bluuebunny/crossref_metadata_2025 huggingface dataset:
Protective Action of Ostreococcus Tauri and Phaeodactylum Tricornutum Extracts towards Benzo[a]Pyrene-Induced Cytotoxicity in Endothelial Cells
Authors: Le Goff Manon , Delbrut Antoine , Quinton Marie , Pradelles Rémi , Bescher Maelle , Burel Agnès , Schoefs Benoît , Sergent Odile , Lagadic-Gossmann Dominique , Le Ferrec Eric , Ulmann Lionel
Published: December 2019

Marine microalgae are known to be a source of bioactive molecules of interest to human health, such as n-3 polyunsaturated fatty acids (n-3 PUFAs) and carotenoids. The fact that some of these natural compounds are known to exhibit anti-inflammatory, antioxidant, anti-proliferative, and apoptosis-inducing effects, demonstrates their potential use in preventing cancers and cardiovascular diseases (CVDs). Benzo[a]pyrene (B[a]P), a polycyclic aromatic hydrocarbon (PAH), is an ubiquitous environmental pollutant known to contribute to the development or aggravation of human diseases, such as cancer, CVDs, and immune dysfunction. Most of these deleterious effects are related to the activation of the polycyclic aromatic hydrocarbon receptor (AhR). In this context, two ethanolic microalgal extracts with concentrations of 0.1 to 5 µg/mL are tested, Ostreoccoccus tauri (OT) and Phaeodactylum tricornutum (PT), in order to evaluate and compare their potential effects towards B[a]P-induced toxicity in endothelial HMEC-1 cells. Our results indicate that the OT extract can influence the toxicity of B[a]P. Indeed, apoptosis and the production of extracellular vesicles were decreased, likely through the reduction of the expression of CYP1A1, a B[a]P bioactivation enzyme. Furthermore, the B[a]P-induced expression of the inflammatory cytokines IL-8 and IL1-β was reduced. The PT extract only inhibited the expression of the B[a]P-induced cytokine IL-8 expression. The OT extract therefore seems to be a good candidate for counteracting the B[a]P toxicity.
Marine Pharmacology in 2014–2015: Marine Compounds with Antibacterial, Antidiabetic, Antifungal, Anti-Inflammatory, Antiprotozoal, Antituberculosis, Antiviral, and Anthelmintic Activities; Affecting the Immune and Nervous Systems, and Other Miscellaneous Mechanisms of Action
Authors: Mayer Alejandro M. S. , Guerrero Aimee J. , Rodríguez Abimael D. , Taglialatela-Scafati Orazio , Nakamura Fumiaki , Fusetani Nobuhiro
Published: December 2019

The systematic review of the marine pharmacology literature from 2014 to 2015 was completed in a manner consistent with the 1998–2013 reviews of this series. Research in marine pharmacology during 2014–2015, which was reported by investigators in 43 countries, described novel findings on the preclinical pharmacology of 301 marine compounds. These observations included antibacterial, antifungal, antiprotozoal, antituberculosis, antiviral, and anthelmintic pharmacological activities for 133 marine natural products, 85 marine compounds with antidiabetic, and anti-inflammatory activities, as well as those that affected the immune and nervous system, and 83 marine compounds that displayed miscellaneous mechanisms of action, and may probably contribute to novel pharmacological classes upon further research. Thus, in 2014–2015, the preclinical marine natural product pharmacology pipeline provided novel pharmacology as well as new lead compounds for the clinical marine pharmaceutical pipeline, and thus continued to contribute to ongoing global research for alternative therapeutic approaches to many disease categories.
Deep-Sea Fungi Could Be the New Arsenal for Bioactive Molecules
Authors: Zain ul Arifeen Muhammad , Ma Yu-Nan , Xue Ya-Rong , Liu Chang-Hong
Published: December 2019

Growing microbial resistance to existing drugs and the search for new natural products of pharmaceutical importance have forced researchers to investigate unexplored environments, such as extreme ecosystems. The deep-sea (>1000 m below water surface) has a variety of extreme environments, such as deep-sea sediments, hydrothermal vents, and deep-sea cold region, which are considered to be new arsenals of natural products. Organisms living in the extreme environments of the deep-sea encounter harsh conditions, such as high salinity, extreme pH, absence of sun light, low temperature and oxygen, high hydrostatic pressure, and low availability of growth nutrients. The production of secondary metabolites is one of the strategies these organisms use to survive in such harsh conditions. Fungi growing in such extreme environments produce unique secondary metabolites for defense and communication, some of which also have clinical significance. Despite being the producer of many important bioactive molecules, deep-sea fungi have not been explored thoroughly. Here, we made a brief review of the structure, biological activity, and distribution of secondary metabolites produced by deep-sea fungi in the last five years.
Proapoptotic Index Evaluation of Two Synthetic Peptides Derived from the Coneshell Californiconus californicus in Lung Cancer Cell Line H1299
Authors: Oroz-Parra Irasema , Álvarez-Delgado Carolina , Cervantes-Luevano Karla , Dueñas-Espinoza Salvador , Licea-Navarro Alexei F.
Published: December 2019

Lung cancer is one of the most common types of cancer, accounting for approximately 15% of all cancer cases worldwide. Apoptosis is the dominant defense mechanism against tumor development. The balance between pro- and antiapoptotic members of the Bcl-2 protein family can determine cellular fate. The venom of predatory marine snails Conus is estimated to have 100–400 toxins called conotoxins. The family of α-conotoxins is known to consist of selective antagonists of nicotinic acetylcholine receptors (nAChRs). Lung cancer cells overexpress several subunits of nAChRs and are considered as an excellent target for new anticancer drugs. We compared the cytotoxic effect of two synthetic peptides derived from Californiconus californicus, Cal14.1a, and Cal14.1b, which only differ by one amino acid in their sequence, and compared their proapoptotic balance by Bax and Bcl-2 mRNA expression. We determined the caspase-3 and -7 activation to demonstrate apoptosis induction. Results showed that Cal14.1a induces a high Bax/Bcl-2 ratio in H1299 (lung cancer cells). Although Cal14.1b has a cytotoxic effect on H1299 cells, reducing cell viability by 30%, it does not increase the Bax/Bcl-2 ratio, which could be explained by the Glu in the 15th residue, which is crucial for the ability of Cal14.1a to induce apoptosis.
Stroke Volume Variation and Stroke Volume Index Can Predict Fluid Responsiveness after Mini-Volume Challenge Test in Patients Undergoing Laparoscopic Cholecystectomy
Authors: Moon Eun-Jin , Lee Seunghwan , Yi Jae-Woo , Kim Ju Hyun , Lee Bong-Jae , Seo Hyungseok
Published: December 2019

Background and Objectives: For using appropriate goal-directed fluid therapy during the surgical conditions of pneumoperitoneum in the reverse Trendelenburg position, we investigated the predictability of various hemodynamic parameters for fluid responsiveness by using a mini-volume challenge test. Materials and Methods: 42 adult patients scheduled for laparoscopic cholecystectomy were enrolled. After general anesthesia was induced, CO2 pneumoperitoneum was applied and the patient was placed in the reverse Trendelenburg position. The mini-volume challenge test was carried out with crystalloid 4 mL/kg over 10 min. Hemodynamic parameters, including stroke volume variation (SVV), cardiac index (CI), stroke volume index (SVI), mean arterial pressure (MAP), and heart rate (HR), were measured before and after the mini-volume challenge test. The positive fluid responsiveness was defined as an increase in stroke volume index ≥10% after the mini-volume challenge. For statistical analysis, a Shapiro–Wilk test was used to test the normality of the data. Continuous variables were compared using an unpaired t-test or the Mann–Whitney rank-sum test. Categorical data were compared using the chi-square test. A receiver operating characteristic curve analysis was used to assess the predictability of fluid responsiveness after the mini-volume challenge. Results: 31 patients were fluid responders. Compared with the MAP and HR, the SVV, CI, and SVI showed good predictability for fluid responsiveness after the mini-volume challenge test (area under the curve was 0.900, 0.833, and 0.909, respectively; all p-values were <0.0001). Conclusions: SVV and SVI effectively predicted fluid responsiveness after the mini-volume challenge test in patients placed under pneumoperitoneum and in the reverse Trendelenburg position.
Reply to Comment on the Paper Entitled “A New Cumulative Fatigue Damage Rule Based on Dynamic Residual S-N Curve and Material Memory Concept” by Peng Z., Huang H., Zhou J. and Li Y. Published in Metals (2018; 8(6): 456)
Authors: Peng Zhaochun , Huang Hong-Zhong , Zhou Jie , Li Yan-Feng
Published: December 2019

Dear Editors, [...]
Impact of Bovine Diet on Metabolomic Profile of Skim Milk and Whey Protein Ingredients
Authors: Magan Jonathan B. , O’Callaghan Tom F. , Zheng Jiamin , Zhang Lun , Mandal Rupasri , Hennessy Deirdre , Fenelon Mark A. , Wishart David S. , Kelly Alan L. , McCarthy Noel A.
Published: December 2019

The influence of bovine diet on the metabolome of reconstituted skim milk powder (SMP) and protein ingredients produced from the milk of cows fed on pasture or concentrate-based diets was investigated. Cows were randomly assigned to diets consisting of perennial ryegrass only (GRS), perennial ryegrass/white clover sward (CLV), or indoor total mixed ration (TMR) for an entire lactation. Raw milk obtained from each group was processed at pilot scale, to produce SMP and sweet whey, and SMP was further processed at laboratory scale, to yield ideal whey and acid whey. The total amino acid composition and metabolome of each sample were analyzed, using high-performance cation exchange and a targeted combination of direct-injection mass spectrometry and reverse-phase liquid chromatography–tandem mass spectrometry (LC–MS/MS), respectively. The nitrogen composition of the products from each of the diets was similar, with one exception being the significantly higher nonprotein nitrogen content in TMR-derived skim milk powder than that from the GRS system. Total amino acid analysis showed significantly higher concentrations of glycine in GRS- and CLV-derived sweet whey and acid whey than in those from TMR. The cysteine contents of CLV-derived ideal whey and acid whey were significantly higher than for TMR, while the valine content of GRS-derived acid whey was significantly higher than TMR. The phenylalanine content of GRS-derived ideal whey was significantly higher than that from CLV. Metabolomic analysis showed significantly higher concentrations of the metabolites glutamine, valine, and phosphocreatine in each ingredient type derived from TMR than those from GRS or CLV, while the serine content of each GRS-derived ingredient type was significantly higher than that in TMR-derived ingredients. These results demonstrate that the type of bovine feeding system used can have a significant effect on the amino acid composition and metabolome of skim milk and whey powders and may aid in the selection of raw materials for product manufacture, while the clear separation between the samples gives further evidence for distinguishing milk products produced from different feeding systems based on LC–MS/MS.
Barth Syndrome: Exploring Cardiac Metabolism with Induced Pluripotent Stem Cell-Derived Cardiomyocytes
Authors: Fatica Erica M. , DeLeonibus Gina A. , House Alisha , Kodger Jillian V. , Pearce Ryan W. , Shah Rohan R. , Levi Liraz , Sandlers Yana
Published: December 2019

Barth syndrome (BTHS) is an X-linked recessive multisystem disorder caused by mutations in the TAZ gene (TAZ, G 4.5, OMIM 300394) that encodes for the acyltransferase tafazzin. This protein is highly expressed in the heart and plays a significant role in cardiolipin biosynthesis. Heart disease is the major clinical manifestation of BTHS with a high incidence in early life. Although the genetic basis of BTHS and tetralinoleoyl cardiolipin deficiency in BTHS-affected individuals are well-established, downstream metabolic changes in cardiac metabolism are still uncovered. Our study aimed to characterize TAZ-induced metabolic perturbations in the heart. Control (PGP1-TAZWT) and TAZ mutant (PGP1-TAZ517delG) iPS-CM were incubated with 13C6-glucose and 13C5-glutamine and incorporation of 13C into downstream Krebs cycle intermediates was traced. Our data reveal that TAZ517delG induces accumulation of cellular long chain acylcarnitines and overexpression of fatty acid binding protein (FABP4). We also demonstrate that TAZ517delG induces metabolic alterations in pathways related to energy production as reflected by high glucose uptake, an increase in glycolytic lactate production and a decrease in palmitate uptake. Moreover, despite mitochondrial dysfunction, in the absence of glucose and fatty acids, TAZ517delG-iPS-CM can use glutamine as a carbon source to replenish the Krebs cycle.
From Samples to Insights into Metabolism: Uncovering Biologically Relevant Information in LC-HRMS Metabolomics Data
Authors: Ivanisevic Julijana , Want Elizabeth J.
Published: December 2019

Untargeted metabolomics (including lipidomics) is a holistic approach to biomarker discovery and mechanistic insights into disease onset and progression, and response to intervention. Each step of the analytical and statistical pipeline is crucial for the generation of high-quality, robust data. Metabolite identification remains the bottleneck in these studies; therefore, confidence in the data produced is paramount in order to maximize the biological output. Here, we outline the key steps of the metabolomics workflow and provide details on important parameters and considerations. Studies should be designed carefully to ensure appropriate statistical power and adequate controls. Subsequent sample handling and preparation should avoid the introduction of bias, which can significantly affect downstream data interpretation. It is not possible to cover the entire metabolome with a single platform; therefore, the analytical platform should reflect the biological sample under investigation and the question(s) under consideration. The large, complex datasets produced need to be pre-processed in order to extract meaningful information. Finally, the most time-consuming steps are metabolite identification, as well as metabolic pathway and network analysis. Here we discuss some widely used tools and the pitfalls of each step of the workflow, with the ultimate aim of guiding the reader towards the most efficient pipeline for their metabolomics studies.
A Foldable Chip Array for the Continuous Investigation of Seed Germination and the Subsequent Root Development of Seedlings
Authors: Song Zhao Xi , Chai Hui Hui , Chen Feng , Yu Ling , Fang Can
Published: December 2019

Seed germination and seedling root development are important indicators of plant development. This work designed and fabricated a foldable microfluidic chip array for conducting nondestructive and continuous evaluation of seed germination and subsequent seedling development in situ. Each plant chamber has two functional units: seed germination part and root-growth part. The root-growth parts are themselves connected to a single channel designed to provide a uniform culture medium for plant growth. The individual chips are connected into an array using elastic hinges that facilitate the folding and unfolding of the array to accommodate different viewing purposes. In the folded state, the seed germination chambers form a closely spaced array platform to facilitate the comparison of seed germination and plant development characteristics. Unfolding the array facilitates a clear examination of root development within the root-growth parts. The observation window of an individual chip facilitates either the direct examination of the developing seedling (e.g., stems and leaves) or the use of a microscope for examining microscale features (e.g., root tips and root hairs). The potential of the proposed foldable chip array as a new cultivation platform for botanic studies is demonstrated by examining the seed germination and seedling development of tobacco (Nicotiana tabacum) under different cultivation conditions.
Efficient Development of Integrated Lab-On-A-Chip Systems Featuring Operational Robustness and Manufacturability
Authors: Ducrée Jens
Published: December 2019

The majority of commercially oriented microfluidic technologies provide novel point-of-use solutions for laboratory automation with important areas in the context of the life sciences such as health care, biopharma, veterinary medicine and agrifood as well as for monitoring of the environment, infrastructures and industrial processes. Such systems are often composed of a modular setup exhibiting an instrument accommodating rather conventional actuation, detection and control units which interfaces with a fluidically integrated “Lab-on-a-Chip” device handling (bio-)sample(s) and reagents. As the complex network of tiny channels, chambers and surface-functionalised zones can typically not be properly cleaned and regenerated, these microfluidic chips are mostly devised as single-use disposables. The availability of cost-efficient materials and associated structuring, functionalisation and assembly schemes thus represents a key ingredient along the commercialisation pipeline and will be a first focus of this work. Furthermore, and owing to their innate variability, investigations on biosamples mostly require the acquisition of statistically relevant datasets. Consequently, intermediate numbers of consistently performing chips are already needed during application development; to mitigate the potential pitfalls of technology migration and to facilitate regulatory compliance of the end products, manufacture of such pilot series should widely follow larger-scale production schemes. To expedite and de-risk the development of commercially relevant microfluidic systems towards high Technology Readiness Levels (TRLs), we illustrate a streamlined, manufacturing-centric platform approach employing the paradigms of tolerance-forgiving Design-for-Manufacture (DfM) and Readiness for Scale-up (RfS) from prototyping to intermediate pilot series and eventual mass fabrication. Learning from mature industries, we further propose pursuing a platform approach incorporating aspects of standardisation in terms of specification, design rules and testing methods for materials, components, interfaces, and operational procedures; this coherent strategy will foster the emergence of dedicated commercial supply chains and also improve the economic viability of Lab-on-a-Chip systems often targeting smaller niche markets by synergistically bundling technology development.
Femtosecond Laser Written Depressed-Cladding Waveguide 2 × 2, 1 × 2 and 3 × 3 Directional Couplers in Tm3+:YAG Crystal
Authors: Skryabin Nikolay , Kalinkin Alexander , Dyakonov Ivan , Kulik Sergei
Published: December 2019

Ion-doped crystal-based compact devices capable of beam splitting and coupling are enthralling for a broad range of classical and quantum integrated photonics applications. In this work, we report on the fabrication of depressed-cladding waveguide 2D 2 × 2, 1 × 2 and 3D 3 × 3 directional couplers in Tm 3 + :YAG crystal by femtosecond laser writing. The performances of the couplers are characterized at 810 nm, showing single-mode guidance, polarization independence, finely matched splitting ratios. These results open up new opportunities in the beneficial fabrication of 3D circuits and devices in crystals.
Simulation Informed CAD for 3D Nanoprinting
Authors: Fowlkes Jason D. , Winkler Robert , Mutunga Eva , Rack Philip D. , Plank Harald
Published: December 2019

A promising 3D nanoprinting method, used to deposit nanoscale mesh style objects, is prone to non-linear distortions which limits the complexity and variety of deposit geometries. The method, focused electron beam-induced deposition (FEBID), uses a nanoscale electron probe for continuous dissociation of surface adsorbed precursor molecules which drives highly localized deposition. Three dimensional objects are deposited using a 2D digital scanning pattern—the digital beam speed controls deposition into the third, or out-of-plane dimension. Multiple computer-aided design (CAD) programs exist for FEBID mesh object definition but rely on the definition of nodes and interconnecting linear nanowires. Thus, a method is needed to prevent non-linear/bending nanowires for accurate geometric synthesis. An analytical model is derived based on simulation results, calibrated using real experiments, to ensure linear nanowire deposition to compensate for implicit beam heating that takes place during FEBID. The model subsequently compensates and informs the exposure file containing the pixel-by-pixel scanning instructions, ensuring nanowire linearity by appropriately adjusting the patterning beam speeds. The derivation of the model is presented, based on a critical mass balance revealed by simulations and the strategy used to integrate the physics-based analytical model into an existing 3D nanoprinting CAD program is overviewed.
Fabrication of Tapered Circular Depressed-Cladding Waveguides in Nd:YAG Crystal by Femtosecond-Laser Direct Inscription
Authors: Romero Carolina , García Ajates Javier , Chen Feng , Vázquez de Aldana Javier R.
Published: December 2019

Crystalline materials are excellent substrates for the integration of compact photonic devices benefiting from the unique optical properties of these materials. The technique of direct inscription with femtosecond lasers, as an advantage over other techniques, has opened the door to the fabrication of true three-dimensional (3D) photonic devices in almost any transparent substrate. Depressed-cladding waveguides have been demonstrated to be an excellent and versatile platform for the integration of 3D photonic circuits in crystals. Here, we present the technique that we have developed to inscribe tapered depressed-cladding waveguides with a circular section for the control of the modal behavior. As a proof of concept, we have applied the technique to fabricate structures in Nd:YAG crystal that efficiently change the modal behavior from highly multimodal to monomodal, in the visible and near infrared, with reduction factors in the waveguide radius of up to 4:1. Our results are interesting for different devices such as waveguide lasers, frequency converters or connectors between external devices with different core sizes.
Correction: Park, J.; et al. Fine-Grained Power Gating Using an MRAM-CMOS Non-Volatile Flip-Flop. Micromachines 2019, 10, 411
Authors: Park Jaeyoung , Yim Young Uk
Published: December 2019

As this research is a personal achievement with no company-related information, and there is no financial support for this paper from Qualcomm Technologies Inc [...]
Anti-Symmetric Mode Vibration of Electrostatically Actuated Clamped–Clamped Microbeams for Mass Sensing
Authors: Li Lei , Zhang Yin-ping , Ma Chi-cheng , Liu Can-chang , Peng Bo
Published: December 2019

This paper details study of the anti-symmetric response to the symmetrical electrostatic excitation of a Micro-electro-mechanical-systems (MEMS) resonant mass sensor. Under higher order mode excitation, two nonlinear coupled flexural modes to describe MEMS mass sensors are obtained by using Hamilton’s principle and Galerkin method. Static analysis is introduced to investigate the effect of added mass on the natural frequency of the resonant sensor. Then, the perturbation method is applied to determine the response and stability of the system for small amplitude vibration. Through bifurcation analysis, the physical conditions of the anti-symmetric mode vibration are obtained. The corresponding stability analysis is carried out. Results show that the added mass can change the bifurcation behaviors of the anti-symmetric mode and affect the voltage and frequency of the bifurcation jump point. Typically, we propose a mass parameter identification method based on the dynamic jump motion of the anti-symmetric mode. Numerical studies are introduced to verify the validity of mass detection method. Finally, the influence of physical parameters on the sensitivity of mass sensor is analyzed. It is found that the DC voltage and mass adsorption position are critical to the sensitivity of the sensor. The results of this paper can be potentially useful in nonlinear mass sensors.
Direct Patterning and Spontaneous Self-Assembly of Graphene Oxide via Electrohydrodynamic Jet Printing for Energy Storage and Sensing
Authors: Zhang Bin , Lee Jaehyun , Kim Mincheol , Lee Naeeung , Lee Hyungdong , Byun Doyoung
Published: December 2019

The macroscopic assembly of two-dimensional materials into a laminar structure has received considerable attention because it improves both the mechanical and chemical properties of the original materials. However, conventional manufacturing methods have certain limitations in that they require a high temperature process, use toxic solvents, and are considerably time consuming. Here, we present a new system for the self-assembly of layer-by-layer (LBL) graphene oxide (GO) via an electrohydrodynamic (EHD) jet printing technique. During printing, the orientation of GO flakes can be controlled by the velocity distribution of liquid jet and electric field-induced alignment spontaneously. Closely-packed GO patterns with an ordered laminar structure can be rapidly realized using an interfacial assembly process on the substrates. The surface roughness and electrical conductivity of the LBL structure were significantly improved compared with conventional dispensing methods. We further applied this technique to fabricate a reduced graphene oxide (r-GO)-based supercapacitor and a three-dimensional (3D) metallic grid hybrid ammonia sensor. We present the EHD-assisted assembly of laminar r-GO structures as a new platform for preparing high-performance energy storage devices and sensors.
Fermented Seeds (“Zgougou”) from Aleppo Pine as a Novel Source of Potentially Probiotic Lactic Acid Bacteria
Authors: Missaoui Jihen , Saidane Dalila , Mzoughi Ridha , Minervini Fabio
Published: December 2019

Microorganisms inhabiting fermented foods represent the main link between the consumption of this food and human health. Although some fermented food is a reservoir of potentially probiotic microorganisms, several foods are still unexplored. This study aimed at characterizing the probiotic potential of lactic acid bacteria isolated from zgougou, a fermented matrix consisting of a watery mixture of Aleppo pine′s seeds. In vitro methods were used to characterize the safety, survival ability in typical conditions of the gastrointestinal tract, and adherence capacity to surfaces, antimicrobial, and antioxidant activities. Strains belonged to the Lactobacillus plantarum group and Enterococcus faecalis showed no DNase, hemolytic, and gelatinase activities. In addition, their susceptibility to most of the tested antibiotics, satisfied some of the safety prerequisites for their potential use as probiotics. All the strains tolerated low pH, gastrointestinal enzymes, and bile salts. They displayed a good antibacterial activity and antibiofilm formation against 10 reference bacterial pathogens, especially when used as a cell-free supernatant. Furthermore, the lactic acid bacteria (LAB) strains inhibited the growth of Aspergillus flavus and Aspergillus carbonarius. Finally, they had good antioxidant activity, although depending on the strain. Overall, the results of this work highlight that zgougou represents an important reservoir of potentially probiotic LAB. Obviously, future studies should be addressed to confirm the health benefits of the LAB strains.
Fungal and Bacterial Communities Exhibit Consistent Responses to Reversal of Soil Acidification and Phosphorus Limitation over Time
Authors: R. Carrino-Kyker Sarah , P. Coyle Kaitlin , A. Kluber Laurel , J. Burke David
Published: December 2019

Chronic acid deposition affects many temperate hardwood forests of the northeastern United States, reduces soil pH and phosphorus (P) availability, and can alter the structure and function of soil microbial communities. The strategies that microorganisms possess for survival in acidic, low P soil come at a carbon (C) cost. Thus, how microbial communities respond to soil acidification in forests may be influenced by plant phenological stage as C allocation belowground varies; however, this remains largely unexplored. In this study, we examined microbial communities in an ecosystem level manipulative experiment where pH and/or P availability were elevated in three separate forests in Northeastern Ohio. Tag-encoded pyrosequencing was used to examine bacterial and fungal community structure at five time points across one year corresponding to plant phenological stages. We found significant effects of pH treatment and time on fungal and bacterial communities in soil. However, we found no interaction between pH treatment and time of sampling for fungal communities and only a weak interaction between pH elevation and time for bacterial communities, suggesting that microbial community responses to soil pH are largely independent of plant phenological stage. In addition, fungal communities were structured largely by site, suggesting that fungi were responding to differences between the forests, such as plant community differences.
Structural and Functional Characterization of Stx2k, a New Subtype of Shiga Toxin 2
Authors: Hughes Anna C. , Zhang Yuzhu , Bai Xiangning , Xiong Yanwen , Wang Yan , Yang Xi , Xu Qingping , He Xiaohua
Published: December 2019

Shiga toxin (Stx) is the major virulence factor of Shiga toxin-producing Escherichia coli (STEC). Stx evolves rapidly and, as such, new subtypes continue to emerge that challenge the efficacy of existing disease management and surveillance strategies. A new subtype, Stx2k, was recently identified in E. coli isolated from a wide range of sources including diarrheal patients, animals, and raw meats, and was poorly detected by existing immunoassays. In this study, the structure of Stx2kE167Q was determined at 2.29 Å resolution and the conservation of structure with Stx2a was revealed. A novel polyclonal antibody capable of neutralizing Stx2k and an immunoassay, with a 10-fold increase in sensitivity compared to assays using extant antibodies, were developed. Stx2k is less toxic than Stx2a in Vero cell assays but is similar to Stx2a in receptor-binding preference, thermostability, and acid tolerance. Although Stx2k does not appear to be as potent as Stx2a to Vero cells, the wide distribution and blended virulence profiles of the Stx2k-producing strains suggest that horizontal gene transfer through Stx2k-converting phages could result in the emergence of new and highly virulent pathogens. This study provides useful information and tools for early detection and control of Stx2k-producing E. coli, which could reduce public risk of infection by less-known STECs.
Tissue- and Population-Level Microbiome Analysis of the Wasp Spider Argiope bruennichi Identified a Novel Dominant Bacterial Symbiont
Authors: Sheffer Monica M. , Uhl Gabriele , Prost Stefan , Lueders Tillmann , Urich Tim , Bengtsson Mia M.
Published: December 2019

Many ecological and evolutionary processes in animals depend upon microbial symbioses. In spiders, the role of the microbiome in these processes remains mostly unknown. We compared the microbiome between populations, individuals, and tissue types of a range-expanding spider, using 16S rRNA gene sequencing. Our study is one of the first to go beyond targeting known endosymbionts in spiders and characterizes the total microbiome across different body compartments (leg, prosoma, hemolymph, book lungs, ovaries, silk glands, midgut, and fecal pellets). Overall, the microbiome differed significantly between populations and individuals, but not between tissue types. The microbiome of the wasp spider Argiope bruennichi features a novel dominant bacterial symbiont, which is abundant in every tissue type in spiders from geographically distinct populations and that is also present in offspring. The novel symbiont is affiliated with the Tenericutes, but has low sequence identity (<85%) to all previously named taxa, suggesting that the novel symbiont represents a new bacterial clade. Its presence in offspring implies that it is vertically transmitted. Our results shed light on the processes that shape microbiome differentiation in this species and raise several questions about the implications of the novel dominant bacterial symbiont on the biology and evolution of its host.
Vegetation-Dependent Response to Drought in Salt Marsh Ammonia-Oxidizer Communities
Authors: Beltz Jack K. , McMahon Hayley , Torres Nunez Isis , Bernhard Anne E.
Published: December 2019

We investigated the impacts of drought on ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a salt marsh and compared the response to the total bacterial community. We analyzed abundance and community composition of amoA genes by QPCR and TRFLP, respectively, in three vegetation zones in 2014 (pre-drought), 2016 (drought), and 2017 (post-drought), and analyzed bacterial 16S rRNA genes by QPCR, TRFLP, and MiSeq analyses. AOA and AOB abundance in the Spartina patens zone increased significantly in 2016, while abundance decreased in the tall S. alterniflora zone, and showed little change in the short S. alterniflora zone. Total bacterial abundance declined annually in all vegetation zones. Significant shifts in community composition were detected in 2016 in two of the three vegetation zones for AOA and AOB, and in all three vegetation zones for total bacteria. Abundance and community composition of AOA and AOB returned to pre-drought conditions by 2017, while bacterial abundance continued to decline, suggesting that nitrifiers may be more resilient to drought than other bacterial communities. Finding vegetation-specific drought responses among N-cycling microbes may have broad implications for changes in N availability and marsh productivity, particularly if vegetation patterns continue to shift as predicted due to sea level rise.
Growth Control of Adherent-Invasive Escherichia coli (AIEC) by the Predator Bacteria Bdellovibrio bacteriovorus: A New Therapeutic Approach for Crohn’s Disease Patients
Authors: Bonfiglio Giulia , Neroni Bruna , Radocchia Giulia , Pompilio Arianna , Mura Francesco , Trancassini Maria , Di Bonaventura Giovanni , Pantanella Fabrizio , Schippa Serena
Published: December 2019

In Crohn’s disease (CD) patients, intestinal dysbiosis with an overgrowth of Proteobacteria, mainly Escherichia coli, has been reported. A new pathotype of E. coli, the adherent-invasive Escherichia coli strain (AIEC), has been isolated from the mucosae of CD patients. AIEC strains play an important role in CD pathogenesis, increasing intestinal mucosa damage and inflammation. Several studies have been undertaken to find possible strategies/treatments aimed at AIEC strain reduction/elimination from CD patients’ intestinal mucosae. To date, a truly effective strategy against AIEC overgrowth is not yet available, and as such, further investigations are warranted. Bdellovibrio bacteriovorus is a predator bacterium which lives by invading Gram-negative bacteria, and is usually present both in natural and human ecosystems. The aim of this study was to evaluate a novel possible strategy to treat CD patients’ mucosae when colonized by AIEC strains, based on the utilization of the Gram-negative predatory bacteria, B. bacteriovorus. The overall results indicate that B. bacteriovorus is able to interfere with important steps in the dynamics of pathogenicity of AIEC strains by its predatory activity. We indicate, for the first time, the possibility of counteracting AIEC strain overgrowth by exploiting what naturally occurs in microbial ecosystems (i.e., predation).
Spontaneous Serpentine Carbonation Controlled by Underground Dynamic Microclimate at the Montecastelli Copper Mine, Italy
Authors: Boschi Chiara , Bedini Federica , Baneschi Ilaria , Rielli Andrea , Baumgartner Lukas , Perchiazzi Natale , Ulyanov Alexey , Zanchetta Giovanni , Dini Andrea
Published: December 2019

Understanding low temperature carbon sequestration through serpentinite–H2O–CO2 interaction is becoming increasingly important as it is considered a potential approach for carbon storage required to offset anthropogenic CO2 emissions. In this study, we present new insights into spontaneous CO2 mineral sequestration through the formation of hydromagnesite + kerolite with minor aragonite incrustations on serpentinite walls of the Montecastelli copper mine located in Southern Tuscany, Italy. On the basis of field, petrological, and geochemical observations coupled with geochemical modeling, we show that precipitation of the wall coating paragenesis is driven by a sequential evaporation and condensation process starting from meteoric waters which emerge from fractures into the mine walls and ceiling. A direct precipitation of the coating paragenesis is not compatible with the chemical composition of the mine water. Instead, geochemical modeling shows that its formation can be explained through evaporation of mine water and its progressive condensation onto the mine walls, where a layer of serpentinite powder was accumulated during the excavation of the mine adits. Condensed water produces a homogeneous film on the mine walls where it can interact with the serpentinite powder and become enriched in Mg, Si, and minor Ca, which are necessary for the precipitation of the observed coating paragenesis. The evaporation and condensation processes are driven by changes in the air flow inside the mine, which in turns are driven by seasonal changes of the outside temperature. The presence of “kerolite”, a Mg-silicate, is indicative of the dissolution of Si-rich minerals, such as serpentine, through the water–powder interaction on the mine walls at low temperature (~17.0 to 18.1 °C). The spontaneous carbonation of serpentine at low temperature is a peculiar feature of this occurrence, which has only rarely been observed in ultramafic outcrops exposed on the Earth’s surface, where instead hydromagnesite predominantly forms through the dissolution of brucite. The high reactivity of serpentine observed, in this study, is most likely due to the presence of fine-grained serpentine fines in the mine walls. Further study of the peculiar conditions of underground environments hosted in Mg-rich lithologies, such as that of the Montecastelli Copper mine, can lead to a better understanding of the physical and chemical conditions necessary to enhance serpentine carbonation at ambient temperature.
Critical Elements in Supergene Phosphates: The Example of the Weathering Profile at the Gavà Neolithic Mines, Catalonia, Spain
Authors: Díaz-Acha Yael , Campeny Marc , Tauler Esperança , Bosch Josep , Melgarejo Joan Carles , Camprubí Antoni , Villanova-de-Benavent Cristina , Jorge-Villar Susana E. , Díaz-Ontiveros Iria , Fernández-Lluch David , Proenza Joaquín A. , Andreazini Aleu , Pastor Míriam
Published: December 2019

The essential role of Critical Elements (CE) in 21st century economy has led to an increasing demand of these metals and promotes the exploration of non-conventional deposits such as weathering profiles. The present work is focused on the study of a weathering profile located at the Archaeological Park of the Gavà Neolithic Mines, Barcelona, Catalonia, Spain. In the Gavà deposit, acid and oxidising meteoric fluids generated intense weathering during the early Pleistocene, affecting series of Llandoverian black shales and associated syn-sedimentary phosphates. The circulation of these acid fluids at deeper levels of the profile generated supergene vein-like mineralisations comprised of secondary phosphates (e.g., variscite, perhamite, crandallite, phosphosiderite) and sulphates (e.g., jarosite, alunite). This supergene mineralisation is significantly enriched in certain CE (e.g., Ga, Sc, REE, In, Co and Sb) that were mobilised from host rock components and later hosted in the crystal lattice of supergene minerals. Weathering processes and corresponding supergene enrichment of CE at the Gavà deposit could be used as an example to determine exploration guidelines of CE in weathering profiles and associated supergene phosphates worldwide.
Early Triassic Conversion from Source to Sink on the Southern Margin of the North China Craton: Constraints by Detrital Zircon U-Pb Ages
Authors: Wang Yanpeng , Yang Wentao , Peng Shenyuan , Qi Shuaishuai , Zheng Deshun
Published: December 2019

Provenance analysis of sediments provides important constraints on basin formation and orogenic processes. With the aim to define the sedimentary provenance and tectonic evolution of the southern margin of the North China Craton, this paper presents new detrital zircon U-Pb data from Early Triassic sediments in the Yiyang area. The results showed major peaks at 1848, 458, 425, and 268 Ma and subordinate peaks at ca. 2500, 872, and 957 Ma on age spectra from the Liujiagou Formation. The Heshanggou Formation exhibited a major age peak at 445 Ma and subordinate peaks at 755 and 947 Ma. Integrated with the analysis of sandstone detrital compositions, we suggest that the sources of the Liujiagou Formation were mainly a mixture of the southern margin of the North China Craton and the North Qinling Orogenic Belt, whereas the Heshanggou Formation was derived primarily from the North Qinling Orogenic Belt. Age comparisons of detrital zircon geochronology collected from different basins in the North China Craton indicated that the paleogeography of the North China Craton during the Early Triassic was strongly asymmetric, wherein the uplifted highland along the southern margin of the North China Craton was relatively lower than the northern margin. Meanwhile, the marked shift in source region from the Liujiagou to the Heshanggou formations provides a constraint regarding the conversion from denuded zone to deposited zone along the southern margin of the North China Craton in the Early Triassic, which controlled the evolution of the provenance and sedimentary system.
Valorization of Lignin as an Immobilizing Agent for Bioinoculant Production using Azospirillum brasilense as a Model Bacteria
Authors: Tapia-Olivares Victor Rogelio , Vazquez-Bello Eimy Alejandra , Aguilar-Garnica Efrén , Escalante Froylán M.E.
Published: December 2019

Plant growth-promoting bacteria (PGPB) have been largely considered as beneficial in harsh and limiting environments given their effects on alleviating plant stress. For practical applications, most of the PGPB are prepared in immobilization matrices to improve the stability and benefits of bacteria. Despite the long list of immobilizing agents/carriers tested to date, a long list of desired requirements is yet to be achieved. Here, lignin stands as a scarcely tested immobilizer for bioinoculants with great potential for this purpose. The aim of this work was to demonstrate the feasibility of lignin as a carrier of the nitrogen-fixing Azospirillum brasilense. These bacteria were cultured in liquid media with recovered organosolv lignin added for bacterial immobilization. Then, lignin was recovered and the immobilized biomass was quantified gravimetrically by DNA extraction and serial dilution plating. Fluorescent microscopy as well as Congo red agar plating showed the immobilization of the bacterial cells in the lignin matrix and crystal violet dyeing showed the biofilms formation in lignin particles. A high number of cells were counted per gram of dried lignin. Lignin can be readily used as low-cost, health-safe bioinoculant carrier to be used in soil and agricultural applications.
Ultrasound-Assisted Solvent Extraction of a Porous Membrane Packed Sample for the Determination of Tobacco-Specific Nitrosamines in the Replacement Liquids for E-Cigarettes
Authors: Kubica Paweł
Published: December 2019

The content of tobacco-specific nitrosamines (TSNAs) possessing carcinogenic properties has been an important area of research since replacement liquids were introduced for e-cigarettes. A method for determining N′-nitrosonornicotine (NNN), 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), N′-nitrosoanatabine (NAT), and N′-nitrosoanabasine (NAB) in replacement liquids for electronic cigarettes was developed using liquid chromatography–tandem mass spectrometry with electrospray ionisation (HPLC-ESI-MS/MS) in the multiple reaction monitoring mode. The sample preparation of replacement liquids was accomplished via the ultrasound-assisted solvent extraction of a porous membrane packed sample. The sample preparation proved to be successful in extracting the analytes, with recoveries from 87% to 105%, with coefficients of variation < 4.9%. Moreover, the linearity and limits of detection and quantitation (LOD, LOQ), together with repeatability and accuracy, were determined for the developed method. The proposed sample preparation and developed chromatographic method were successfully applied to the determination of TSNAs in 9 replacement liquid samples. The NNK and NNN were found to be most frequently detected (89 and 67%, respectively), with concentration ranges from 1.2–54.3 ng/mL and 4.1–30.2 ng/mL, respectively, while NAT was detected with frequency of 22% with range 1.7–2.5 ng/mL and NAB were found to be below the LOD in all samples.
Nucleic Acid Nanoparticles at a Crossroads of Vaccines and Immunotherapies
Authors: Dobrovolskaia Marina A.
Published: December 2019

Vaccines and immunotherapies involve a variety of technologies and act through different mechanisms to achieve a common goal, which is to optimize the immune response against an antigen. The antigen could be a molecule expressed on a pathogen (e.g., a disease-causing bacterium, a virus or another microorganism), abnormal or damaged host cells (e.g., cancer cells), environmental agent (e.g., nicotine from a tobacco smoke), or an allergen (e.g., pollen or food protein). Immunogenic vaccines and therapies optimize the immune response to improve the eradication of the pathogen or damaged cells. In contrast, tolerogenic vaccines and therapies retrain or blunt the immune response to antigens, which are recognized by the immune system as harmful to the host. To optimize the immune response to either improve the immunogenicity or induce tolerance, researchers employ different routes of administration, antigen-delivery systems, and adjuvants. Nanocarriers and adjuvants are of particular interest to the fields of vaccines and immunotherapy as they allow for targeted delivery of the antigens and direct the immune response against these antigens in desirable direction (i.e., to either enhance immunogenicity or induce tolerance). Recently, nanoparticles gained particular attention as antigen carriers and adjuvants. This review focuses on a particular subclass of nanoparticles, which are made of nucleic acids, so-called nucleic acid nanoparticles or NANPs. Immunological properties of these novel materials and considerations for their clinical translation are discussed.