arising from the inorganic phase was observed for the cells incubated in osteogenic induction medium with vibration. Our results showed that filter paper can be used as a model scaffold system for studying the effects of mechanical loads on cells, and LMHF vibrations induced the osteogenic differentiation of stem cells.

Interaction network effects on position- and velocity-based models of collective motion

We study how the structure of the interaction network affects self-organized collective motion in two minimal models of self-propelled agents: the Vicsek model and the Active-Elastic (AE) model. We perform simulations with topologies that interpolate between a nearest-neighbour network and random networks with different degree distributions to analyse the relationship between the interaction topology and the resilience to noise of the ordered state. For the Vicsek case, we find that a higher fraction of random connections with homogeneous or power-law degree distribution increases the critical noise, and thus the resilience to noise, as expected due to small-world effects. Surprisingly, for the AE model, a higher fraction of random links with power-law degree distribution can decrease this resilience, despite most links being long-range. We explain this effect through a simple mechanical analogy, arguing that the larger presence of agents with few connections contributes localized low-energy modes that are easily excited by noise, thus hindering the collective dynamics. These results demonstrate the strong effects of the interaction topology on self-organization. Our work suggests potential roles of the interaction network structure in biological collective behaviour and could also help improve decentralized swarm robotics control and other distributed consensus systems.

Structural analysis of the PATZ1 BTB domain homodimer

PATZ1 is a ubiquitously expressed transcriptional repressor belonging to the ZBTB family that is functionally expressed in T lymphocytes. PATZ1 targets the CD8 gene in lymphocyte development and interacts with the p53 protein to control genes that are important in proliferation and in the DNA-damage response. PATZ1 exerts its activity through an N-terminal BTB domain that mediates dimerization and co-repressor interactions and a C-terminal zinc-finger motif-containing domain that mediates DNA binding. Here, the crystal structures of the murine and zebrafish PATZ1 BTB domains are reported at 2.3 and 1.8 Å resolution, respectively. The structures revealed that the PATZ1 BTB domain forms a stable homodimer with a lateral surface groove, as in other ZBTB structures. Analysis of the lateral groove revealed a large acidic patch in this region, which contrasts with the previously resolved basic co-repressor binding interface of BCL6. A large 30-amino-acid glycine- and alanine-rich central loop, which is unique to mammalian PATZ1 amongst all ZBTB proteins, could not be resolved, probably owing to its flexibility. Molecular-dynamics simulations suggest a contribution of this loop to modulation of the mammalian BTB dimerization interface.

Messinian vegetation and climate of the intermontane Florina-Ptolemais-Servia Basin, NW Greece inferred from palaeobotanical data: how well do plant fossils reflect past environments?

The late Miocene is marked by pronounced environmental changes and the appearance of strong temperature and precipitation seasonality. Although environmental heterogeneity is to be expected during this time, it is challenging to reconstruct palaeoenvironments using plant fossils. We investigated leaves and dispersed spores/pollen from 6.4 to 6 Ma strata in the intermontane Florina-Ptolemais-Servia Basin (FPS) of northwestern Greece. To assess how well plant fossils reflect the actual vegetation of the FPS, we assigned fossil taxa to biomes providing a measure for environmental heterogeneity. Additionally, the palynological assemblage was compared with pollen spectra from modern lake sediments to assess biases in spore/pollen representation in the pollen record. We found a close match of the Vegora assemblage with modern Fagus-Abies forests of Turkey. Using taxonomic affinities of leaf fossils, we further established close similarities of the Vegora assemblage with modern laurophyllous oak forests of Afghanistan. Finally, using information from sedimentary environment and taphonomy, we distinguished local and distantly growing vegetation types. We then subjected the plant assemblage of Vegora to different methods of climate reconstruction and discussed their potentials and limitations. Leaf and spore/pollen records allow accurate reconstructions of palaeoenvironments in the FPS, whereas extra-regional vegetation from coastal lowlands is probably not captured.

Genome-wide association study identifies various loci underlying agronomic and morphological traits in diversified potato panel

Potato is one of the most important food crops all over the world. Breeding activities for this crop are mainly aimed to improve the quality and yield of tuber. However, genetic architecture of various traits contributing to the quality and yield of potato are not yet completely understood. Genome wide association studies provides a broader way to identify the genomic regions associated with various traits. Panels of 237 tetraploid potato genotypes from different countries were grown for two consecutive years 2016 and 2017 at experimental research area of Potato research center Niğde, Turkey. A genome wide association study using SolCAP 12K array was performed for various morpho-agronomic traits. Structure algorithm and neighborhood joining analysis clearly divided all genotypes into 4 clusters on the basis of their origin. For the marker trait association, Mixed Linear Model in TASSEL was performed and 36 genomic regions were found for the traits under study. The mean r² value was found to be 0.92 and mean significant LD was 47.5% in the populations. LD patterns reflected the breeding history of potato. The findings of present study provide a framework which could be useful for future potato breeding programs to enhance the production and to reduce the challenges in the coming years to feed world's population.

Toprak M. Composition Tuning of Nanostructured Binary Copper Selenides through Rapid Chemical Synthesis and their Thermoelectric Property Evaluation

Reduced energy consumption and environmentally friendly, abundant constituents are gaining more attention for the synthesis of energy materials. A rapid, highly scalable, and process-temperature-sensitive solution synthesis route is demonstrated for the fabrication of thermoelectric Cu2-xSe. The process relies on readily available precursors and microwave-assisted thermolysis, which is sensitive to reaction conditions; yielding Cu1.8Se at 200 °C and Cu2Se at 250 °C within 6-8 min reaction time. Transmission electron microscopy (TEM) revealed crystalline nature of as-made particles with irregular truncated morphology, which exhibit a high phase purity as identified by X-ray powder diffraction (XRPD) analysis. Temperature-dependent transport properties were characterized via electrical conductivity, Seebeck coefficient, and thermal diffusivity measurements. Subsequent to spark plasma sintering, pure Cu1.8Se exhibited highly compacted and oriented grains that were similar in size in comparison to Cu2Se, which led to its high electrical and low thermal conductivity, reaching a very high power-factor (24 µW/K-2cm-1). Density-of-states (DOS) calculations confirm the observed trends in electronic properties of the material, where Cu-deficient phase exhibits metallic character. The TE figure of merit (ZT) was estimated for the materials, demonstrating an unprecedentedly high ZT at 875 K of 2.1 for Cu1.8Se sample, followed by 1.9 for Cu2Se. Synthetic and processing methods presented in this work enable large-scale production of TE materials and components for niche applications.

Optical spatial modulation design

Visible light communication (VLC) systems are inherently signal-to-noise ratio (SNR) limited due to link budget constraints. One favourable method to overcome this limitation is to focus on the pre-log factors of the channel capacity. Multiple-input multiple-output (MIMO) techniques are therefore a promising avenue of research. However, inter-channel interference in MIMO limits the achievable capacity. Spatial modulation (SM) avoids this limitation. Furthermore, the performance of MIMO systems in VLC is limited by the similarities among spatial channels. This limitation becomes particularly severe in intensity modulation/direct detection (IM/DD) systems because of the lack of phase information. The motivation of this paper is to propose a system that results in a multi-channel transmission system that enables reliable multi-user optical MIMO SM transmission without the need for a precoder, power allocation algorithm or additional optics at the receiver. A general bit error performance model for the SM system is developed for an arbitrary number of light-emitting diodes (LEDs) in conjunction with pulse amplitude modulation. Based on this model, an LED array structure is designed to result in spatially separated multiple channels by manipulating the transmitter geometry. This article is part of the theme issue 'Optical wireless communication'.

In Vivo Dielectric Properties of Healthy and Benign Rat Mammary Tissues from 500 MHz to 18 GHz

This work investigates the in vivo dielectric properties of healthy and benign rat mammary tissues in an attempt to expand the dielectric property knowledge of animal models. The outcomes of this study can enable testing of microwave medical technologies on animal models and interpretation of tissue alteration-dependent in vivo dielectric properties of mammary tissues. Towards this end, in vivo dielectric properties of healthy rat mammary tissues and chemically induced benign rat mammary tumors including low-grade adenosis, sclerosing adenosis, and adenosis were collected with open-ended coaxial probes from 500 MHz to 18 GHz. The in vivo measurements revealed that the dielectric properties of benign rat mammary tumors are higher than the healthy rat mammary tissues by 9.3% to 35.5% and 19.6% to 48.7% for relative permittivity and conductivity, respectively. Furthermore, to our surprise, we found that the grade of the benign tissue affects the dielectric properties for this study. Finally, a comparison with ex vivo healthy human mammary tissue dielectric properties revealed that the healthy rat mammary tissues best replicate the dielectric properties of healthy medium density human samples.

Statistical Approaches for the Analysis of Dependency Among Neurons Under Noise

Neuronal noise is a major factor affecting the communication between coupled neurons. In this work, we propose a statistical toolset to infer the coupling between two neurons under noise. We estimate these statistical dependencies from data which are generated by a coupled Hodgkin-Huxley (HH) model with additive noise. To infer the coupling using observation data, we employ copulas and information-theoretic quantities, such as the mutual information (MI) and the transfer entropy (TE). Copulas and MI between two variables are symmetric quantities, whereas TE is asymmetric. We demonstrate the performances of copulas and MI as functions of different noise levels and show that they are effective in the identification of the interactions due to coupling and noise. Moreover, we analyze the inference of TE values between neurons as a function of noise and conclude that TE is an effective tool for finding out the direction of coupling between neurons under the effects of noise.

Mechanochemical generation of singlet oxygen

Controlled generation of singlet oxygen is very important due to its involvement in scheduled cellular maintenance processes and therapeutic potential. As a consequence, precise manipulation of singlet oxygen release rates under mild conditions, is crucial. In this work, a cross-linked polyacrylate, and a polydimethylsiloxane elastomer incorporating anthracene-endoperoxide modules with chain extensions at the 9,10-positions were synthesized. We now report that on mechanical agitation in cryogenic ball mill, fluorescence emission due to anthracene units in the PMA (polymethacrylate) polymer is enhanced, with a concomitant generation of singlet oxygen as proved by detection with a selective probe. The PDMS (polydimethylsiloxane) elastomer with the anthracene endoperoxide mechanophore, is also similarly sensitive to mechanical force.

Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics

Kombucha, a fermented tea generated from the co-culture of yeasts and bacteria, has gained worldwide popularity in recent years due to its potential benefits to human health. As a result, many studies have attempted to characterize both its biochemical properties and microbial composition. Here, we have applied a combination of whole metagenome sequencing (WMS) and amplicon (16S rRNA and Internal Transcribed Spacer 1 [ITS1]) sequencing to investigate the microbial communities of homemade Kombucha fermentations from day 3 to day 15. We identified the dominant bacterial genus as Komagataeibacter and dominant fungal genus as Zygosaccharomyces in all samples at all time points. Furthermore, we recovered three near complete Komagataeibacter genomes and one Zygosaccharomyces bailii genome and then predicted their functional properties. Also, we determined the broad taxonomic and functional profile of plasmids found within the Kombucha microbial communities. Overall, this study provides a detailed description of the taxonomic and functional systems of the Kombucha microbial community. Based on this, we conject that the functional complementarity enables metabolic cross talks between Komagataeibacter species and Z. bailii, which helps establish the sustained a relatively low diversity ecosystem in Kombucha.

Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul

BACKGROUND

Several bioinformatics tools have been designed for assembly and annotation of chloroplast (cp) genomes, making it difficult to decide which is most useful and applicable to a specific case. The increasing number of plant genomes provide an opportunity to accurately obtain cp genomes from whole genome shotgun (WGS) sequences. Due to the limited genetic information available for European hazelnut (Corylus avellana L.) and as part of a genome sequencing project, we analyzed the complete chloroplast genome of the cultivar 'Tombul' with multiple annotation tools.

RESULTS

Three different annotation strategies were tested, and the complete cp genome of C. avellana cv Tombul was constructed, which was 161,667 bp in length, and had a typical quadripartite structure. A large single copy (LSC) region of 90,198 bp and a small single copy (SSC) region of 18,733 bp were separated by a pair of inverted repeat (IR) regions of 26,368 bp. In total, 125 predicted functional genes were annotated, including 76 protein-coding, 25 tRNA, and 4 rRNA unique genes. Comparative genomics indicated that the cp genome sequences were relatively highly conserved in species belonging to the same order. However, there were still some variations, especially in intergenic regions, that could be used as molecular markers for analyses of phylogeny and plant identification. Simple sequence repeat (SSR) analysis showed that there were 83 SSRs in the cp genome of cv Tombul. Phylogenetic analysis suggested that C. avellana cv Tombul had a close affinity to the sister group of C. fargesii and C. chinensis, and then a closer evolutionary relationship with Betulaceae family than other species of Fagales.

CONCLUSION

In this study, the complete cp genome of Corylus avellana cv Tombul, the most widely cultivated variety in Turkey, was obtained and annotated, and additionally phylogenetic relationships were predicted among Fagales species. Our results suggest a very accurate assembly of chloroplast genome from next generation whole genome shotgun (WGS) sequences. Enhancement of taxon sampling in Corylus species provide genomic insights into phylogenetic analyses. The nucleotide sequences of cv Tombul cp genomes can provide comprehensive genetic insight into the evolution of genus Corylus.

3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients

Glioblastoma multiforme (GBM) is the most aggressive type of brain tumor. Molecular heterogeneity is a hallmark of GBM tumors that is a barrier in developing treatment strategies. In this study, we used the nonsynonymous mutations of GBM tumors deposited in The Cancer Genome Atlas (TCGA) and applied a systems level approach based on biophysical characteristics of mutations and their organization in patient-specific subnetworks to reduce inter-patient heterogeneity and to gain potential clinically relevant insights. Approximately 10% of the mutations are located in "patches" which are defined as the set of residues spatially in close proximity that are mutated across multiple patients. Grouping mutations as 3D patches reduces the heterogeneity across patients. There are multiple patches that are relatively small in oncogenes, whereas there are a small number of very large patches in tumor suppressors. Additionally, different patches in the same protein are often located at different domains that can mediate different functions. We stratified the patients into five groups based on their potentially affected pathways that are revealed from the patient-specific subnetworks. These subnetworks were constructed by integrating mutation profiles of the patients with the interactome data. Network-guided clustering showed significant association between the groups and patient survival (P-value = 0.0408). Also, each group carries a set of signature 3D mutation patches that affect predominant pathways. We integrated drug sensitivity data of GBM cell lines with the mutation patches and the patient groups to analyze the possible therapeutic outcome of these patches. We found that Pazopanib might be effective in Group 3 by targeting CSF1R. Additionally, inhibiting ATM that is a mediator of PTEN phosphorylation may be ineffective in Group 2. We believe that from mutations to networks and eventually to clinical and therapeutic data, this study provides a novel perspective in the network-guided precision medicine.

Retinal ischemia induces α-SMA-mediated capillary pericyte contraction coincident with perivascular glycogen depletion

Increasing evidence indicates that pericytes are vulnerable cells, playing pathophysiological roles in various neurodegenerative processes. Microvascular pericytes contract during cerebral and coronary ischemia and do not relax after re-opening of the occluded artery, causing incomplete reperfusion. However, the cellular mechanisms underlying ischemia-induced pericyte contraction, its delayed emergence, and whether it is pharmacologically reversible are unclear. Here, we investigate i) whether ischemia-induced pericyte contractions are mediated by alpha-smooth muscle actin (α-SMA), ii) the sources of calcium rise in ischemic pericytes, and iii) if peri-microvascular glycogen can support pericyte metabolism during ischemia. Thus, we examined pericyte contractility in response to retinal ischemia both in vivo, using adaptive optics scanning light ophthalmoscopy and, ex vivo, using an unbiased stereological approach. We found that microvascular constrictions were associated with increased calcium in pericytes as detected by a genetically encoded calcium indicator (NG2-GCaMP6) or a fluoroprobe (Fluo-4). Knocking down α-SMA expression with RNA interference or fixing F-actin with phalloidin or calcium antagonist amlodipine prevented constrictions, suggesting that constrictions resulted from calcium- and α-SMA-mediated pericyte contractions. Carbenoxolone or a Cx43-selective peptide blocker also reduced calcium rise, consistent with involvement of gap junction-mediated mechanisms in addition to voltage-gated calcium channels. Pericyte calcium increase and capillary constrictions became significant after 1 h of ischemia and were coincident with depletion of peri-microvascular glycogen, suggesting that glucose derived from glycogen granules could support pericyte metabolism and delay ischemia-induced microvascular dysfunction. Indeed, capillary constrictions emerged earlier when glycogen breakdown was pharmacologically inhibited. Constrictions persisted despite recanalization but were reversible with pericyte-relaxant adenosine administered during recanalization. Our study demonstrates that retinal ischemia, a common cause of blindness, induces α-SMA- and calcium-mediated persistent pericyte contraction, which can be delayed by glucose driven from peri-microvascular glycogen. These findings clarify the contractile nature of capillary pericytes and identify a novel metabolic collaboration between peri-microvascular end-feet and pericytes.