bluuebunny/crossref_metadata_2025 huggingface dataset:
Seven New Cytotoxic and Antimicrobial Xanthoquinodins from Jugulospora vestita
Authors: Shao Lulu , Marin-Felix Yasmina , Surup Frank , Stchigel Alberto M. , Stadler Marc
Published: September 2020

During the course of a screening for novel biologically active secondary metabolites produced by the Sordariomycetes (Ascomycota, Fungi), the ex-type strain of Jugulospora vestita was found to produce seven novel xanthone-anthraquinone heterodimers, xanthoquinodin A11 (1) and xanthoquinodins B10–15 (2–7), together with the already known compound xanthoquinodin B4 (8). The structures of the xanthoquinodins were determined by analysis of the nuclear magnetic resonance (NMR) spectroscopic and mass spectrometric data. Moreover, the absolute configurations of these metabolites were established by analysis of the 1H−1H coupling constants, nuclear Overhauser effect spectroscopy (NOESY) correlations, and Electronic Circular Dichroism (ECD) spectroscopic data. Antifungal and antibacterial activities as well as cytotoxicity of all compounds were tested. Xanthoquinodin B11 showed fungicidal activities against Mucor hiemalis [minimum inhibitory concentration (MIC) 2.1 µg/mL], Rhodotorula glutinis (MIC 2.1 µg/mL), and Pichia anomala (MIC 8.3 µg/mL). All the compounds 1–8 displayed anti-Gram-positive bacteria activity (MIC 0.2–8.3 µg/mL). In addition, all these eight compounds showed cytotoxicity against KB 3.1, L929, A549, SK-OV-3, PC-3, A431, and MCF-7 mammalian cell lines. The six novel compounds (1–3, 5–7), together with xanthoquinodin B4, were also found in the screening of other strains belonging to Jugulospora rotula, revealing the potential chemotaxonomic significance of the compound class for the genus.
Review of the Novel Echinocandin Antifungal Rezafungin: Animal Studies and Clinical Data
Authors: Zhao Yanan , Perlin David S.
Published: September 2020

Rezafungin is a novel echinocandin drug being developed as a first-line option for treatment and prevention of invasive fungal infections. As a result of a structural modification in its parent molecule anidulafungin, rezafungin has acquired unique chemical stability conferring prolonged pharmacokinetics, as well as an administration advantage in the clinical setting compared to other drugs in the same class. Rezafungin displays potent in vitro activity against a wide spectrum of fungal pathogens, which is reflected in robust in vivo efficacy and/or pharmacodynamic studies using various animal models as well as in promising clinical trials data. This review describes in vivo characterization of rezafungin using animal models, current status of clinical development and key findings from these studies.
Paracoccidioides HSP90 Can Be Found in the Cell Surface and Is a Target for Antibodies with Therapeutic Potential
Authors: Moura Ágata , Oliveira Diane , Paredes Verenice , Rocha Letícia , Oliveira Fabiana , Lessa Gustavo , Riasco-Palacios Juan , Casadevall Arturo , Albuquerque Patrícia , Felipe Maria , Piazza Roxane , Nicola André
Published: September 2020

Paracoccidioidomycosis (PCM) is one of the most frequent systemic mycoses in Latin America. It affects mainly male rural workers in impoverished regions, and the therapy can last up to two years or use drugs that are very toxic. Given the need for novel safe and effective approaches to treat PCM, we have been developing monoclonal antibodies (mAbs) that could be used not only to block specific fungal targets, but also modulate the host’s antifungal immunity. In this work we show the generation of and promising results with an mAb against Heat Shock Protein (HSP)90, a molecular chaperone that is an important virulence factor in fungi. Using recombinant Paracoccidioides lutzii (Pb01) and P. brasiliensis (Pb18) HSP90 proteins produced in E. coli, we immunized mice and generated polyclonal antibodies and an IgG1 hybridoma mAb. The proteins were very immunogenic and both the polyclonal serum and mAb were used in immunofluorescence experiments, which showed binding of antibodies to the yeast cell surface. The mAb successfully opsonized P. lutzii and P. brasiliensis cells in co-incubations with J774.16 macrophage-like cells. Our results suggest that this mAb could serve as the basis for new immunotherapy regimens for PCM.
The Impact of Interphase Precipitation on the Mechanical Behavior of Fire-Resistant Steels at an Elevated Temperature
Authors: Cong Jinghua , Li Jiangwen , Fan Jiajie , Liu Pengcheng , Misra Raja Devesh Kumar , Shang Chengjia , Wang Xuemin
Published: September 2020

In this study, we address the challenge of obtaining high strength at ambient and elevated temperatures in fire-resistant Ti–Mo–V steel with ferrite microstructures through thermo-mechanical controlled processing (TMCP). Thermally stable interphase precipitation of (Ti, Mo, V)C was an important criterion for retaining strength at elevated temperatures. Electron microscopy indicated that interphase precipitation occurred during continuous cooling after controlled rolling, where the volume fraction of interphase precipitation was controlled by the laminar cooling temperature. The interphase precipitation of MC carbides with an NaCl-type crystal structure indicated a Baker–Nutting (B–N) orientation relationship with ferrite. When the steel was isothermally held at 600 °C for up to 3 h, interphase precipitation occurred during TMCP with high thermal stability. At the same time, some random precipitation took place during isothermal holding. The interphase precipitation increased the elastic modulus of the experimental steels at an elevated temperature. It is proposed that fire-resistant steel with thermally stable interphase precipitation is preferred, which enhances precipitation strengthening and dislocation strengthening at elevated temperatures.
Synthesis and Formation Mechanism of Limestone-Derived Porous Rod Hierarchical Ca-based Metal–Organic Framework for Efficient CO2 Capture
Authors: Chang Po-Hsueh , Hsu Hua-Pei , Wu Szu-Chen , Peng Cheng-Hsiung
Published: September 2020

Limestone is a relatively abundant and low-cost material used for producing calcium oxide as a CO2 adsorbent. However, the CO2 capture capacity of limestone decreases rapidly after multiple carbonation/calcination cycles. To improve the CO2 capture performance, we developed a process using limestone to transform the material into a rod Ca-based metal–organic framework (Ca-MOF) via a hydrothermal process with the assistance of acetic acid and terephthalic acid (H2BDC). The structural formation of rod Ca-MOF may result from the (200) face-oriented attachment growth of Ca-MOF sheets. Upon heat treatment, a highly stable porous rod network with a calcined Ca-MOF-O structure was generated with a pore distribution of 50–100 nm, which allowed the rapid diffusion of CO2 into the interior of the sorbent and enhanced the CO2 capture capacity with high multiple carbonation–calcination cycle stability compared to limestone alone at the intermediate temperature of 450 °C. The CO2 capture capacity of the calcined porous Ca-MOF-O network reached 52 wt% with a CO2 capture stability of 80% after 10 cycles. The above results demonstrated that rod Ca-MOF can be synthesized from a limestone precursor to form a porous network structure as a CO2 capture sorbent to improve CO2 capture performance at an intermediate temperature, thus suggesting its potential in environmental applications.
Coupling of Anodic Oxidation and Soil Remediation Processes: A Review
Authors: Barbosa Ferreira Maiara , Sales Solano Aline Maria , Vieira dos Santos Elisama , Martínez-Huitle Carlos A. , Ganiyu Soliu O.
Published: September 2020

In recent years, due to industrial modernization and agricultural mechanization, several environmental consequences have been observed, which make sustainable development difficult. Soil, as an important component of ecosystem and a key resource for the survival of human and animals, has been under constant contamination from different human activities. Contaminated soils and sites require remediation not only because of the hazardous threat it possess to the environment but also due to the shortage of fresh land for both agriculture and urbanization. Combined or coupled remediation technologies are one of the efficient processes for the treatment of contaminated soils. In these technologies, two or more soil remediation techniques are applied simultaneously or sequentially, in which one technique complements the other, making the treatment very efficient. Coupling anodic oxidation (AO) and soil remediation for the treatment of soil contaminated with organics has been studied via two configurations: (i) soil remediation, ex situ AO, where AO is used as a post-treatment stage for the treatment of effluents from soil remediation process and (ii) soil remediation, in situ AO, where both processes are applied simultaneously. The former is the most widely investigated configuration of the combined processes, while the latter is less common due to the greater diffusion dependency of AO as an electrode process. In this review, the concept of soil washing (SW)/soil flushing (SF) and electrokinetic as soil remediation techniques are briefly explained followed by a discussion of different configurations of combined AO and soil remediation.
Performance of Rice Husk Ash as Supplementary Cementitious Material after Production in the Field and in the Lab
Authors: Thiedeitz Mareike , Schmidt Wolfram , Härder Michelle , Kränkel Thomas
Published: September 2020

Supplementary cementitious materials (SCM) can reduce the total amount of Portland cement clinker in concrete production. Rice husk ashes (RHA) can be converted from an agricultural by-product to a high-performance concrete constituent due to a high amount of reactive silica with pozzolanic properties if they are burnt under controlled conditions. The way and duration of combustion, the cooling process as well as the temperature have an effect on the silica form and thus, the chemical and physical performance of the RHA. Various studies on the best combustion technique have been published to investigate the ideal combustion techniques. Yet, the process mostly took place under laboratory conditions. Investigating the difference between the performance of RHA produced in a rural environment and laboratory conditions is useful for the assessment and future enhancement of RHA production, and its application both as building material, for example in rural areas where it is sourced in large quantities, and as additive for high performance concrete. Thus, the paper presents a comparison between RHA produced under rudimentary conditions in a self-made furnace in the rural Bagamoyo, Tanzania and under controlled laboratory conditions at the Technical University of Munich, Germany, with different combustion methods and temperatures. In a second step, RHA was ground to reach particle size distributions comparable to cement. In a third step, cement pastes were prepared with 10%, 20% and 40% of cement replacement, and compared to the performance of plain and fly ash blended cement pastes. The results show that controlled burning conditions around 650 °C lead to high reactivity of silica and, therefore, to good performance as SCM. However, also the RHA burnt under less controlled conditions in the field provided reasonably good properties, if the process took place with proper burning parameters and adequate grinding. The knowledge can be implemented in the field to improve the final RHA performance as SCM in concrete.
Thermal Load of Mine Rescuer in the Underwear and Protective Clothing with Phase Change Materials in Simulated Utility Conditions
Authors: Bartkowiak Grażyna , Marszałek Anna , Dąbrowska Anna
Published: September 2020

A new set of underwear and protective clothing with phase change materials (PCM) for mine rescuers has been developed in order to increase their safety of work. It includes PCM pouches absorbing excess heat from the body. In order to evaluate thermal load of mine rescuers, physiological tests were carried out for three variants of possible use of the developed set of clothing: for mine rescuers wearing only the underwear with PCM; for a set of underwear and protective clothing; and for a complete set of clothing with closed-circuit compressed oxygen breathing apparatus. Tests were performed in difficult microclimate conditions, reflecting the typical working conditions of rescuers that cause a significant thermal load. The use of outer clothing shortened safe time of exposure to such conditions by about 36%, while the addition of respiratory protective device to this set further shortened this time to a lesser extent (by another 13%).
Nonnegative Inverse Elementary Divisors Problem for Lists with Nonnegative Real Parts
Authors: Nina Hans , Flores Callisaya Hector , Pickmann-Soto H. , Rodriguez Jonnathan
Published: September 2020

In this paper, sufficient conditions for the existence and construction of nonnegative matrices with prescribed elementary divisors for a list of complex numbers with nonnegative real part are obtained, and the corresponding nonnegative matrices are constructed. In addition, results of how to perturb complex eigenvalues of a nonnegative matrix while keeping its elementary divisors and its nonnegativity are derived.
Is There a Connection between Sovereign CDS Spreads and the Stock Market? Evidence for European and US Returns and Volatilities
Authors: Ballester Laura , González-Urteaga Ana
Published: September 2020

This study complements the current literature, providing a thorough investigation of the lead–lag connection between stock indices and sovereign credit default swap (CDS) returns for 14 European countries and the US over the period 2004–2016. We use a rolling VAR framework that enables us to analyse the connection process over time covering both crisis and non-crisis periods. In addition, we analyse the relationship between stock market volatility and CDS returns. We find that the connection between the credit and equity markets does exist and that it is time variable and seems to be related to financial crises. We also observe that stock market returns anticipate sovereign CDS returns, and sovereign CDSs anticipate the conditional volatility of equity returns, closing a connectedness circle between markets. Contribution percentages in terms of returns are more intense in the US than in Europe and the opposite result is found with respect to volatilities. Within Europe, a greater impact in Eurozone countries compared to non-Eurozone countries is observed. Finally, an additional analysis is also carried out for the financial sector, obtaining results largely consistent with those found using sovereign data.
Venous Thromboembolism and Its Association with COVID-19: Still an Open Debate
Authors: Di Micco Pierpaolo , Russo Vincenzo , Lodigiani Corrado
Published: September 2020

Asreported by the World Health Organization, a novel coronavirus (COVID-19) was identified as the causative virus of new viral pneumonia of unknown etiology by Chinese authorities on 7 January 2020. The virus was named COVID-19 and because of its ability to cause severe acute respiratory syndrome (i.e., SARS) this infection has also been defined as SARS-CoV2.Furthermore, an association between COVID-19 infection and venous thromboembolism has been reported in several series around the world.For this reason, methods used to improve diagnostic tools, pharmacological thromboprophylaxis and type of anticoagulants are discussed in this expert opinion.
Effects of the Substrate on Interfacial Polymerization: Tuning the Hydrophobicity via Polyelectrolyte Deposition
Authors: Liu Xin , Liu Ge , Li Weiyi , Wang Qinyu , Deng Baolin
Published: September 2020

Interfacial polymerization (IP) has been the key method for the fabrication of the thin film composite (TFC) membranes that are extensively employed in reverse osmosis (RO) and forward osmosis (FO). However, the role of the substrate surface hydrophilicity in the formation of the IP-film remains a controversial issue to be further addressed. This study characterized the IP films formed on a series of polyacrylonitrile (PAN) substrates whose hydrophilicities (from ~38 to ~93 degrees) were varied via different approaches, including the alkaline treatment and the deposition of various polycations. It was revealed that delamination could occur when the IP film was formed on a relatively hydrophilic surface; the integrity of the TFC membranes was substantially improved, owing to the modification of the polyelectrolyte deposition. On the other hand, the characterization indicated that the TFC membrane could have an enhanced efficiency (with a factor of ~2) when the substrate was relatively hydrophilic. It was established that the polyelectrolyte deposition could be exploited to effectively tune the substrate surface hydrophobicity, thereby providing more degrees of freedom for the optimization of the TFC membranes fabrication.
Shear Strength and Aging Characteristics of Sn-3.0Ag-0.5Cu/Cu Solder Joint Reinforced with ZrO2 Nanoparticles
Authors: Rajendran Sri Harini , Hwang Seung Jun , Jung Jae Pil
Published: September 2020

This study investigates the shear strength and aging characteristics of Sn-3.0Ag-0.5Cu (SAC 305)/Cu joints by the addition of ZrO2 nanoparticles (NPs) having two different particle size: 5–15 nm (ZrO2A) and 70–90 nm (ZrO2B). Nanocomposite pastes were fabricated by mechanically mixing ZrO2 NPs and the solder paste. ZrO2 NPs decreased the β-Sn grain size and Ag3Sn intermetallic compound (IMC) in the matrix and reduced the Cu6Sn5 IMC thickness at the interface of lap shear SAC 305/Cu joints. The effect is pronounced for ZrO2A NPs added solder joint. The solder joints were isothermally aged at 175 °C for 24, 48, 144 and 256 h. NPs decreased the diffusion coefficient from 1.74 × 10–16 m/s to 3.83 × 10–17 m/s and 4.99 × 10–17 m/s for ZrO2A and ZrO2B NPs added SAC 305/Cu joints respectively. The shear strength of the solder joints decreased with the aging time due to an increase in the thickness of interfacial IMC and coarsening of Ag3Sn in the solder. However, higher shear strength exhibited by SAC 305-ZrO2A/Cu joints was attributed to the fine Ag3Sn IMC’s dispersed in the solder matrix. Fracture analysis of SAC 305-ZrO2A/Cu joints displayed mixed solder/IMC mode upon 256 h of aging.
Towards Best Practice in Hair Metabolomic Studies: Systematic Investigation on the Impact of Hair Length and Color
Authors: Eisenbeiss Lisa , Binz Tina M. , Baumgartner Markus R. , Kraemer Thomas , Steuer Andrea E.
Published: September 2020

Untargeted metabolomic studies are used for large-scale analysis of endogenous compounds. Due to exceptional long detection windows of incorporated substances in hair, analysis of hair samples for retrospective monitoring of metabolome changes has recently been introduced. However, information on the general behavior of metabolites in hair samples is scarce, hampering correct data interpretation so far. The presented study aimed to investigate endogenous metabolites depending on hair color and along the hair strand and to propose recommendations for best practice in hair metabolomic studies. A metabolite selection was analyzed using untargeted data acquisition in genuine hair samples from different hair colors and after segmentation in 3 cm segments. Significant differences in metabolites among hair colors and segments were found. In conclusion, consideration of hair color and hair segments is necessary for hair metabolomic studies and, subsequently, recommendations for best practice in hair metabolomic studies were proposed.
Lactate Kinetics Reflect Organ Dysfunction and Are Associated with Adverse Outcomes in Intensive Care Unit Patients with COVID-19 Pneumonia: Preliminary Results from a GREEK Single-Centre Study
Authors: Vassiliou Alice G. , Jahaj Edison , Ilias Ioannis , Markaki Vassiliki , Malachias Sotirios , Vrettou Charikleia , Ischaki Eleni , Mastora Zafeiria , Douka Evangelia , Keskinidou Chrysi , Tsipilis Stamatios , Vassiliadi Dimitra A. , Kotanidou Anastasia , Dimopoulou Ioanna
Published: September 2020

Coronavirus disease-19 (COVID-19) continues to be a health threat worldwide. Increased blood lactate is common in intensive care unit (ICU) patients; however, its association with outcomes in ICU COVID-19 patients remains currently unexplored. In this retrospective, observational study we assessed whether lactate is associated with outcomes in COVID-19 patients. Blood lactate was measured on ICU admission and thereafter daily up to day 14 in 45 patients with confirmed COVID-19 pneumonia. Acute physiology and chronic health evaluation (APACHE II) was calculated on ICU admission, and sequential organ failure assessment (SOFA) score was assessed on admission and every second day. The cohort was divided into survivors and non-survivors based on 28-day ICU mortality (24.4%). Cox regression analysis revealed that maximum lactate on admission was independently related to 28-day ICU mortality with time in the presence of APACHE II (RR = 2.45, p = 0.008). Lactate’s area under the curve for detecting 28-day ICU mortality was 0.77 (p = 0.008). Mixed model analysis showed that mean daily lactate levels were higher in non-survivors (p < 0.0001); the model applied on SOFA scores showed a similar time pattern. Thus, initial blood lactate was an independent outcome predictor in COVID-19 ICU patients. The time course of lactate mirrors organ dysfunction and is associated with poor clinical outcomes.
Pore Structures for High-Throughput Nanopore Devices
Authors: Ryuzaki Sou , Matsuda Rintaro , Taniguchi Masateru
Published: September 2020

Nanopore devices are expected to advance the next-generation of nanobiodevices because of their strong sensing and analyzing capabilities for single molecules and bioparticles. However, the device throughputs are not sufficiently high. Although analytes pass through a nanopore by electrophoresis, the electric field gradient is localized inside and around a nanopore structure. Thus, analytes located far from a nanopore cannot be driven by electrophoresis. Here, we report nanopore structures for high-throughput sensing, namely, inverted pyramid (IP)-shaped nanopore structures. Silicon-based IP-shaped nanopore structures create a homogeneous electric field gradient within a nanopore device, indicating that most of the analytes can pass through a nanopore by electrophoresis, even though the analytes are suspended far from the nanopore entrance. In addition, the nanostructures can be fabricated only by photolithography. The present study suggests a high potential for inverted pyramid shapes to serve as nanopore devices for high-throughput sensing.
A Capacitive Pressure Sensor Interface IC with Wireless Power and Data Transfer
Authors: Zhang Chaoping , Gallichan Robert , Budgett David , McCormick Daniel
Published: September 2020

This paper presents a capacitive pressure sensor interface circuit design in 180 nm XH018 CMOS technology for an implantable capacitive pressure sensor, which has a wireless power supply and wireless data transfer function. It integrates full-bridge rectifiers, shorting control switches, low-dropout regulators, bandgap references, analog front end, single slope analog to digital converter (ADC), I2C, and an RC oscillator. The low-dropout regulators regulate the wireless power supply coming from the rectifier and provide a stable and accurate 1.8 V DC voltage to other blocks. The capacitance of the pressure sensor is sampled to a discrete voltage by the analog front end. The single slope ADC converts the discrete voltage into 11 bits of digital data, which is then converted into 1 kbps serial data out by the I2C block. The “1” of serial data is modulated to a 500 kHz digital signal that is used to control the shorting switch for wireless data transfer via inductive back scatter. This capacitive pressure sensor interface IC has a resolution of 0.98 mmHg (1.4 fF), average total power consumption of 7.8 mW, and ±3.2% accuracy at the worst case under a −20 to 80 °C temperature range, which improves to ±0.86% when operated between 20 and 60 °C.
Haloferax profundi sp. nov. and Haloferax marisrubri sp. nov., Isolated from the Discovery Deep Brine-Seawater Interface in the Red Sea
Authors: Zhang Guishan , Dong Xiaoyan , Sun Yingjiao , Antunes André , Hikmawan Tyas , Haroon Mohamed Fauzi , Wang Junru , Stingl Ulrich
Published: September 2020

Two extremely halophilic archaeal strains, designated SB29T and SB3T, were isolated from the brine-seawater interface of Discovery Deep in the Red Sea. Cells of both strains were pleomorphic (irregular polyhedrals, ovals, and rods) and stained Gram-negative; colonies were pigmented pink. The sequence similarity of the 16S rRNA gene of strain SB29T with that of its most closely related validly described species (Hfx. sulfurifontis DSM 16227T) and that of strain SB3T with its closest validly described relative (Hfx. denitrificans ATCC 35960T) was 98.1% and 98.6%, respectively. The incomplete draft genomes of SB29T and SB3T are 3,871,125 bp and 3,904,985 bp in size, respectively, and their DNA G + C contents are 60.75% and 65.64%, respectively. The highest ANI values between the genomes of SB29T and SB3T and the most closely related genomes in GenBank were determined as 82.6% (Hfx. sulfurifontis ATCC BAA-897T, GenBank accession no. GCA_000337835.1) and 92.6% (Haloferax denitrificans ATCC 35960T, GenBank accession no. GCA_000337795.1), respectively. These data indicate that the two new isolates cannot be classified into any recognized species of the genus Haloferax, and, therefore, two novel species of the genus Haloferax are proposed: Haloferax profundi sp. nov. (type strain SB29T = JCM 19567T = CGMCC 1.14960T) and Haloferax marisrubri sp. nov. (type strain SB3T = JCM 19566T = CGMCC 1.14958T).
Environmental Influences of High-Density Agricultural Animal Operation on Human Forearm Skin Microflora
Authors: Peng Mengfei , Biswas Debabrata
Published: September 2020

The human forearm skin microbiome ecosystem contains rich and diverse microbes, which are influenced by environmental exposures. The microbial representatives can be exchanged between human and environment, specifically animals, by which they share certain or similar epidermal microbes. Livestock and poultry are the microbial sources that are associated with the transmission of community-based pathogenic infections. Here, in this study, we proposed investigating the environmental influences introduced by livestock/poultry operations on forearm skin microflora of on-site farm workers. A total of 30 human skin swab samples were collected from 20 animal workers in dairy or integrated farms and 10 healthy volunteer controls. The skin microbiome was 16S metagenomics that were sequenced with Illumina MiSeq system. For skin microbial community analysis, the abundance of major phyla and genera as well as alpha and beta diversities were compared across groups. We identified distinctive microbial compositional patterns on skin of workers in farm with different animal commodities. Workers in integrated farms containing various animals were associated with higher abundances of epidermal Proteobacteria, especially Pseudomonas and Acinetobacter, but lower Actinobacteria, especially Corynebacterium and Propionibacterium. For those workers with frequent dairy cattle operations, their Firmicutes in the forearm skin microbiota were enriched. Furthermore, farm animal operations also reduced Staphylococcus and Streptococcus, as well as modulated the microbial biodiversity in farm workers’ skin microbiome. The alterations of forearm skin microflora in farm workers, influenced by their frequent farm animal operations, may increase their risk in skin infections with unusual pathogens and epidermal diseases.
Different Bacteroides Species Colonise Human and Chicken Intestinal Tract
Authors: Kollarcikova Miloslava , Faldynova Marcela , Matiasovicova Jitka , Jahodarova Eva , Kubasova Tereza , Seidlerova Zuzana , Babak Vladimir , Videnska Petra , Cizek Alois , Rychlik Ivan
Published: September 2020

Bacteroidaceae are common gut microbiota members in all warm-blooded animals. However, if Bacteroidaceae are to be used as probiotics, the species selected for different hosts should reflect the natural distribution. In this study, we therefore evaluated host adaptation of bacterial species belonging to the family Bacteroidaceae. B. dorei, B. uniformis, B. xylanisolvens, B. ovatus, B. clarus, B. thetaiotaomicron and B. vulgatus represented human-adapted species while B. gallinaceum, B. caecigallinarum, B. mediterraneensis, B. caecicola, M. massiliensis, B. plebeius and B. coprocola were commonly detected in chicken but not human gut microbiota. There were 29 genes which were present in all human-adapted Bacteroides but absent from the genomes of all chicken isolates, and these included genes required for the pentose cycle and glutamate or histidine metabolism. These genes were expressed during an in vitro competitive assay, in which human-adapted Bacteroides species overgrew the chicken-adapted isolates. Not a single gene specific for the chicken-adapted species was found. Instead, chicken-adapted species exhibited signs of frequent horizontal gene transfer, of KUP, linA and sugE genes in particular. The differences in host adaptation should be considered when the new generation of probiotics for humans or chickens is designed.
High Colonization Rate and Heterogeneity of ESBL- and Carbapenemase-Producing Enterobacteriaceae Isolated from Gull Feces in Lisbon, Portugal
Authors: Aires-de-Sousa Marta , Fournier Claudine , Lopes Elizeth , de Lencastre Hermínia , Nordmann Patrice , Poirel Laurent
Published: September 2020

In order to evaluate whether seagulls living on the Lisbon coastline, Portugal, might be colonized and consequently represent potential spreaders of multidrug-resistant bacteria, a total of 88 gull fecal samples were screened for detection of extended-spectrum β-lactamase (ESBL)- or carbapenemase-producing Enterobacteriaceae for methicillin-resistant Staphylococcus aureus (MRSA) and for vancomycin-resistant Enterococci (VRE). A large proportion of samples yielded carbapenemase- or ESBL-producing Enterobacteriaceae (16% and 55%, respectively), while only two MRSA and two VRE were detected. Mating-out assays followed by PCR and whole-plasmid sequencing allowed to identify carbapenemase and ESBL encoding genes. Among 24 carbapenemase-producing isolates, there were mainly Klebsiella pneumoniae (50%) and Escherichia coli (33%). OXA-181 was the most common carbapenemase identified (54%), followed by OXA-48 (25%) and KPC-2 (17%). Ten different ESBLs were found among 62 ESBL-producing isolates, mainly being CTX-M-type enzymes (87%). Co-occurrence in single samples of multiple ESBL- and carbapenemase producers belonging to different bacterial species was observed in some cases. Seagulls constitute an important source for spreading multidrug-resistant bacteria in the environment and their gut microbiota a formidable microenvironment for transfer of resistance genes within bacterial species.
Probing the Local Atomic Structure of In and Cu in Sphalerite by XAS Spectroscopy Enhanced by Reverse Monte Carlo Algorithm
Authors: Trigub Alexander L. , Trofimov Nikolay D. , Tagirov Boris R. , Nickolsky Max S. , Kvashnina Kristina O.
Published: September 2020

The distortion of atomic structure around In and Cu dopants in sphalerite ZnS was explored by extended X-ray absorption fine structure (EXAFS) spectroscopy enhanced by reverse Monte Carlo (RMC) simulation (RMC-EXAFS method). These data were complemented with quantum chemical Density Functional Theory (DFT) calculations and theoretical modeling of X-ray absorption near edge spectroscopy (XANES) spectra. The RMC-EXAFS method showed that in the absence of Cu, the In-bearing solid solution is formed via the charge compensation scheme 3Zn2+↔2In3+ + □, where □ is a Zn vacancy. The coordination spheres of In remain undistorted. Formation of the solid solution in the case of (In, Cu)-bearing sphalerites follows the charge compensation scheme 2Zn2+↔Cu+ + In3+. In the solid solution, splitting of the interatomic distances in the 2nd and 3rd coordination spheres of In and Cu is observed. The dopants’ local atomic structure is slightly distorted around In but highly distorted around Cu. The DFT calculations showed that the geometries with close arrangement (clustering) of the impurities—In and Cu atoms, or the In atom and a vacancy—are energetically more favorable than the random distribution of the defects. However, as no heavy In atoms were detected in the 2nd shell of Cu by means of EXAFS, and the 2nd shell of In was only slightly distorted, we conclude that the defects are distributed randomly (or at least, not close to each other). The disagreement of the RMC-EXAFS fittings with the results of the DFT calculations, according to which the closest arrangement of dopants is the most stable configuration, can be explained by the presence of other defects of the sphalerite crystal lattice, which were not considered in the DFT calculations.
The Reduction Behavior of Ocean Manganese Nodules by Pyrolysis Technology Using Sawdust as the Reductant
Authors: Deng Xiang-yi , He Dong-sheng , Chi Ru-an , Xiao Chun-qiao , Hu Jin-gang
Published: September 2020

Ocean manganese nodules, which contain abundant Cu, Co, Ni and Mn resources, were reduced using biomass (sawdust) pyrolysis technology. Valuable metals were further extracted by acid leaching after the reduction process with high efficiency. The effects of sawdust dosage, reduction temperature, and time were investigated to obtain optimal operating parameters. The extraction rates of Mn, Cu, Co, and Ni reached as high as 96.1%, 91.7%, 92.5%, and 94.4%, respectively. Results from TGA show that the main pyrolysis process of sawdust occurs at temperature range of 250–375 °C with a mass loss of 59%, releasing a large amount of volatile substances to reduce the ocean manganese nodules. The pyrolysis activation energy of sawdust was calculated to be 52.68 kJ∙mol−1 by the non-isothermal kinetic model. Additionally, the main reduction reaction behind the main sawdust pyrolysis process was identified by the comparison of the assumed and actual TG curve. The thermodynamic analysis showed that the high valence manganese minerals were gradually reduced to Mn2O3, Mn3O4, and MnO by CO generated from sawdust pyrolysis. The shrinking core model showed that the reduction process is controlled by the surface chemical reaction with activation energy of 45.5 kJ∙mol−1. The surface of reduced ore and acid leached residue exhibited a structure composed of relatively finer pores and rougher morphology than the raw ore.
Sustainable Reuse of Coal Mine Waste: Experimental and Economic Assessments for Embankments and Pavement Layer Applications in Morocco
Authors: Amrani Mustapha , Taha Yassine , El Haloui Yassine , Benzaazoua Mostafa , Hakkou Rachid
Published: September 2020

This paper deals with the potential reuse of coal mine waste rocks (CMWR) as an alternative material for road construction to conserve the natural resources and sustainable management of mining waste. The investigation was conducted through the determination of the chemical, mineralogical, geotechnical properties, and acid mine drainage formulation of CMWR as well as economic feasibility. This waste was used either alone for embankments and mixed with stabilizing agents fly ash (FA) and hydraulic road binder (HRB) for pavement applications. The experimental results confirmed that weathered CMWR can be successfully used alone as a sustainable alternative material for the embankment. Furthermore, the use of stabilizing agents in the following ratio CMWR:FA:HRB = 80:20:5 allow the use of CMWR in road sub-base layers for high-traffic pavements. Also, the environmental investigations showed that CMWR does not present any potential contaminating risk on the surrounding environment and most of the pyrite particles were already oxidized. Therefore, the environmental impact of acid mine drainage produced by pyritic waste throughout its life cycle can be neglected. Finally, an economic case study confirmed the workability of CMWR reuse in a radius of 29 km around their dumps by resulting in a lower cost compared with conventional materials.
LncMirNet: Predicting LncRNA–miRNA Interaction Based on Deep Learning of Ribonucleic Acid Sequences
Authors: Yang Sen , Wang Yan , Lin Yu , Shao Dan , He Kai , Huang Lan
Published: September 2020

Long non-coding RNA (LncRNA) and microRNA (miRNA) are both non-coding RNAs that play significant regulatory roles in many life processes. There is cumulating evidence showing that the interaction patterns between lncRNAs and miRNAs are highly related to cancer development, gene regulation, cellular metabolic process, etc. Contemporaneously, with the rapid development of RNA sequence technology, numerous novel lncRNAs and miRNAs have been found, which might help to explore novel regulated patterns. However, the increasing unknown interactions between lncRNAs and miRNAs may hinder finding the novel regulated pattern, and wet experiments to identify the potential interaction are costly and time-consuming. Furthermore, few computational tools are available for predicting lncRNA–miRNA interaction based on a sequential level. In this paper, we propose a hybrid sequence feature-based model, LncMirNet (lncRNA–miRNA interactions network), to predict lncRNA–miRNA interactions via deep convolutional neural networks (CNN). First, four categories of sequence-based features are introduced to encode lncRNA/miRNA sequences including k-mer (k = 1, 2, 3, 4), composition transition distribution (CTD), doc2vec, and graph embedding features. Then, to fit the CNN learning pattern, a histogram-dd method is incorporated to fuse multiple types of features into a matrix. Finally, LncMirNet attained excellent performance in comparison with six other state-of-the-art methods on a real dataset collected from lncRNASNP2 via five-fold cross validation. LncMirNet increased accuracy and area under curve (AUC) by more than 3%, respectively, over that of the other tools, and improved the Matthews correlation coefficient (MCC) by more than 6%. These results show that LncMirNet can obtain high confidence in predicting potential interactions between lncRNAs and miRNAs.
Computational Study of C-X-C Chemokine Receptor (CXCR)3 Binding with Its Natural Agonists Chemokine (C-X-C Motif) Ligand (CXCL)9, 10 and 11 and with Synthetic Antagonists: Insights of Receptor Activation towards Drug Design for Vitiligo
Authors: Aguilera-Durán Giovanny , Romo-Mancillas Antonio
Published: September 2020

Vitiligo is a hypopigmentary skin pathology resulting from the death of melanocytes due to the activity of CD8+ cytotoxic lymphocytes and overexpression of chemokines. These include CXCL9, CXCL10, and CXCL11 and its receptor CXCR3, both in peripheral cells of the immune system and in the skin of patients diagnosed with vitiligo. The three-dimensional structure of CXCR3 and CXCL9 has not been reported experimentally; thus, homology modeling and molecular dynamics could be useful for the study of this chemotaxis-promoter axis. In this work, a homology model of CXCR3 and CXCL9 and the structure of the CXCR3/Gαi/0βγ complex with post-translational modifications of CXCR3 are reported for the study of the interaction of chemokines with CXCR3 through all-atom (AA-MD) and coarse-grained molecular dynamics (CG-MD) simulations. AA-MD and CG-MD simulations showed the first activation step of the CXCR3 receptor with all chemokines and the second activation step in the CXCR3-CXCL10 complex through a decrease in the distance between the chemokine and the transmembrane region of CXCR3 and the separation of the βγ complex from the α subunit in the G-protein. Additionally, a general protein–ligand interaction model was calculated, based on known antagonists binding to CXCR3. These results contribute to understanding the activation mechanism of CXCR3 and the design of new molecules that inhibit chemokine binding or antagonize the receptor, provoking a decrease of chemotaxis caused by the CXCR3/chemokines axis.
Expanding the Scope of Orthogonal Translation with Pyrrolysyl-tRNA Synthetases Dedicated to Aromatic Amino Acids
Authors: Tseng Hsueh-Wei , Baumann Tobias , Sun Huan , Wang Yane-Shih , Ignatova Zoya , Budisa Nediljko
Published: September 2020

In protein engineering and synthetic biology, Methanosarcina mazei pyrrolysyl-tRNA synthetase (MmPylRS), with its cognate tRNAPyl, is one of the most popular tools for site-specific incorporation of non-canonical amino acids (ncAAs). Numerous orthogonal pairs based on engineered MmPylRS variants have been developed during the last decade, enabling a substantial genetic code expansion, mainly with aliphatic pyrrolysine analogs. However, comparatively less progress has been made to expand the substrate range of MmPylRS towards aromatic amino acid residues. Therefore, we set to further expand the substrate scope of orthogonal translation by a semi-rational approach; redesigning the MmPylRS efficiency. Based on the randomization of residues from the binding pocket and tRNA binding domain, we identify three positions (V401, W417 and S193) crucial for ncAA specificity and enzyme activity. Their systematic mutagenesis enabled us to generate MmPylRS variants dedicated to tryptophan (such as β-(1-Azulenyl)-l-alanine or 1-methyl-l-tryptophan) and tyrosine (mainly halogenated) analogs. Moreover, our strategy also significantly improves the orthogonal translation efficiency with the previously activated analog 3-benzothienyl-l-alanine. Our study revealed the engineering of both first shell and distant residues to modify substrate specificity as an important strategy to further expand our ability to discover and recruit new ncAAs for orthogonal translation
Apigenin and Hesperidin Downregulate DNA Repair Genes in MCF-7 Breast Cancer Cells and Augment Doxorubicin Toxicity
Authors: Korga-Plewko Agnieszka , Michalczyk Monika , Adamczuk Grzegorz , Humeniuk Ewelina , Ostrowska-Lesko Marta , Jozefczyk Aleksandra , Iwan Magdalena , Wojcik Marta , Dudka Jaroslaw
Published: September 2020

A number of studies have confirmed anti-tumor activity of flavonoids and their ability to enhance the effectiveness of classical anticancer drugs. The mechanism of this phenomenon is difficult to explain because of the ambivalent nature of these compounds. Many therapeutic properties of these compounds are attributed to their antioxidant activity; however, it is known that they can act as oxidants. The aim of this study was to assess the influence of apigenin and hesperidin on MCF-7 breast cancer cells with doxorubicin. The cytotoxic effect was determined using an MTT test and cell cycle analysis. To evaluate the possible interaction mechanism, reduced glutathione levels, as well as the DNA oxidative damage and the double strand breaks, were evaluated. Additionally, mRNA expression of genes related to DNA repair was assessed. It was demonstrated that flavonoids intensified the cytotoxic effect of doxorubicin despite flavonoids reduced oxidative damage caused by the drug. At the same time, the number of double strand breaks significantly increased and expression of tested genes was downregulated. In conclusion, both apigenin and hesperidin enhance the cytotoxic effects of doxorubicin on breast cancer cells, and this phenomenon occurs regardless of oxidative stress but is accompanied by disorders of DNA damage response mechanisms.
Consumption of Anacardium occidentale L. (Cashew Nuts) Inhibits Oxidative Stress through Modulation of the Nrf2/HO−1 and NF-kB Pathways
Authors: Fusco Roberta , Cordaro Marika , Siracusa Rosalba , Peritore Alessio Filippo , Gugliandolo Enrico , Genovese Tiziana , D’Amico Ramona , Crupi Rosalia , Smeriglio Antonella , Mandalari Giuseppina , Impellizzeri Daniela , Cuzzocrea Salvatore , Di Paola Rosanna
Published: September 2020

Ischemia/reperfusion injury is a severe disorder associated with a high mortality. Several antioxidant and pharmacological properties of cashew nuts (Anacardium occidentale L.) and its metabolites from different countries have recently been described. It is a medicinal plant with important therapeutic effects. This study aimed to verify the effect of an oral administration of cashew nuts in a rat model of ischemia/reperfusion (I/R). Adult male rats were subjected to intestinal I/R injury by clamping the superior mesenteric artery for 30 min and then allowing animals to 1 h of reperfusion. Rats subjected to I/R of the gut showed a significant increase in different biochemical markers. In particular, we evaluated lipid peroxidation, tissue myeloperoxidase activity, protein carbonyl content, reactive oxygen species generation and decreased antioxidant enzyme activities. Western blot analysis showed the activation of the NRF2 and NF-kB pathways. Increased immunoreactivity to nitrotyrosine, PARP, P-selectin, and ICAM-1 was observed in the ileum of rats subjected to I/R. Administration of cashew nuts (100 mg/kg) significantly reduced the mortality rate, the fall in arterial blood pressure, and oxidative stress and restored the antioxidant enzyme activities by a mechanism involving both NRF2 and NF-kB pathways. Cashew nuts treatments reduced cytokines plasma levels, nitrotyrosine, and PARP expression as well as adhesion molecules expressions. Additionally, cashew nuts decreased the intestinal barrier dysfunction and mucosal damage, the translocation of toxins and bacteria, which leads to systemic inflammation and associated organs injuries in particular of liver and kidney. Our study demonstrates that cashew nuts administration exerts antioxidant and pharmacological protective effects in superior mesenteric artery occlusion–reperfusion shock.
Isoliquiritigenin Pretreatment Induces Endoplasmic Reticulum Stress-Mediated Hormesis and Attenuates Cisplatin-Induced Oxidative Stress and Damage in LLC-PK1 Cells
Authors: Gómez-Sierra Tania , Medina-Campos Omar Noel , Solano José D. , Ibarra-Rubio María Elena , Pedraza-Chaverri José
Published: September 2020

Isoliquiritigenin (IsoLQ) is a flavonoid with antioxidant properties and inducer of endoplasmic reticulum (ER) stress. In vitro and in vivo studies show that ER stress-mediated hormesis is cytoprotective; therefore, natural antioxidants and ER stress inducers have been used to prevent renal injury. Oxidative stress and ER stress are some of the mechanisms of damage involved in cisplatin (CP)-induced nephrotoxicity. This study aims to explore whether IsoLQ pretreatment induces ER stress and produces hormesis to protect against CP-induced nephrotoxicity in Lilly Laboratories Cell-Porcine Kidney 1 (LLC-PK1) cells. During the first stage of this study, both IsoLQ protective concentration and pretreatment time against CP-induced toxicity were determined by cell viability. At the second stage, the effect of IsoLQ pretreatment on cell viability, ER stress, and oxidative stress were evaluated. IsoLQ pretreatment in CP-treated cells induces expression of glucose-related proteins 78 and 94 kDa (GRP78 and GRP94, respectively), attenuates CP-induced cell death, decreases reactive oxygen species (ROS) production, and prevents the decrease in glutathione/glutathione disulfide (GSH/GSSG) ratio, free thiols levels, and glutathione reductase (GR) activity. These data suggest that IsoLQ pretreatment has a moderately protective effect on CP-induced toxicity in LLC-PK1 cells, through ER stress-mediated hormesis, as well as by the antioxidant properties of IsoLQ.