bluuebunny/crossref_metadata_2025 huggingface dataset:
Using Oxidative Electrodes to Enrich Novel Members in the Desulfobulbaceae Family from Intertidal Sediments
Authors: Li Cheng , Reimers Clare E. , Alleau Yvan
Published: November 2021

Members in the family of Desulfobulbaceae may be influential in various anaerobic microbial communities, including those in anoxic aquatic sediments and water columns, and within wastewater treatment facilities and bioelectrochemical systems (BESs) such as microbial fuel cells (MFCs). However, the diversity and roles of the Desulfobulbaceae in these communities have received little attention, and large portions of this family remain uncultured. Here we expand on findings from an earlier study (Li, Reimers, and Alleau, 2020) to more fully characterize Desulfobulbaceae that became prevalent in biofilms on oxidative electrodes of bioelectrochemical reactors. After incubations, DNA extraction, microbial community analyses, and microscopic examination, we found that a group of uncultured Desulfobulbaceae were greatly enriched on electrode surfaces. These Desulfobulbaceae appeared to form filaments with morphological features ascribed to cable bacteria, but the majority were taxonomically distinct from recognized cable bacteria genera. Thus, the present study provides new information about a group of Desulfobulbaceae that can exhibit filamentous morphologies and respire on the oxidative electrodes. While the phylogeny of cable bacteria is still being defined and updated, further enriching these members can contribute to the overall understanding of cable bacteria and may also lead to identification of successful isolation strategies.
Microfluidics as a Novel Technique for Tuberculosis: From Diagnostics to Drug Discovery
Authors: Molloy Antonia , Harrison James , McGrath John S. , Owen Zachary , Smith Clive , Liu Xin , Li Xin , Cox Jonathan A. G.
Published: November 2021

Tuberculosis (TB) remains a global healthcare crisis, with an estimated 5.8 million new cases and 1.5 million deaths in 2020. TB is caused by infection with the major human pathogen Mycobacterium tuberculosis, which is difficult to rapidly diagnose and treat. There is an urgent need for new methods of diagnosis, sufficient in vitro models that capably mimic all physiological conditions of the infection, and high-throughput drug screening platforms. Microfluidic-based techniques provide single-cell analysis which reduces experimental time and the cost of reagents, and have been extremely useful for gaining insight into monitoring microorganisms. This review outlines the field of microfluidics and discusses the use of this novel technique so far in M. tuberculosis diagnostics, research methods, and drug discovery platforms. The practices of microfluidics have promising future applications for diagnosing and treating TB.
Bhalin, an Essential Cytoskeleton-Associated Protein of Trypanosoma brucei Linking TbBILBO1 of the Flagellar Pocket Collar with the Hook Complex
Authors: Broster Reix Christine E. , Florimond Célia , Cayrel Anne , Mailhé Amélie , Agnero-Rigot Corentin , Landrein Nicolas , Dacheux Denis , Havlicek Katharina , Bonhivers Mélanie , Morriswood Brooke , Robinson Derrick R.
Published: November 2021

Background: In most trypanosomes, endo and exocytosis only occur at a unique organelle called the flagellar pocket (FP) and the flagellum exits the cell via the FP. Investigations of essential cytoskeleton-associated structures located at this site have revealed a number of essential proteins. The protein TbBILBO1 is located at the neck of the FP in a structure called the flagellar pocket collar (FPC) and is essential for biogenesis of the FPC and parasite survival. TbMORN1 is a protein that is present on a closely linked structure called the hook complex (HC) and is located anterior to and overlapping the collar. TbMORN1 is essential in the bloodstream form of T. brucei. We now describe the location and function of BHALIN, an essential, new FPC-HC protein. Methodology/Principal Findings: Here, we show that a newly characterised protein, BHALIN (BILBO1 Hook Associated LINker protein), is localised to both the FPC and HC and has a TbBILBO1 binding domain, which was confirmed in vitro. Knockdown of BHALIN by RNAi in the bloodstream form parasites led to cell death, indicating an essential role in cell viability. Conclusions/Significance: Our results demonstrate the essential role of a newly characterised hook complex protein, BHALIN, that influences flagellar pocket organisation and function in bloodstream form T. brucei parasites.
Overcoming the Prokaryote/Eukaryote Barrier in Tuberculosis Treatment: A Prospect for the Repurposing and Use of Antiparasitic Drugs
Authors: Ezquerra-Aznárez José Manuel , Almeida da Silva Pedro E. , Aínsa José A.
Published: November 2021

Antimicrobial resistance, the so-called silent pandemic, is pushing industry and academia to find novel antimicrobial agents with new mechanisms of action in order to be active against susceptible and drug-resistant microorganisms. In the case of tuberculosis, the need of novel anti-tuberculosis drugs is specially challenging because of the intricate biology of its causative agent, Mycobacterium tuberculosis. The repurposing of medicines has arisen in recent years as a fast, low-cost, and efficient strategy to identify novel biomedical applications for already approved drugs. This review is focused on anti-parasitic drugs that have additionally demonstrated certain levels of anti-tuberculosis activity; along with this, natural products with a dual activity against parasites and against M. tuberculosis are discussed. A few clinical trials have tested antiparasitic drugs in tuberculosis patients, and have revealed effective dose and toxicity issues, which is consistent with the natural differences between tuberculosis and parasitic infections. However, through medicinal chemistry approaches, derivatives of drugs with anti-parasitic activity have become successful drugs for use in tuberculosis therapy. In summary, even when the repurposing of anti-parasitic drugs for tuberculosis treatment does not seem to be an easy job, it deserves attention as a potential contributor to fuel the anti-tuberculosis drug pipeline.
Outer Membrane Protein F Is Involved in Biofilm Formation, Virulence and Antibiotic Resistance in Cronobacter sakazakii
Authors: Gao Jianxin , Han Zhonghui , Li Ping , Zhang Hongyan , Du Xinjun , Wang Shuo
Published: November 2021

In some Gram-negative bacteria, ompF encodes outer membrane protein F (OmpF), which is a cation-selective porin and is responsible for the passive transport of small molecules across the outer membrane. However, there are few reports about the functions of this gene in Cronobacter sakazakii. To investigate the role of ompF in detail, an ompF disruption strain (ΔompF) and a complementation strain (cpompF) were successfully obtained. We find that OmpF can affect the ability of biofilm formation in C. sakazakii. In addition, the variations in biofilm composition of C. sakazakii were examined using Raman spectroscopy analyses caused by knocking out ompF, and the result indicated that the levels of certain biofilm components, including lipopolysaccharide (LPS), were significantly decreased in the mutant (ΔompF). Then, SDS-PAGE was used to further analyze the LPS content, and the result showed that the LPS levels were significantly reduced in the absence of ompF. Therefore, we conclude that OmpF affects biofilm formation in C. sakazakii by reducing the amount of LPS. Furthermore, the ΔompF mutant showed decreased (2.7-fold) adhesion to and invasion of HCT-8 cells. In an antibiotic susceptibility analysis, the ΔompF mutant showed significantly smaller inhibition zones than the WT, indicating that OmpF had a positive effect on the influx of antibiotics into the cells. In summary, ompF plays a positive regulatory role in the biofilm formation and adhesion/invasion, which is achieved by regulating the amount of LPS, but is a negative regulator of antibiotic resistance in C. sakazakii.
Transcriptomic Analysis of the Effects of Chemokine Receptor CXCR3 Deficiency on Immune Responses in the Mouse Brain during Toxoplasma gondii Infection
Authors: Umeda Kousuke , Goto Youta , Watanabe Kenichi , Ushio Nanako , Fereig Ragab M. , Ihara Fumiaki , Tanaka Sachi , Suzuki Yutaka , Nishikawa Yoshifumi
Published: November 2021

The obligate intracellular parasite Toxoplasma gondii infects warm-blooded animals, including humans. We previously revealed through a whole-brain transcriptome analysis that infection with T. gondii in mice causes immune response-associated genes to be upregulated, for instance, chemokines and chemokine receptors such as CXC chemokine receptor 3 (CXCR3) and its ligand CXC chemokine ligand 10 (CXCL10). Here, we describe the effect of CXCR3 on responses against T. gondii infection in the mouse brain. In vivo assays using CXCR3-deficient mice showed that the absence of CXCR3 delayed the normal recovery of body weight and increased the brain parasite burden, suggesting that CXCR3 plays a role in the control of pathology in the brain, the site where chronic infection occurs. Therefore, to further analyze the function of CXCR3 in the brain, we profiled the gene expression patterns of primary astrocytes and microglia by RNA sequencing and subsequent analyses. CXCR3 deficiency impaired the normal upregulation of immune-related genes during T. gondii infection, in astrocytes and microglia alike. Collectively, our results suggest that the immune-related genes upregulated by CXCR3 perform a particular role in controlling pathology when the host is chronically infected with T. gondii in the brain.
Phenotypic and Molecular Characterization of Commensal, Community-Acquired and Nosocomial Klebsiella spp.
Authors: Gómez Marta , Valverde Arancha , del Campo Rosa , Rodríguez Juan Miguel , Maldonado-Barragán Antonio
Published: November 2021

Klebsiella spp. is a relevant pathogen that can present acquired resistance to almost all available antibiotics, thus representing a serious threat for public health. While most studies have been focused on isolates causing community-acquired and nosocomial infections, little is known about the commensal isolates colonizing healthy subjects. We describe the molecular identification and the phenotypic characterization of commensal Klebsiella spp. from breast milk of healthy women and faeces from healthy breast-fed infants, which were compared with isolates from community-acquired infections and from a nosocomial NICU outbreak. The phylogenetic analysis of a 454-bp sequence of the rpoB gene was useful for species identification (K. pneumoniae, K. variicola, K. quasipneumoniae, K. oxytoca, K. grimontii, K. michiganensis, Raoultella planticola and R. ornithinolytica), previously misidentified as K. pneumoniae or K. oxytoca by biochemical methods. Globally, we report that commensal strains present virulence traits (virulence genes, siderophores and biofilms) comparable to community-acquired and NICU-infective isolates, thus suggesting that the human microbiota could constitute a reservoir for infection. Isolates causing NICU outbreak were multi-drug resistant (MDR) and ESBLs producers, although an imipenem-resistant commensal MDR K. quasipneumoniae isolate was also found. A commensal K. pneumoniae strain showed a potent bacteriocin-like inhibitory activity against MDR Klebsiella isolates, thus highlighting the potential role of commensal Klebsiella spp. in health and disease.
Rapid Full-Cycle Technique to Control Adulteration of Meat Products: Integration of Accelerated Sample Preparation, Recombinase Polymerase Amplification, and Test-Strip Detection
Authors: Ivanov Aleksandr V. , Popravko Demid S. , Safenkova Irina V. , Zvereva Elena A. , Dzantiev Boris B. , Zherdev Anatoly V.
Published: November 2021

Verifying the authenticity of food products is essential due to the recent increase in counterfeit meat-containing food products. The existing methods of detection have a number of disadvantages. Therefore, simple, cheap, and sensitive methods for detecting various types of meat are required. In this study, we propose a rapid full-cycle technique to control the chicken or pig adulteration of meat products, including 3 min of crude DNA extraction, 20 min of recombinase polymerase amplification (RPA) at 39 °C, and 10 min of lateral flow assay (LFA) detection. The cytochrome B gene was used in the developed RPA-based test for chicken and pig identification. The selected primers provided specific RPA without DNA nuclease and an additional oligonucleotide probe. As a result, RPA–LFA, based on designed fluorescein- and biotin-labeled primers, detected up to 0.2 pg total DNA per μL, which provided up to 0.001% w/w identification of the target meat component in the composite meat. The RPA–LFA of the chicken and pig meat identification was successfully applied to processed meat products and to meat after heating. The results were confirmed by real-time PCR. Ultimately, the developed analysis is specific and enables the detection of pork and chicken impurities with high accuracy in raw and processed meat mixtures. The proposed rapid full-cycle technique could be adopted for the authentication of other meat products.
Evaluation of Sample Preparation Strategies for Human Milk and Plasma Proteomics
Authors: Milkovska-Stamenova Sanja , Wölk Michele , Hoffmann Ralf
Published: November 2021

Sample preparation is the most critical step in proteomics as it directly affects the subset of proteins and peptides that can be reliably identified and quantified. Although a variety of efficient and reproducible sample preparation strategies have been developed, their applicability and efficacy depends much on the biological sample. Here, three approaches were evaluated for the human milk and plasma proteomes. Protein extracts were digested either in an ultrafiltration unit (filter-aided sample preparation, FASP) or in-solution (ISD). ISD samples were desalted by solid-phase extraction prior to nRPC-ESI-MS/MS. Additionally, milk and plasma samples were directly digested by FASP without prior protein precipitation. Each strategy provided inherent advantages and disadvantages for milk and plasma. FASP appeared to be the most time efficient procedure with a low miscleavage rate when used for a biological sample aliquot, but quantitation was less reproducible. A prior protein precipitation step improved the quantitation by FASP due to significantly higher peak areas for plasma and a much better reproducibility for milk. Moreover, the miscleavage rate for milk, the identification rate for plasma, and the carbamidomethylation efficiency were improved. In contrast, ISD of both milk and plasma resulted in higher miscleavage rates and is therefore less suitable for targeted proteomics.
Persistence Enhancement of a Promising Tick Repellent, Benzyl Isothiocyanate, by Yeast Microcarriers
Authors: Kim Hui-Ju , Jeong Ah-Hyeon , Lee Ji-Hoon , Park Jun-Hwan
Published: November 2021

Phenethyl isothiocyanate isolated from Armoracia rusticana root oil and its derivatives were tested at different doses in a bioassay designed to evaluate repellency against individual Haemaphysalis longicornis nymphs. Among the tested compounds, benzyl isothiocyanate exhibited repellency against H. longicornis nymphs at the lowest dose of 0.00625 mg/cm2, followed by phenethyl isothiocyanate (0.0125 mg/cm2) and phenyl isothiocyanate (0.025 mg/cm2). The behavioral responses of H. longicornis nymphs exposed to benzyl isothiocyanate and phenethyl isothiocyanate indicated that the mode of action of these compounds can be mainly attributed to the vapor phase. Encapsulated benzyl isothiocyanate showed repellency up to 120 min post-application at 0.1 mg/cm2, whereas pure benzyl isothiocyanate showed repellency up to 60 min post-application at 0.1 mg/cm2. The present study suggests that benzyl isothiocyanate is a potential repellent for protection against H. longicornis nymphs, and encapsulation in yeast cells may enhance the repellency effect.
Characterization of the Synergistic Effect between Ligands of Opioid and Free Fatty Acid Receptors in the Mouse Model of Colitis
Authors: Binienda Agata , Makaro Adam , Talar Marcin , Krajewska Julia B. , Tarasiuk Aleksandra , Bartoszek Adrian , Fabisiak Adam , Mosińska Paula , Niewinna Karolina , Dziedziczak Katarzyna , Świerczyński Mikołaj , Kordek Radzisław , Salaga Maciej , Fichna Jakub
Published: November 2021

Background: Recent studies suggest that lipids, including free fatty acids (FFAs), are necessary for proper μ opioid receptor (MOR) binding and that activation of opioid receptors (ORs) improves intestinal inflammation. The objective of the study was to investigate a possible interaction between the ORs and FFA receptors (FFARs) ligands in the colitis. Methods: The potential synergistic effect of ORs and FFARs ligands was evaluated using mouse model of acute colitis induced by dextran sulfate sodium (DSS, 4%). Compounds were injected intraperitoneally (i.p.) once or twice daily at the doses of 0.01 or 0.02 mg/kg body weight (BW) (DAMGO—an MOR agonist), 0.3 mg/kg BW (DPDPE—a δ OR (DOR) agonist) and 1 mg/kg BW (naloxone—a non-selective OR antagonist, GLPG 0974—a FFAR2 antagonist, GSK 137647—a FFAR4 agonist and AH 7614—a FFAR4 antagonist) for 4 days. Results: Myeloperoxidase (MPO) activity was significantly decreased after DAMGO (0.02 mg/kg BW) and GSK 137647 (1 mg/kg BW) administration and co-administration as compared to DSS group. Conclusions: Treatment with ligands of ORs and FFARs may affect the immune cells in the inflammation; however, no significant influence on the severity of colitis and no synergistic effect were observed.
A 110 Year Sediment Record of Polycyclic Aromatic Hydrocarbons Related to Economic Development and Energy Consumption in Dongping Lake, North China
Authors: Guo Wei , Yue Junhui , Zhao Qian , Li Jun , Yu Xiangyi , Mao Yan
Published: November 2021

A sedimentary record of the 16 polycyclic aromatic hydrocarbon (PAH) pollutants from Dongping Lake, north China, is presented in this study. The influence of regional energy structure changes for 2–6-ring PAHs was investigated, in order to assess their sources and the impact of socioeconomic developments on the observed changes in concentration over time. The concentration of the ΣPAH16 ranged from 77.6 to 628.0 ng/g. Prior to the 1970s, the relatively low concentration of ΣPAH16 and the average presence of 44.4% 2,3-ring PAHs indicated that pyrogenic combustion from grass, wood, and coal was the main source of PAHs. The rapid increase in the concentration of 2,3-ring PAHs between the 1970s and 2006 was attributed to the growth of the urban population and the coal consumption, following the implementation of the Reform and Open Policy in 1978. The source apportionment, which was assessed using a positive matrix factorization model, revealed that coal combustion was the most important regional source of PAHs pollution (>51.0%). The PAHs were mainly transported to the site from the surrounding regions by atmospheric deposition rather than direct discharge.
Compression Behavior and Vibrational Properties of New Energetic Material LLM-105 Analyzed Using the Dispersion-Corrected Density Functional Theory
Authors: Li Tianming , Fan Junyu , Wang Zhuoran , Qi Hanhan , Su Yan , Zhao Jijun
Published: November 2021

The 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) is a newly energetic material with an excellent performance and low sensitivity and has attracted considerable attention. On the basis of the dispersion-corrected density functional theory (DFT-D), the high-pressure responses of vibrational properties, in conjunction with structural properties, are used to understand its intermolecular interactions and anisotropic properties under hydrostatic and uniaxial compressions. At ambient and pressure conditions, the DFT-D scheme could reasonably describe the structural parameters of LLM-105. The hydrogen bond network, resembling a parallelogram shape, links two adjacent molecules and contributes to the structure stability under hydrostatic compression. The anisotropy of LLM-105 is pronounced, especially for Raman spectra under uniaxial compression. Specifically, the red-shifts of modes are obtained for [100] and [010] compressions, which are caused by the pressure-induced enhance of the strength of the hydrogen bonds. Importantly, coupling modes and discontinuous Raman shifts are observed along [010] and [001] compressions, which are related to the intramolecular vibrational redistribution and possible structural transformations under uniaxial compressions. Overall, the detailed knowledge of the high-pressure responses of LLM-105 is established from the atomistic level. Uniaxial compression responses provide useful insights for realistic shock conditions.
Synthesis and Physico-Chemical Properties of Homoleptic Copper(I) Complexes with Asymmetric Ligands as a DSSC Dye
Authors: Inomata Tomohiko , Hatano Mayuka , Kawai Yuya , Matsunaga Ayaka , Kitagawa Takuma , Wasada-Tsutsui Yuko , Ozawa Tomohiro , Masuda Hideki
Published: November 2021

To develop low-cost and efficient dye-sensitized solar cells (DSSCs), we designed and prepared three homoleptic Cu(I) complexes with asymmetric ligands, M1, M2, and Y3, which have the advantages of heteroleptic-type complexes and compensate for their synthetic challenges. The three copper(I) complexes were characterized by elemental analysis, UV-vis absorption spectroscopy, and electrochemical measurements. Their absorption spectra and orbital energies were evaluated and are discussed in the context of TD-DFT calculations. The complexes have high VOC values (0.48, 0.60, and 0.66 V for M1, M2, and Y3, respectively) which are similar to previously reported copper(I) dyes with symmetric ligands, although their energy conversion efficiencies are relatively low (0.17, 0.64, and 2.66%, respectively).
Predicting Finite-Bias Tunneling Current Properties from Zero-Bias Features: The Frontier Orbital Bias Dependence at an Exemplar Case of DNA Nucleotides in a Nanogap
Authors: Djurišić Ivana , Jovanović Vladimir P. , Dražić Miloš S. , Tomović Aleksandar Ž. , Zikic Radomir
Published: November 2021

The electrical current properties of single-molecule sensing devices based on electronic (tunneling) transport strongly depend on molecule frontier orbital energy, spatial distribution, and position with respect to the electrodes. Here, we present an analysis of the bias dependence of molecule frontier orbital properties at an exemplar case of DNA nucleotides in the gap between H-terminated (3, 3) carbon nanotube (CNT) electrodes and its relation to transversal current rectification. The electronic transport properties of this simple single-molecule device, whose characteristic is the absence of covalent bonding between electrodes and a molecule between them, were obtained using density functional theory and non-equilibrium Green’s functions. As in our previous studies, we could observe two distinct bias dependences of frontier orbital energies: the so-called strong and the weak pinning regimes. We established a procedure, from zero-bias and empty-gap characteristics, to estimate finite-bias electronic tunneling transport properties, i.e., whether the molecular junction would operate in the weak or strong pinning regime. We also discuss the use of the zero-bias approximation to calculate electric current properties at finite bias. The results from this work could have an impact on the design of new single-molecule applications that use tunneling current or rectification applicable in high-sensitivity sensors, protein, or DNA sequencing.
Force Dependence of Proteins’ Transition State Position and the Bell–Evans Model
Authors: Rico-Pasto Marc , Zaltron Annamaria , Ritort Felix
Published: November 2021

Single-molecule force spectroscopy has opened a new field of research in molecular biophysics and biochemistry. Pulling experiments on individual proteins permit us to monitor conformational transitions with high temporal resolution and measure their free energy landscape. The force–extension curves of single proteins often present large hysteresis, with unfolding forces that are higher than refolding ones. Therefore, the high energy of the transition state (TS) in these molecules precludes kinetic rates measurements in equilibrium hopping experiments. In irreversible pulling experiments, force-dependent kinetic rates measurements show a systematic discrepancy between the sum of the folding and unfolding TS distances derived by the kinetic Bell–Evans model and the full molecular extension predicted by elastic models. Here, we show that this discrepancy originates from the force-induced movement of TS. Specifically, we investigate the highly kinetically stable protein barnase, using pulling experiments and the Bell–Evans model to characterize the position of its kinetic barrier. Experimental results show that while the TS stays at a roughly constant distance relative to the native state, it shifts with force relative to the unfolded state. Interestingly, a conversion of the protein extension into amino acid units shows that the TS position follows the Leffler–Hammond postulate: the higher the force, the lower the number of unzipped amino acids relative to the native state. The results are compared with the quasi-reversible unfolding–folding of a short DNA hairpin.
Tailoring the Structural and Optical Properties of Germanium Telluride Phase-Change Materials by Indium Incorporation
Authors: Wang Xudong , Shen Xueyang , Sun Suyang , Zhang Wei
Published: November 2021

Chalcogenide phase-change materials (PCMs) based random access memory (PCRAM) enter the global memory market as storage-class memory (SCM), holding great promise for future neuro-inspired computing and non-volatile photonic applications. The thermal stability of the amorphous phase of PCMs is a demanding property requiring further improvement. In this work, we focus on indium, an alloying ingredient extensively exploited in PCMs. Starting from the prototype GeTe alloy, we incorporated indium to form three typical compositions along the InTe-GeTe tie line: InGe3Te4, InGeTe2 and In3GeTe4. The evolution of structural details, and the optical properties of the three In-Ge-Te alloys in amorphous and crystalline form, was thoroughly analyzed via ab initio calculations. This study proposes a chemical composition possessing both improved thermal stability and sizable optical contrast for PCM-based non-volatile photonic applications.
Modal Properties of Photonic Crystal Cavities and Applications to Lasers
Authors: Saldutti Marco , Xiong Meng , Dimopoulos Evangelos , Yu Yi , Gioannini Mariangela , Mørk Jesper
Published: November 2021

Photonic crystal cavities enable strong light–matter interactions, with numerous applications, such as ultra-small and energy-efficient semiconductor lasers, enhanced nonlinearities and single-photon sources. This paper reviews the properties of the modes of photonic crystal cavities, with a special focus on line-defect cavities. In particular, it is shown how the fundamental resonant mode in line-defect cavities gradually turns from Fabry–Perot-like to distributed-feedback-like with increasing cavity size. This peculiar behavior is directly traced back to the properties of the guided Bloch modes. Photonic crystal cavities based on Fano interference are also covered. This type of cavity is realized through coupling of a line-defect waveguide with an adjacent nanocavity, with applications to Fano lasers and optical switches. Finally, emerging cavities for extreme dielectric confinement are covered. These cavities promise extremely strong light–matter interactions by realizing deep sub-wavelength mode size while keeping a high quality factor.
Functionalized Protein Nanotubes Based on the Bacteriophage vB_KleM-RaK2 Tail Sheath Protein
Authors: Labutytė Greta , Povilonienė Simona , Šimoliūnas Eugenijus , Gabrielaitis Dovydas , Skapas Martynas , Noreika Algirdas , Meškys Rolandas , Časaitė Vida
Published: November 2021

We report on the construction of functionalized nanotubes based on tail sheath protein 041 from vB_KleM-RaK2 bacteriophage. The truncated 041 protein (041Δ200) was fused with fluorescent proteins GFP and mCherry or amidohydrolase YqfB. The generated chimeric proteins were successfully synthesized in E. coli BL21 (DE3) cells and self-assembled into tubular structures. We detected the fluorescence of the structures, which was confirmed by stimulated emission depletion microscopy. When 041Δ200GFP and 041Δ200mCherry were coexpressed in E. coli BL21 (DE3) cells, the formed nanotubes generated Förster resonance energy transfer, indicating that both fluorescent proteins assemble into a single nanotube. Chimeric 041Δ200YqfB nanotubes possessed an enzymatic activity, which was confirmed by hydrolysis of N4-acetyl-2′-deoxycytidine. The enzymatic properties of 041Δ200YqfB were similar to those of a free wild-type YqfB. Hence, we conclude that 041-based chimeric nanotubes have the potential for the development of delivery vehicles and targeted imaging and are applicable as scaffolds for biocatalysts.
Nanocellulose Xerogel as Template for Transparent, Thick, Flame-Retardant Polymer Nanocomposites
Authors: Sakuma Wataru , Fujisawa Shuji , Berglund Lars A. , Saito Tsuguyuki
Published: November 2021

Cellulose nanofibers (CNFs) have excellent properties, such as high strength, high specific surface areas (SSA), and low coefficients of thermal expansion (CTE), making them a promising candidate for bio-based reinforcing fillers of polymers. A challenge in the field of CNF-reinforced composite research is to produce strong and transparent CNF/polymer composites that are sufficiently thick for use as load-bearing structural materials. In this study, we successfully prepared millimeter-thick, transparent CNF/polymer composites using CNF xerogels, with high porosity (~70%) and high SSA (~350 m2 g−1), as a template for monomer impregnation. A methacrylate was used as the monomer and was cured by UV irradiation after impregnation into the CNF xerogels. The CNF xerogels effectively reinforced the methacrylate polymer matrix, resulting in an improvement in the flexural modulus (up to 546%) and a reduction in the CTE value (up to 78%) while maintaining the optical transparency of the matrix polymer. Interestingly, the composites exhibited flame retardancy at high CNF loading. These unique features highlight the applicability of CNF xerogels as a reinforcing template for producing multifunctional and load-bearing polymer composites.
Thermal and Rheological Properties of Hydrophobic Nanosilica in Sunflower Oil Suspensions at High Pressures
Authors: Martín-Alfonso María J. , Pozo Javier , Delgado-Sánchez Clara , Martínez-Boza Francisco José
Published: November 2021

Nowadays, the reduction of the environmental impact associated with the operation of the oil industry is a primary concern. A growing trend is to develop low-toxicity formulations based on biodegradable components. In this sense, vegetable oils structured with nanomaterials could be an alternative to mineral or synthetic oils for sustainable fluid formulations. Hydrophobic fumed silica nanoparticles have the capability to change the rheological behavior of oil in suspensions, providing a large variety of non-Newtonian behaviors over a wide range of temperatures, from shear-thinning to gel-like, depending on the concentration and the nanosilica’s hydrophobicity, that permits the design of fluids with selected characteristic and applications. This work explores the microstructure and the rheological behavior of hydrophobic fumed silica dispersed in a sunflower oil as a function of temperature and pressure. The results suggest that the suspensions of hydrophobic silica in sunflower oil reveals appropriate rheological and thermal properties over a wide range of temperatures and pressures to serve as components of sustainable drilling fluids.
Investigation of the Tribological Characteristics of Aluminum 6061-Reinforced Titanium Carbide Metal Matrix Composites
Authors: Veeresh Kumar G. B. , Pramod R. , Hari Kiran Reddy R. , Ramu P. , Kunaal Kumar B. , Madhukar Pagidi , Chavali Murthy , Mohammad Faruq , Khiste Sachin K.
Published: November 2021

The current trend in the materials engineering sector is to develop newer materials that can replace the existing materials in various engineering sectors in order to be more and more efficient. Therefore, the present research work is aimed at fabricating and determining the physical, mechanical, and dry sliding wear properties of titanium carbide (TiC)-reinforced aluminum alloy (Al6061) metal matrix composites (MMCs). For the study, the Al6061-TiC microparticle-reinforced composites were fabricated via the liquid metallurgy route through the stir casting method, where the reinforcement of the TiC particles into the Al6061 alloy matrix was added in the range of 0 to 8.0 wt.%, i.e., in the steps of 2.0 wt.%. The synthesis procedure followed the investigation of the various mechanical properties of Al6061-TiC MMCs, such as the density and structure, as well as mechanical and dry wear experimentation. The tests performed on the casted Al6061, as well as its TiC composites, were in harmony with ASTM standards. As per the experimental outcome, it can be confirmed that the increase in the weight percentage of TiC into the Al6061 alloy substantially increases the density, hardness, and tensile strength, at the expense of the percentage of elongation. In addition, the dry wear experiments, performed on a pin-on-disc tribometer, showed that the Al6061-TiC MMCs have superior wear-resistance properties, as compared to those of pure Al6061 alloy. Furthermore, optical micrograph (OM), powdered X-ray diffraction (XRD), energy dispersive spectroscopy (EDS), and scanning electron microscopy (SEM) analyses were employed for the developed Al6061-TiC MMCs before and after the fracture and wear test studies. From the overall analysis of the results, it can be observed that the Al6061-TiC composite material with higher TiC reinforcement displays superior mechanical characteristics.
Between the Devil and the Deep Blue Sea: Non-Coding RNAs Associated with Transmissible Cancers in Tasmanian Devil, Domestic Dog and Bivalves
Authors: Lister Nicholas C. , Milton Ashley M. , Hanrahan Benjamin J. , Waters Paul D.
Published: November 2021

Currently there are nine known examples of transmissible cancers in nature. They have been observed in domestic dog, Tasmanian devil, and six bivalve species. These tumours can overcome host immune defences and spread to other members of the same species. Non-coding RNAs (ncRNAs) are known to play roles in tumorigenesis and immune system evasion. Despite their potential importance in transmissible cancers, there have been no studies on ncRNA function in this context to date. Here, we present possible applications of the CRISPR/Cas system to study the RNA biology of transmissible cancers. Specifically, we explore how ncRNAs may play a role in the immortality and immune evasion ability of these tumours.
Management of Phantom Limb Pain through Thalamotomy of the Centro-Median Nucleus
Authors: Pérez de la Torre Ramiro A. , Rodríguez Hernández Job J. , Al-Ramadan Ali , Gharaibeh Abeer
Published: November 2021

Background: Phantom limb syndrome is defined as the perception of intense pain or other sensations that are secondary to a neural lesion in a limb that does not exist. It can be treated using pharmacological and surgical interventions. Most medications are prescribed to improve patients’ lives; however, the response rate is low. In this case report, we present a case of phantom limb syndrome in a 42-year-old female with a history of transradial amputation of the left thoracic limb due to an accidental compression one year before. The patient underwent placement of a deep brain stimulator at the ventral posteromedial nucleus (VPM) on the right side and removal secondary to loss of battery. The patient continued to have a burning pain throughout the limb with a sensation of still having the limb, which was subsequently diagnosed as phantom limb syndrome. After a thorough discussion with the patient, a right stereotactic centro-median thalamotomy was offered. An immediate response was reported with a reduction in pain severity on the visual analogue scale (VAS) from a value of 9–10 preoperative to a value of 2 postoperative, with no postoperative complications. Although phantom limb pain is one of the most difficult to treat conditions, centro-median thalamotomy may provide an effective stereotactic treatment procedure with adequate outcomes.
Impact of Exercise on Gut Microbiota in Obesity
Authors: Aragón-Vela Jerónimo , Solis-Urra Patricio , Ruiz-Ojeda Francisco Javier , Álvarez-Mercado Ana Isabel , Olivares-Arancibia Jorge , Plaza-Diaz Julio
Published: November 2021

Physical activity, exercise, or physical fitness are being studied as helpful nonpharmacological therapies to reduce signaling pathways related to inflammation. Studies describing changes in intestinal microbiota have stated that physical activity could increase the microbial variance and enhance the ratio of Firmicutes/Bacteroidetes, and both actions could neutralize the obesity progression and diminish body weight. The aim of this review is to provide an overview of the literature describing the relationship between physical activity profiles and gut microbiota and in obesity and some associated comorbidities. Promoting physical activity could support as a treatment to maintain the gut microbiota composition or to restore the balance toward an improvement of dysbiosis in obesity; however, these mechanisms need to be studied in more detail. The opportunity to control the microbiota by physical activity to improve health results and decrease obesity and related comorbidities is very attractive. Nevertheless, several incompletely answered questions need to be addressed before this strategy can be implemented.
Mineral Micronutrients in Asthma
Authors: Zajac Dominika
Published: November 2021

Asthma represents one of the most common medical issues in the modern world. It is a chronic inflammatory disease characterized by persistent inflammation of the airways and disturbances in redox status, leading to hyperresponsiveness of bronchi and airway obstruction. Apart from classical risk factors such as air pollution, family history, allergies, or obesity, disturbances of the levels of micronutrients lead to impairments in the defense mechanisms of the affected organism against oxidative stress and proinflammatory stimuli. In the present review, the impact of micronutrients on the prevalence, severity, and possible risk factors of asthma is discussed. Although the influence of classical micronutrients such as selenium, copper, or zinc are well known, the effects of those such as iodine or manganese are only rarely mentioned. As a consequence, the aim of this paper is to demonstrate how disturbances in the levels of micronutrients and their supplementation might affect the course of asthma.
Food Composition and Dedicated Databases: Key Tools for Human Health and Public Nutrition
Authors: Durazzo Alessandra , Lucarini Massimo
Published: November 2021

To better understand nutrition, food chemistry, and medicine, it is important to investigate biologically active constituents, which requires a detailed knowledge and coverage of the composition of compounds of nutritional and nutraceutical character [...]
Higher Serum Phosphorus Is Not an Independent Risk Factor of Mortality in Heart Failure with Reduced Ejection Fraction
Authors: Robert Partyka , Alina Mroczek , Sylwia Duda , Jolanta Malinowska-Borowska , Marta Buczkowska , Anna Głogowska-Gruszka , Jacek Niedziela , Bartosz Hudzik , Mariusz Gąsior , Piotr Rozentryt
Published: November 2021

Higher serum phosphorus has detrimental health effects. Even high-normal rage sP is associated with worse outcomes. The relationship of serum phosphorus with prognostic markers in heart failure remains unclear. We investigated the association of serum phosphorus with heart failure prognostic factors and risk of mortality related to serum phosphorus. In 1029 stable heart failure patients, we investigated the distribution of markers of more advanced heart failure stage across quintiles of serum phosphorus and estimated the relative risk of mortality in comparison to reference. Higher serum phosphorus levels sP were associated with markers of a worse outcome. The best survival was observed in low-normal serum levels. The unadjusted hazard ratio for mortality increased toward higher phosphorus quintiles but not to lower levels of sP. The correction for age, sex, BMI, percent weight loss, inflammation, kidney function, and LVEF did not modify the risk profile substantially. The adjustment for NYHA, natriuretic peptides, serum sodium, and treatment characteristics broke down the risk relationship completely. A higher serum phosphorus is associated with markers of a more risky profile of heart failure. Elevated serum levels of phosphorus sP does not provide independent prognostic information beyond the strongest markers of the severity of the syndrome. The potential involvement of higher serum phosphorus as a mediator in the pathophysiology of heart failure warrants further study.
Reply to Cantarelli et al. Chronic Recurrent Multifocal Osteomyelitis Associated with Crohn Disease: A Potential Role of Exclusion Diet? Comment on “Starz et al. The Modification of the Gut Microbiota via Selected Specific Diets in Patients with Crohn’s Disease. Nutrients 2021, 13, 2125”
Authors: Starz Eliza , Wzorek Karolina , Folwarski Marcin , Kaźmierczak-Siedlecka Karolina , Stachowska Laura , Przewłócka Katarzyna , Stachowska Ewa , Skonieczna-Żydecka Karolina
Published: November 2021

We congratulate Erika Cantarelli and colleagues for the presented case report in the comment entitled “Chronic Recurrent Multifocal Osteomyelitis associated to Crohn Disease (CD): a potential role of exclusion diet [...]
Iron Deficiency Anemia in Inflammatory Bowel Diseases—A Narrative Review
Authors: Mahadea Dagmara , Adamczewska Ewelina , Ratajczak Alicja Ewa , Rychter Anna Maria , Zawada Agnieszka , Eder Piotr , Dobrowolska Agnieszka , Krela-Kaźmierczak Iwona
Published: November 2021

Inflammatory bowel disease (IBD), which includes Crohn’s disease and ulcerative colitis, is characterized by chronic inflammation of the gastrointestinal tract. IBD has been associated with numerous symptoms and complications, with the most common being iron deficiency anemia (IDA). Iron deficiency in IBD is caused by inadequate intake, malabsorption (including duodenal involvement and surgical removal), and chronic blood loss by mucosal ulcerations. Therefore, an appropriate diet should be enforced. Iron deficiency and iron supplementation have been associated with alterations to gut microbiota. IBD-associated anemia, in particular iron deficiency anemia, is associated with a significant decrease in quality of life and with clinical symptoms such as chronic fatigue, headaches and dizziness, reduced exercise tolerance, pale skin, nails, conjunctiva, and fainting. However, despite these numerous adverse symptoms, IDA remains undertreated. The European Crohn’s and Colitis Organisation (ECCO) guidelines state that patients should be monitored for anemia. Adequate treatment, whether oral or intravenous, should be implemented while taking into consideration C-reactive protein values (CRP), hemoglobin levels, and therapeutic response. It should be stressed that every case of anemia in IBD patients should be treated. Intravenous iron formulations, which are more superior compared to the oral form, should be used. There is a need to increase awareness and implementation of international guidelines on iron supplementation in patients with IBD.
Beneficial Effects of Slow-Release Large Neutral Amino Acids after a Phenylalanine Oral Load in Patients with Phenylketonuria
Authors: Scala Iris , Concolino Daniela , Nastasi Anna , Esposito Giulia , Crisci Daniela , Sestito Simona , Ferraro Stefania , Albano Lucia , Ruoppolo Margherita , Parenti Giancarlo , Strisciuglio Pietro
Published: November 2021

The mainstay of phenylketonuria treatment is a low protein diet, supplemented with phenylalanine (Phe)-free protein substitutes and micronutrients. Adhering to this diet is challenging, and even patients with good metabolic control who follow the dietary prescriptions in everyday life ignore the recommendations occasionally. The present study explores the ability of slow-release large neutral amino acids (srLNAAs) to prevent Phe increase following a Phe dietary load. Fourteen phenylketonuric patients aged ≥13 years were enrolled in a 6-week protocol. Oral acute Phe loads of 250 and 500 mg were added to the evening meal together with srLNAAs (0.5 gr/kg). Phe and tyrosine were dosed before dinner, 2h-after dinner, and after the overnight fast. After oral Phe loads, mean plasma Phe remained stable and below 600 µmol/L. No Phe peaks were registered. Tyrosine levels significantly increased, and Phe/Tyrosine ratio decreased. No adverse events were registered. In conclusion, a single oral administration of srLNAAs at the dose of 0.5 gr/kg is effective in maintaining stable plasma Phe during acute oral loads with Phe-containing food and may be added to the dietetic scheme in situations in which patients with generally good adherence to diet foresee a higher than prescribed Phe intake due to their commitments.
The Role of Vitamin Deficiency in Liver Disease: To Supplement or Not Supplement?
Authors: Licata Anna , Zerbo Maddalena , Como Silvia , Cammilleri Marcella , Soresi Maurizio , Montalto Giuseppe , Giannitrapani Lydia
Published: November 2021

Over the past few years, growing interest has been shown for the impact of dietary requirements and nutritional factors on chronic diseases. As a result, nutritional programs have been reinforced by public health policies. The precise role of micronutrients in chronic liver disease is currently receiving particular attention since abnormalities in vitamin levels are often detected. At present, treatment programs are focused on correcting vitamin deficiencies, which are frequently correlated to higher rates of comorbidities with poor outcomes. The literature reviewed here indicates that liver diseases are often related to vitamin disorders, due to both liver impairment and abnormal intake. More specific knowledge about the role of vitamins in liver disease is currently emerging from various results and recent evidence. The most significant benefits in this area may be observed when improved vitamin intake is combined with a pharmacological treatment that may also affect the progression of the liver disease, especially in the case of liver tumors. However, further studies are needed.
Six Oligosaccharides’ Variation in Breast Milk: A Study in South China from 0 to 400 Days Postpartum
Authors: Liu Shuang , Cai Xiaokun , Wang Jin , Mao Yingyi , Zou Yan , Tian Fang , Peng Bo , Hu Jiaqiang , Zhao Yanrong , Wang Shuo
Published: November 2021

This study investigated the variation in oligosaccharide levels in the breast milk of south Chinese mothers in a prolonged breastfeeding period of up to 400 days postpartum. A total of 488 breast milk samples were collected from 335 healthy mothers at five different time points: 0–5 days, 10–15 days, 40–45 days, 200–240 days, and 300–400 days postpartum. A high-performance anion-exchange chromatography-pulsed amperometric detector (HPAEC-PAD) was used to quantify 2′-fucosyllactose (2′-FL), 3-fucosyllactose (3-FL), lacto-N-tetraose (LNT), lacto-N-neotetraose (LNnT), 3′-sialyllactose (3′-SL) and 6′-sialyllactose (6′-SL). In this study, we found six oligosaccharides that were present in breast milk from 0 to 400 days postpartum. The median value ranges of individual oligosaccharide components in this study were 1013–2891 mg/L 2′-FL, 193–1421 mg/L 3-FL, 314–1478 mg/L LNT, 44–255 mg/L LNnT, 111–241 mg/L 3′-SL, and 23–602 mg/L6′-SL. HMO levels decreased over the lactation periods, except for 3-FL, which increased throughout lactation. The predominant fucosylated and sialylated HMOs were 2′-FL and 6′-SL at 40–45 days postpartum and changed to 3-FL and 3′-SL at 200–240 days postpartum. Results from this study showed that lactating women continue to provide their offspring with a high level of 2′-FL one year after delivery, suggesting that 2′-FL may play an important role for infants in early life. Our findings also provide further evidence in support of breastfeeding after one-year postpartum.