bluuebunny/crossref_metadata_2025 huggingface dataset:
Toxic Metabolites and Inborn Errors of Amino Acid Metabolism: What One Informs about the Other
Authors: Lee Namgyu , Kim Dohoon
Published: June 2022

In inborn errors of metabolism, such as amino acid breakdown disorders, loss of function mutations in metabolic enzymes within the catabolism pathway lead to an accumulation of the catabolic intermediate that is the substrate of the mutated enzyme. In patients of such disorders, dietarily restricting the amino acid(s) to prevent the formation of these catabolic intermediates has a therapeutic or even entirely preventative effect. This demonstrates that the pathology is due to a toxic accumulation of enzyme substrates rather than the loss of downstream products. Here, we provide an overview of amino acid metabolic disorders from the perspective of the ‘toxic metabolites’ themselves, including their mechanism of toxicity and whether they are involved in the pathology of other disease contexts as well. In the research literature, there is often evidence that such metabolites play a contributing role in multiple other nonhereditary (and more common) disease conditions, and these studies can provide important mechanistic insights into understanding the metabolite-induced pathology of the inborn disorder. Furthermore, therapeutic strategies developed for the inborn disorder may be applicable to these nonhereditary disease conditions, as they involve the same toxic metabolite. We provide an in-depth illustration of this cross-informing concept in two metabolic disorders, methylmalonic acidemia and hyperammonemia, where the pathological metabolites methylmalonic acid and ammonia are implicated in other disease contexts, such as aging, neurodegeneration, and cancer, and thus there are opportunities to apply mechanistic or therapeutic insights from one disease context towards the other. Additionally, we expand our scope to other metabolic disorders, such as homocystinuria and nonketotic hyperglycinemia, to propose how these concepts can be applied broadly across different inborn errors of metabolism and various nonhereditary disease conditions.
Sanitary Conditions on the Farm Alters Fecal Metabolite Profile in Growing Pigs
Authors: Kar Soumya , te Pas Marinus , Kruijt Leo , Vervoort Jacques , Jansman Alfons , Schokker Dirkjan
Published: June 2022

The aim of this study was to use fecal metabolite profiling to evaluate the effects of contrasting sanitary conditions and the associated subclinical health status of pigs. We analyzed fecal metabolite profiles by nuclear magnetic resonance (1H NMR) from pigs aged 14 and 22 weeks. Pigs kept under low and high sanitary conditions differed in fecal metabolites related to the degradation of dietary starch, metabolism of the gut microbiome, and degradation of components of animal (host) origin. The metabolites that differed significantly (FDR < 0.1) were from metabolic processes involved in either maintaining nutrient digestive capacity, including purine metabolism, energy metabolism, bile acid breakdown and recycling, or immune system metabolism. The results show that the fecal metabolite profiles reflect the sanitary conditions under which the pigs are kept. The fecal metabolite profiles closely resembled the profiles of metabolites found in the colon of pigs. Fecal valerate and kynurenic acid could potentially be used as “non-invasive” biomarkers of immune or inflammatory status that could form the basis for monitoring subclinical health status in pigs.
Impact of Imperfect Artefacts and the Modus Operandi on Uncertainty Quantification Using Virtual Instruments
Authors: Kok Gertjan , Wübbeler Gerd , Elster Clemens
Published: June 2022

The usage of virtual instruments (VIs) to analyze measurements and calculate uncertainties is increasing. Well-known examples are virtual coordinate measurement machines (VCMMs) which are often used and even commercially offered to assess measurement uncertainties of CMMs. A more recent usage of the VI concept is posed by the modeling of scatterometers. These VIs can be used to assess the measurement uncertainty after the measurement has been performed based on the real measurement data or prior to the measurement to predict the measurement uncertainty using a type of simulated measurement data. The research question addressed in this paper is to assess if this predicted uncertainty will be similar in magnitude to the calculated uncertainty based on the measurement data. It turns out that this is not necessarily the case. The main observation of this paper was that the uncertainty predicted by a VI can be highly sensitive to the chosen way of operating the VI. To amend this situation, a simple procedure was proposed that can be used prior to performing the real measurement and that is believed to produce a conservative prediction of the measurement uncertainty in most cases. This was verified in a case study involving the measurement of the asphericity of an imperfect sphere using a CMM, with the uncertainty calculated by means of a VCMM.
Comparative Analysis of Microbiome Metagenomics in Reintroduced Wild Horses and Resident Asiatic Wild Asses in the Gobi Desert Steppe
Authors: Tang Liping , Gao Yunyun , Yan Liping , Jia Huiping , Chu Hongjun , Ma Xinping , He Lun , Wang Xiaoting , Li Kai , Hu Defu , Zhang Dong
Published: June 2022

The gut microbiome offers important ecological benefits to the host; however, our understanding of the functional microbiome in relation to wildlife adaptation, especially for translocated endangered species, is lagging. In this study, we adopted a comparative metagenomics approach to test whether the microbiome diverges for translocated and resident species with different adaptive potentials. The composition and function of the microbiome of sympatric Przewalski’s horses and Asiatic wild asses in desert steppe were compared for the first time using the metagenomic shotgun sequencing approach. We identified a significant difference in microbiome composition regarding the microbes present and their relative abundances, while the diversity of microbe species was similar. Furthermore, the functional profile seemed to converge between the two hosts, with genes related to core metabolism function tending to be more abundant in wild asses. Our results indicate that sympatric wild equids differ in their microbial composition while harboring a stable microbial functional core, which may enable them to survive in challenging habitats. A higher abundance of beneficial taxa, such as Akkermansia, and genes related to metabolism pathways and enzymes, such as lignin degradation, may contribute to more diverse diet choices and larger home ranges of wild asses.
B Vitamins and Their Roles in Gut Health
Authors: Hossain Khandkar Shaharina , Amarasena Sathya , Mayengbam Shyamchand
Published: June 2022

B vitamins act as coenzymes in a myriad of cellular reactions. These include energy production, methyl donor generation, neurotransmitter synthesis, and immune functions. Due to the ubiquitous roles of these vitamins, their deficiencies significantly affect the host’s metabolism. Recently, novel roles of B vitamins in the homeostasis of gut microbial ecology and intestinal health continue to be unravelled. This review focuses on the functional roles and biosynthesis of B vitamins and how these vitamins influence the growth and proliferation of the gut microbiota. We have identified the gut bacteria that can produce vitamins, and their biosynthetic mechanisms are presented. The effects of B vitamin deficiencies on intestinal morphology, inflammation, and its effects on intestinal disorders are also discussed.
Assessing the Synergistic Activity of Clarithromycin and Therapeutic Oils Encapsulated in Sodium Alginate Based Floating Microbeads
Authors: Khan Ikram Ullah , Shoukat Mehwish , Asif Muhammad , Khalid Syed Haroon , Asghar Sajid , Munir Muhammad Usman , Irfan Muhammad , Rasul Akhtar , Qari Sameer H. , Qumsani Alaa T. , Hassan Mohamed M. , Alahdal Maryam A. , Usman Muhammad , Khan Zulqurnain
Published: June 2022

We developed alginate-based floating microbeads of clarithromycin with therapeutic oils for the possible eradication of Helicobacter pylori (H. pylori) infections by enhancing the residence time of the carrier at the site of infection. In pursuit of this endeavor, the alginate was blended with hydroxy propyl methyl cellulose (HPMC) as an interpenetrating polymer to develop beads by ionotropic gelation using calcium carbonate as a gas generating agent. The developed microbeads remained buoyant under gastric conditions for 24 h. These microbeads initially swelled and afterwards decreased in size, possibly due to the erosion of the polymer. Furthermore, swelling was also affected by the type of encapsulated oil, i.e., swelling decreased with increasing concentrations of eucalyptus oil and increased with increasing concentrations of oleic acid. Antibacterial assays of the formulations showed significant antibacterial activity against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli); these assays also showed synergistic activity between clarithromycin and therapeutic oils as evident from the higher zone of inhibition of the microbeads as compared to the pure drug and oils. Scanning electron microscopy (SEM) images revealed a smoother surface for oleic acid containing the formulation as compared to eucalyptus oil containing the formulation. Differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) revealed the development of a stable formulation, while Fourier transform infrared spectrophotometry (FTIR) studies did not reveal any interaction between the polymers and the active ingredients. Optimized formulations (CLM3 and CLM6) were designed to release the drug in a controlled manner in gastric media by Fickian diffusion. Conclusively, the developed microbeads are a promising carrier to overcome the narrow therapeutic index and low bioavailability of clarithromycin, while the presence of therapeutic oils will produce synergistic effects with the drug to eradicate infection effectively.
Complete Genome Analysis of Rhodococcus opacus S8 Capable of Degrading Alkanes and Producing Biosurfactant Reveals Its Genetic Adaptation for Crude Oil Decomposition
Authors: Delegan Yanina , Petrikov Kirill , Frantsuzova Ekaterina , Rudenko Natalia , Solomentsev Viktor , Suzina Nataliya , Travkin Vasili , Solyanikova Inna P.
Published: June 2022

Microorganisms capable of decomposing hydrophobic substrates in cold climates are of considerable interest both in terms of studying adaptive reactions to low temperatures and in terms of their application in biotechnologies for cleaning up oil spills in a crude-oil polluted soil. The aim of this work was to investigate the genome of Rhodococcus opacus S8 and explore behavior traits of this strain grown in the presence of hexadecane. The genome size of strain S8 is 8.78 Mb, of which the chromosome size is 7.75 Mb. The S8 strain contains 2 circular plasmids of 135 kb and 105 kb and a linear plasmid with a size of 788 kb. The analysis of the genome revealed the presence of genes responsible for the degradation of alkanes and synthesis of biosurfactants. The peculiarities of morphology of microbial cells when interacting with a hydrophobic substrate were revealed. An adaptive mechanism responsible in the absence of oxygen for maintaining the process of degradation of hexadecane is discussed. The data obtained show that the strain S8 has great potential to be used in biotechnologies.
Estimation of Carbon Metabolism in Saccharomyces cerevisiae Acclimatized to Glycerol Assimilation with Quantitative PCR
Authors: Nakanishi Akihito , Zhang Kuan , Matsumoto Riri , Yamamoto Naotaka
Published: June 2022

Saccharomyces cerevisiae has the potential to produce value-added chemicals; however, this strain is restricted by using glycerol as a carbon source. Although acclimatization of S. cerevisiae as a glycerol-assimilating strain was confirmed so far, the reason why S. cerevisiae can be acclimatized was not clear in detail with limited information on the metabolic changes. In this report, glycerol-assimilating strains from S. cerevisiae BY4741 were isolated, and the biomass production, ethanol fermentation, and transcription levels related to glycolysis and the tricarboxylic acid cycle under aerobic and slightly anaerobic conditions were analyzed. As the results show, although µmax was equal to 0.15 h−1 between wildtype and glycerol-assimilating strains in an aerobic culture including glucose, the differences in max biomass production and percentage yields of ethanol and transcription levels between the two strains were shown. In slightly anaerobic culture, the differences in transcription levels downstream of glycolysis were also displayed. In the case of the glycerol-assimilating strain with glycerol under aerobic conditions, although the transcription levels related to ethanol production were sufficient, the ethanol production was not detected. Additionally, the biomass production reached a plateau even in the culture containing sufficient glycerol, indicating that the redox imbalance even in the cells of the glycerol-acclimatized strain could disturb the utilization of glycerol. The obtained knowledge will promote the use of glycerol resources with the glycerol-acclimatized S. cerevisiae in view of carbon recycling.
Recombinant PilS: Cloning, Expression and Biochemical Characterization of a Pil-Fimbriae Subunit
Authors: Munhoz Danielle D. , Silva Jessika C. A. , Freitas Natalia C. , Iwai Leo K. , Aires Karina A. , Ozaki Christiane Y. , Souza Cristiane S. , Rocha Letícia B. , Silva Miriam A. , Henrique Izabella M. , Elias Waldir P. , Carvalho Eneas , Morganti Ligia , Chura-Chambi Rosa M. , Piazza Roxane M. F.
Published: June 2022

Pil-fimbriae is a type IV pili member, which is a remarkably versatile component with a wide variety of functions, including motility, attachment to different surfaces, electrical conductance, DNA acquisition, and secretion of a broad range of structurally distinct protein substrates. Despite the previous functional characterization of Pil, more studies are required to understand the regulation of Pil expression and production, since the exact mechanisms involved in these steps are still unknown. Therefore it is extremely important to have a protein with the correct secondary and tertiary structure that will enable an accurate characterization and a specific antisera generation. For this reason, the aim of this work was to generate potential tools for further investigations to comprehend the mechanisms involved in Pil regulation and its role in pathogenic E. coli infections with the obtaining of a precise native-like recombinant PilS and the corresponding antisera. The pilS gene was successfully cloned into an expression vector, and recombinant PilS (rPilS) was efficiently solubilized and purified by metal affinity chromatography. Protein characterization analyses indicated that rPilS presented native-like secondary and tertiary structures after the refolding process. The generated anti-rPilS sera efficiently recognized recombinant and native proteins from atypical enteropathogenic E. coli strains.
Use of Flavin-Related Cellular Autofluorescence to Monitor Processes in Microbial Biotechnology
Authors: Müllerová Lucie , Marková Kateřina , Obruča Stanislav , Mravec Filip
Published: June 2022

Cellular autofluorescence is usually considered to be a negative phenomenon because it can affect the sensitivity of fluorescence microscopic or flow cytometric assays by interfering with the signal of various fluorescent probes. Nevertheless, in our work, we adopted a different approach, and green autofluorescence induced by flavins was used as a tool to monitor fermentation employing the bacterium Cupriavidus necator. The autofluorescence was used to distinguish microbial cells from abiotic particles in flow cytometry assays, and it was also used for the determination of viability or metabolic characteristics of the microbial cells. The analyses using two complementary techniques, namely fluorescence microscopy and flow cytometry, are simple and do not require labor sample preparation. Flavins and their autofluorescence can also be used in a combination with other fluorophores when the need for multi-parametrical analyses arises, but it is wise to use dyes that do not emit a green light in order to not interfere with flavins’ emission band (500–550 nm).
Fungal Enzymes Involved in Plastics Biodegradation
Authors: Temporiti Marta Elisabetta Eleonora , Nicola Lidia , Nielsen Erik , Tosi Solveig
Published: June 2022

Plastic pollution is a growing environmental problem, in part due to the extremely stable and durable nature of this polymer. As recycling does not provide a complete solution, research has been focusing on alternative ways of degrading plastic. Fungi provide a wide array of enzymes specialized in the degradation of recalcitrant substances and are very promising candidates in the field of plastic degradation. This review examines the present literature for different fungal enzymes involved in plastic degradation, describing their characteristics, efficacy and biotechnological applications. Fungal laccases and peroxidases, generally used by fungi to degrade lignin, show good results in degrading polyethylene (PE) and polyvinyl chloride (PVC), while esterases such as cutinases and lipases were successfully used to degrade polyethylene terephthalate (PET) and polyurethane (PUR). Good results were also obtained on PUR by fungal proteases and ureases. All these enzymes were isolated from many different fungi, from both Basidiomycetes and Ascomycetes, and have shown remarkable efficiency in plastic biodegradation under laboratory conditions. Therefore, future research should focus on the interactions between the genes, proteins, metabolites and environmental conditions involved in the processes. Further steps such as the improvement in catalytic efficiency and genetic engineering could lead these enzymes to become biotechnological applications in the field of plastic degradation.
Alloiococcus otitidis—Cause of Nonspecific Acute Sinusitis: First Case Report and Review of Literature
Authors: Grubić Kezele Tanja , Abram Maja , Bubonja-Šonje Marina
Published: June 2022

Although most sinus infections are viral, potential bacterial pathogens such as Streptococcus pneumoniae, Haemophilus influenza and Moraxella catarrhalis can migrate during a viral respiratory infection from the nasopharynx into the sinus cavity causing sinusitis. Alloiococcus otitidis is a commensal of the external auditory canal and is considered one of the potential middle ear pathogens. Unlike most otopathogens, A. otitidis is rarely found in the nasopharynx of healthy individuals. This difficult-to-culture organism has not previously been described as a causative agent of sinusitis. Here we describe one case of acute sinusitis due to A. otitidis and review previous knowledge of this controversial organism based on recent literature.
Characterization of Lactic Acid Bacteria Isolated from Banana and Its Application in Silage Fermentation of Defective Banana
Authors: Yang Jinsong , Tang Kai , Tan Haisheng , Cai Yimin
Published: June 2022

To effectively utilize banana by-products, we prepared silage with defective bananas using screened lactic acid bacteria (LAB), sucrose, and tannase as additives. Eleven strains of LAB were isolated from the fruits and flowers of defective bananas, all of which were Gram-positive and catalase-negative bacteria that produced lactic acid from glucose. Among these LAB, homofermentative strain CG1 was selected as the most suitable silage additive due to its high lactic acid production and good growth in a low pH environment. Based on its physiological and biochemical properties and 16S rRNA gene sequence analysis, strain CG1 was identified as Lactiplantibacillus plantarum. Defective bananas contain 74.8–76.3% moisture, 7.2–8.2% crude protein, 5.9–6.5% ether extract, and 25.3–27.8% neutral detergent fibre on a dry matter basis. After 45 d of fermentation, the silage of deficient bananas treated with LAB or sucrose alone improved fermentation quality, with significantly (p < 0.05) lower pH and higher lactic acid contents than the control. The combination of LAB and sucrose had a synergistic effect on the fermentation quality of silage. The tannase-treated silage significantly (p < 0.05) decreased the tannin content, while the combination of tannase and LAB in silage not only decreased (p < 0.05) the tannin content, but also improved the fermentation quality. The study confirmed that defective bananas are rich in nutrients, can prepare good quality silage, and have good potential as a feed source for livestock.
Natural Protein Kinase Inhibitors, Staurosporine, and Chelerythrine Suppress Wheat Blast Disease Caused by Magnaporthe oryzae Triticum
Authors: Chakraborty Moutoshi , Rabby S. M. Fajle , Gupta Dipali Rani , Rahman Mahfuzur , Paul Sanjoy Kumar , Mahmud Nur Uddin , Rahat Abdullah Al Mahbub , Jankuloski Ljupcho , Islam Tofazzal
Published: June 2022

Protein kinases (PKs), being key regulatory enzymes of a wide range of signaling pathways, are potential targets for antifungal agents. Wheat blast disease, caused by Magnaporthe oryzae Triticum (MoT), is an existential threat to world food security. During the screening process of natural metabolites against MoT fungus, we find that two protein kinase inhibitors, staurosporine and chelerythrine chloride, remarkably inhibit MoT hyphal growth. This study further investigates the effects of staurosporine and chelerythrine chloride on MoT hyphal growth, conidia production, and development as well as wheat blast inhibition in comparison to a commercial fungicide, Nativo®75WG. The growth of MoT mycelia is significantly inhibited by these compounds in a dose-dependent manner. These natural compounds greatly reduce conidia production in MoT mycelia along with suppression of conidial germination and triggered lysis, resulting in deformed germ tubes and appressoria. These metabolites greatly suppress blast development in artificially inoculated wheat plants in the field. This is the first report of the antagonistic effect of these two natural PKC inhibitory alkaloids on MoT fungal developmental processes in vitro and suppression of wheat blast disease on both leaves and spikes in vivo. Further research is needed to identify their precise mechanism of action to consider them as biopesticides or lead compounds for controlling wheat blast.
Phylogenomic Analysis of Salmonella enterica subsp. enterica Serovar Bovismorbificans from Clinical and Food Samples Using Whole Genome Wide Core Genes and kmer Binning Methods to Identify Two Distinct Polyphyletic Genome Pathotypes
Authors: Gopinath Gopal R. , Jang Hyein , Beaubrun Junia Jean-Gilles , Gangiredla Jayanthi , Mammel Mark K. , Müller Andrea , Tamber Sandeep , Patel Isha R. , Ewing Laura , Weinstein Leah M. , Wang Caroline Z. , Finkelstein Samantha , Negrete Flavia , Muruvanda Tim , Allard Marc , Sockett Donald C. , Pagotto Franco , Tall Ben D. , Stephan Roger
Published: June 2022

Salmonella enterica subsp. enterica serovar Bovismorbificans has caused multiple outbreaks involving the consumption of produce, hummus, and processed meat products worldwide. To elucidate the intra-serovar genomic structure of S. Bovismorbificans, a core-genome analysis with 2690 loci (based on 150 complete genomes representing Salmonella enterica serovars developed as part of this study) and a k-mer-binning based strategy were carried out on 95 whole genome sequencing (WGS) assemblies from Swiss, Canadian, and USA collections of S. Bovismorbificans strains from foodborne infections. Data mining of a digital DNA tiling array of legacy SARA and SARB strains was conducted to identify near-neighbors of S. Bovismorbificans. The core genome analysis and the k-mer-binning methods identified two polyphyletic clusters, each with emerging evolutionary properties. Four STs (2640, 142, 1499, and 377), which constituted the majority of the publicly available WGS datasets from >260 strains analyzed by k-mer-binning based strategy, contained a conserved core genome backbone with a different evolutionary lineage as compared to strains comprising the other cluster (ST150). In addition, the assortment of genotypic features contributing to pathogenesis and persistence, such as antimicrobial resistance, prophage, plasmid, and virulence factor genes, were assessed to understand the emerging characteristics of this serovar that are relevant clinically and for food safety concerns. The phylogenomic profiling of polyphyletic S. Bovismorbificans in this study corresponds to intra-serovar variations observed in S. Napoli and S. Newport serovars using similar high-resolution genomic profiling approaches and contributes to the understanding of the evolution and sequence divergence of foodborne Salmonellae. These intra-serovar differences may have to be thoroughly understood for the accurate classification of foodborne Salmonella strains needed for the uniform development of future food safety mitigation strategies.
Translational Frameshifting in the chlD Gene Gives a Clue to the Coevolution of the Chlorophyll and Cobalamin Biosyntheses
Authors: Kuznetsov Stepan , Milenkin Alexander , Antonov Ivan
Published: June 2022

Today, hundreds of prokaryotic species are able to synthesize chlorophyll and cobalamin (vitamin B12). An important step in the biosynthesis of these coenzymes is the insertion of a metal ion into a porphyrin ring. Namely, Mg-chelatase ChlIDH and aerobic Co-chelatase CobNST are utilized in the chlorophyll and vitamin B12 pathways, respectively. The corresponding subunits of these enzymes have common evolutionary origin. Recently, we have identified a highly conserved frameshifting signal in the chlD gene. This unusual regulatory mechanism allowed production of both the small and the medium chelatase subunits from the same gene. Moreover, the chlD gene appeared early in the evolution and could be at the starting point in the development of the chlorophyll and B12 pathways. Here, we studied the possible coevolution of these two pathways through the analysis of the chelatase genes. To do that, we developed a specialized Web database with comprehensive information about more than 1200 prokaryotic genomes. Further analysis allowed us to split the coevolution of the chlorophyll and B12 pathway into eight distinct stages.
Landscape Composition and Soil Physical–Chemical Properties Drive the Assemblages of Bacteria and Fungi in Conventional Vegetable Fields
Authors: Kumar Uttam , Saqib Hafiz Sohaib Ahmed , Islam Waqar , Prashant Parmar , Patel Nidhibahen , Chen Wei , Yang Feiying , You Minsheng , He Weiyi
Published: June 2022

The soil microbiome is crucial for improving the services and functioning of agroecosystems. Numerous studies have demonstrated the potential of soil physical–chemical properties in driving the belowground microbial assemblages in different agroecosystems. However, not much is known about the assemblage of bacteria and fungi in response to soil physical–chemical properties and the surrounding landscape composition in different vegetable fields of a highly intensive agricultural system. Here, we investigated the effects of soil physical–chemical properties and landscape composition on the community trends of bacteria and fungi in two different soil compartments (bulk and rhizospheric soils) of two different brassica crop types (Chinese cabbage and flower cabbage). The results revealed that bulk soil had a higher alpha diversity of both bacteria and fungi than rhizospheric soil. Each of the soil physical–chemical properties and landscape compositions contributed differently to driving the community structure of distinct bacterial and fungal taxa in both soil compartments and crop types. The higher proportions of forest, grassland, and cultivated land, along with the higher amount of soil calcium in flower cabbage fields, promote the assemblage of Gammaproteobacteria, Actinobacteria, Oxyophotobacteria, Agaricomycetes, and Eurotiomycetes. On the other hand, in Chinese cabbage fields, the increased amounts of iron, zinc, and manganese in the soil together with higher proportions of non-brassica crops in the surrounding landscape strongly support the assemblage of Deltaproteobacteria, Gemmatimonadetes, Bacilli, Clostridia, Alphaproteobacteria, an unknown bacterial species Subgroup-6, Mortierellomycetes, Rhizophlyctidomycetes, and Chytridiomycetes. The findings of this study provide the most comprehensive, comparative, and novel insights related to the bacterial and fungal responses in a highly intensive vegetable growing system for the improvement of the soil fertility and structure. These are important clues for the identification of key bacteria and fungi contributing to the plant–environment interactions and are of a practical significance for landscape-based ecological pest management.
Deep Learning-Based Method for Compound Identification in NMR Spectra of Mixtures
Authors: Wei Weiwei , Liao Yuxuan , Wang Yufei , Wang Shaoqi , Du Wen , Lu Hongmei , Kong Bo , Yang Huawu , Zhang Zhimin
Published: June 2022

Nuclear magnetic resonance (NMR) spectroscopy is highly unbiased and reproducible, which provides us a powerful tool to analyze mixtures consisting of small molecules. However, the compound identification in NMR spectra of mixtures is highly challenging because of chemical shift variations of the same compound in different mixtures and peak overlapping among molecules. Here, we present a pseudo-Siamese convolutional neural network method (pSCNN) to identify compounds in mixtures for NMR spectroscopy. A data augmentation method was implemented for the superposition of several NMR spectra sampled from a spectral database with random noises. The augmented dataset was split and used to train, validate and test the pSCNN model. Two experimental NMR datasets (flavor mixtures and additional flavor mixture) were acquired to benchmark its performance in real applications. The results show that the proposed method can achieve good performances in the augmented test set (ACC = 99.80%, TPR = 99.70% and FPR = 0.10%), the flavor mixtures dataset (ACC = 97.62%, TPR = 96.44% and FPR = 2.29%) and the additional flavor mixture dataset (ACC = 91.67%, TPR = 100.00% and FPR = 10.53%). We have demonstrated that the translational invariance of convolutional neural networks can solve the chemical shift variation problem in NMR spectra. In summary, pSCNN is an off-the-shelf method to identify compounds in mixtures for NMR spectroscopy because of its accuracy in compound identification and robustness to chemical shift variation.
Magnetophotoselection in the Investigation of Excitonically Coupled Chromophores: The Case of the Water-Soluble Chlorophyll Protein
Authors: Ciuti Susanna , Agostini Alessandro , Barbon Antonio , Bortolus Marco , Paulsen Harald , Di Valentin Marilena , Carbonera Donatella
Published: June 2022

A magnetophotoselection (MPS) investigation of the photoexcited triplet state of chlorophyll a both in a frozen organic solvent and in a protein environment, provided by the water-soluble chlorophyll protein (WSCP) of Lepidium virginicum, is reported. The MPS experiment combines the photoselection achieved by exciting with linearly polarized light with the magnetic selection of electron paramagnetic resonance (EPR) spectroscopy, allowing the determination of the relative orientation of the optical transition dipole moment and the zero-field splitting tensor axes in both environments. We demonstrate the robustness of the proposed methodology for a quantitative description of the excitonic interactions among pigments. The orientation of the optical transition dipole moments determined by the EPR analysis in WSCP, identified as an appropriate model system, are in excellent agreement with those calculated in the point-dipole approximation. In addition, MPS provides information on the electronic properties of the triplet state, localized on a single chlorophyll a pigment of the protein cluster, in terms of orientation of the zero-field splitting tensor axes in the molecular frame.
P2X7 Receptors in Astrocytes: A Switch for Ischemic Tolerance
Authors: Hirayama Yuri , Anzai Naohiko , Kinouchi Hiroyuki , Koizumi Schuichi
Published: June 2022

A sub-lethal ischemic episode (preconditioning [PC]) protects neurons against a subsequent lethal ischemic injury. This phenomenon is known as ischemic tolerance. PC itself does not cause brain damage, but affects glial responses, especially astrocytes, and transforms them into an ischemia-resistant phenotype. P2X7 receptors (P2X7Rs) in astrocytes play essential roles in PC. Although P2X7Rs trigger inflammatory and toxic responses, PC-induced P2X7Rs in astrocytes function as a switch to protect the brain against ischemia. In this review, we focus on P2X7Rs and summarize recent developments on how astrocytes control P2X7Rs and what molecular mechanisms they use to induce ischemic tolerance.
Synthesis and Characterization of Chelating Hyperbranched Polyester Nanoparticles for Cd(II) Ion Removal from Water
Authors: Alregeb Faten , Khalili Fawwaz , Sweileh Bassam , Ali Dalia Khalil
Published: June 2022

Chelating hyperbranched polyester (CHPE) nanoparticles have become an attractive new material family for developing high-capacity nanoscale chelating agents with highly branched structures and many functional groups in the main chains and end groups that can be used to remove heavy metals from water. In this study, a hyperbranched polyester with a particle size of 180–643 nm was synthesized with A2+B3 interfacial polymerization, using dimethylmalonyl chloride as the difunctional monomer (A2) and 1,1,1-tris(4-hydroxyphenyl)ethane (THPE) as the trifunctional monomer (B3). FTIR and NMR were used to characterize the CHPE and confirm the structure. The CHPE nanoparticles were generally considered hydrophilic, with an observed swelling capacity of 160.70%. The thermal properties of the CHPE nanoparticles were studied by thermal gravimetric analysis (TGA) with 1% mass loss at temperatures above 185 °C. The XRD of the CHPE nanoparticles showed a semi-crystalline pattern, as evident from the presence of peaks at positions ~18° and 20°. The nature of the surface of the CHPE was examined using SEM. Batch equilibrium was used to investigate the removal properties of the CHPE nanoparticles towards Cd(II) ions as a function of temperature, contact time, and Cd(II) concentration. The Cd(II) ion thermodynamics, kinetics, and desorption data on the CHPE nanoparticles were also studied.
The Ameliorative Effect of Empagliflozin in Vigabatrin-Induced Cerebellar/Neurobehavioral Deficits: Targeting mTOR/AMPK/SIRT-1 Signaling Pathways
Authors: Amer Rabab M. , Eltokhy Amira Kamel , Elesawy Rasha Osama , Barakat Amany Nagy , Basha Eman , Eldeeb Omnia Safwat , Aboalsoud Alshimaa , Elgharabawy Nancy Mohamed , Ismail Radwa
Published: June 2022

Introduction. Vigabatrin (VGB) is an antiepileptic drug that acts to irreversibly inhibit the γ-aminobutyric acid (GABA) transaminase enzyme, elevating GABA levels. Broad studies have established that long-term treatment and/or high doses of VGB lead to variable visual defects. However, little attention has been paid to its other side effects, especially those demonstrating cerebellar involvement. Sodium glucose-linked co-transporter 2 (SGLT2) inhibitors are antidiabetic agents with protective effects far greater than expected based on their anti-hyperglycemic effect. Method. Our study herein was designed to investigate the possible ameliorative effect of empagliflozin, the SGLT2 inhibitors, in VGB-induced cerebellar toxicity. A total of 40 male Wistar rats were allocated equally into 4 groups: Group I: control group; Group II: VGB group; Group III empagliflozin treated VGB group; and Group IV: empagliflozin treated group. All groups were subjected to the detection of cerebellar messenger RNA gene expression of silent mating type information regulation 2 homolog 1 (SIRT1) and Nucleoporin p62 (P62). Mammalian target of rapamycin (mTOR), adenosine monophosphate-activated protein kinase (AMPK), and beclin1 levels were assessed by the ELISA technique while malondialdehyde (MDA) level and superoxide dismutase (SOD) activity were detected spectrophotometrically. Immuno-histochemical studies, focusing on glial fibrillary acidic protein (GFAP) and S100 were performed, and the optical color density and the mean area percentage of GFAP positive astrocytes and the number of S 100 positive cells were also counted. Results. Following empagliflozin treatment, we documented significant upregulation of both SIRT1 and P62 mRNA gene expression. Additionally, AMPK, Beclin1 levels, and SOD activity were significantly improved, while both mTOR and MDA levels were significantly reduced. Conclusions. We concluded for the first time that empagliflozin efficiently ameliorated the VGB-induced disrupted mTOR/AMPK/SIRT-1 signaling axis with subsequent improvement of the autophagy machinery and mitigation of the oxidative and inflammatory cellular environment, paving the way for an innovative therapeutic potential in managing VGB-induced neurotoxicity.
Dystrophin Protein Quantification as a Duchenne Muscular Dystrophy Diagnostic Biomarker in Dried Blood Spots Using Multiple Reaction Monitoring Tandem Mass Spectrometry: A Preliminary Study
Authors: Nimer Refat M. , Sumaily Khalid M. , Almuslat Arwa , Abdel Jabar Mai Abdel , Sabi Essa M. , Al-Muhaizea Mohammad A. , Abdel Rahman Anas M. Abdel
Published: June 2022

Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder characterized by progressive muscle loss, leading to difficulties in movement. Mutations in the DMD gene that code for the protein dystrophin are responsible for the development of DMD disorder, where the synthesis of this protein is completely halted. Therefore, circulating dystrophin protein could be a promising biomarker of DMD disease. Current methods for diagnosing DMD have sensitivity, specificity, and reproducibility limitations. Herein, a quantitative liquid chromatography–tandem spectrometry (LC–MS/MS) technique in multiple reaction monitoring (MRM) mode was designed and validated for accurate dystrophin protein measurement in a dried blood spot (DBS). The method was successfully validated on the basis of international guidelines regarding calibration curves, precision, and accuracy. In addition, patients and healthy controls were used to test the amount of dystrophin protein circulating in DBS samples as a potential biomarker for DMD disorders. DMD patients were found to have considerably lower levels than controls. To the best of our knowledge, this is the first study to report dystrophin levels in DBS through LC–MS/MS as a diagnostic marker for DMD to the proposed MRM method, providing a highly specific and sensitive approach to dystrophin quantification in a DBS that can be applied in DMD screening.
Nanocomposites Based on Antiferroelectric Liquid Crystal (S)-MHPOBC Doping with Au Nanoparticles
Authors: Lalik Sebastian , Stefańczyk Olaf , Dardas Dorota , Deptuch Aleksandra , Yevchenko Tetiana , Ohkoshi Shin-ichi , Marzec Monika
Published: June 2022

Modification of the physical properties of the (S)-MHPOBC antiferroelectric liquid crystal (AFLC) by doping with low concentrations of gold nanoparticles is presented for the first time. We used several complementary experimental methods to determine the effect of Au nanoparticles on AFLC in the metal–organic composites. It was found that the dopant inhibits the matrix crystallization process and modifies the phase transitions temperatures and switching time, as well as increases the helical pitch and spontaneous polarization, while the tilt angle slightly changes. We also showed that both the LC matrix and Au nanoparticles show strong fluorescence in the green light range, and the contact angle depends on the temperature and dopant concentration.
Study of the Electrical Conductivity Characteristics of Micro and Nano-ZnO/LDPE Composites
Authors: Yu Guang , Cheng Yujia , Duan Zhuohua
Published: June 2022

Polyethylene, a thermoplastic resin made by ethylene polymerization, is widely used in electrical insulation. In this study, low-density polyethylene (LDPE) is used as a matrix with micro- and nano-ZnO particles as a filler to produce different proportions of micro- and nano-ZnO composites by melt blending. These samples are characterized by Polarized Light Microscopy (PLM) and FTIR tests, with their conductance measured under different field strengths. The current density vs. electric field strength (J-E) curve of micro- and nano-ZnO composites under different field strengths are measured and analyzed. The J-E curves of different composites at different temperatures are measured to explore conductance with temperature. The results of these tests showed that nano-ZnO composites successfully suppressed conductivity at elevated temperatures and electric field strengths, while micro-ZnO composites increased the conductivity relative to pure LDPE.
The Expression and Bioinformatics Analysis of Circular RNAs in Endometritis Mouse Uterus Tissues
Authors: Li Zhiqiang , Shi Liying , Li Qianqing , Zhao Jing , Lu Wenfa , Wang Jun
Published: June 2022

Previous studies have shown that circular RNAs are directly or indirectly involved in the occurrence of various diseases by regulating gene expression. However, the acting mechanism of circular RNAs in endometritis remains unclear. In this study, we successfully established an endometritis model in mouse using Escherichia coli; endometrial integrity was destroyed, inflammatory cells infiltrated and the expression of IL-6, IL-1β, TNF-α was significantly up-regulated. We analyzed and screened the circular RNA expression profiles between healthy and endometritis-stricken mice by the Illumina HiSeq platform, and used qRT-PCR method to verify the different expressions of circular RNAs. Gene ontology (GO) analysis showed that circular RNAs were mainly involved in biological processes such as the positive regulation of transcription from RNA polymerase POL II promoter and the negative regulation of cell proliferation. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of circular RNAs target genes may be involved in the TGF-β signaling pathway. We verified the expression of TGF-β and its related factors; the mRNA of TGF-β1 and smad7 were significantly up-regulated in endometritis mouse (p < 0.01) and the protein expression level of p-smad3 was significantly decreased (p < 0.01). Finally, we constructed a circular RNAs–miRNA network to elucidate the potential regulatory relationship between two small molecules. This research may provide new ideas for circular RNAs in the treatment of endometritis.
Neurotoxin (N-Oxalyl-L-α,β-Diamino Propionic Acid) Content in Different Plant Parts of Grass Pea (Lathyrus sativus L.) Spanning Seedling to Maturity Stage: Does It Increase over Time?
Authors: Barpete Surendra , Gupta Priyanka , Sen Gupta Debjyoti , Kumar Jitendra , Bhowmik Arpan , Kumar Shiv
Published: June 2022

ODAP (N-oxalyl-L-2,3-diaminopropionic acid) is present in the seeds of grass pea. In this study, variation of total ODAP accumulation in leaves throughout the crop growth starting from 40 days after sowing to maturity, and the distribution pattern of ODAP in different plant parts including the seeds at the mature stage was analyzed. Five grass pea accessions were evaluated for two subsequent growing seasons in one location of ICARDA, Aleppo (Syria). The results found that the rate of accumulation of total ODAP varied during plant development. Increased rates of synthesis were noticed in young leaves of grass pea. The highest total ODAP content in leaves was noted in the early growth stage (40–50 days after sowing). Mean total ODAP content in leaves ranged from 0.17 to 0.96 percent during 2010–2011 and from 0.19 to 1.28 percent during 2011–2012. During maturity, the total ODAP content was lowest in the seeds than in leaves, stems, pod cover, seed coat, and cotyledons. The ranges of total ODAP content were 0.13 (seed)–0.34 (stem), 0.20 (seed)–1.01 (leaf), 0.22 (seed)–0.62 (leaf), 0.21 (seed)–0.66 (leaf), and 0.21 (seed)–0.78 (leaf) percent in B387, B222, B390, Bio-520, and B587 accessions, respectively, during maturity. The results indicated that the rate of accumulation and synthesis of total ODAP varied during the plant lifespan. The lowest total ODAP content of leaves was observed after 130 days of sowing. The lower total ODAP content after the early vegetative stage of grass pea plants makes them suitable as a feed.
Influence of Multiple Binding Sites on the Supramolecular Assembly of N-[(3-pyridinylamino) Thioxomethyl] Carbamates
Authors: Shunje Kelly N. , Averkiev Boris B. , Aakeröy Christer B.
Published: June 2022

In this study, we investigated how the presence of multiple intermolecular interaction sites influences the heteromeric supramolecular assembly of N-[(3-pyridinylamino) thioxomethyl] carbamates with fluoroiodobenzenes. Three targets—R-N-[(3-pyridinylamino) thioxomethyl] carbamate (R = methyl, ethyl, and isobutyl)—were selected and crystallized, resulting in three parent structures, five co-crystals, and one co-crystal solvate. Three hydrogen-bonded parent crystal structures were stabilized by N-H···N hydrogen bonding and assembled into layers that stacked on top of one another. Molecular electrostatic potential surfaces were employed to rank binding sites (Npyr > C=S > C=O) in order to predict the dominant interactions. The N-H⋯H hydrogen bond was replaced by I⋯Npyr in 3/6 cases, I⋯C=S in 4/6 cases, and I⋯O=C in 1 case. Interestingly, the I⋯C=S halogen bond coexisted twice with I⋯Npyr and I⋯O=C. Overall, the MEPs were fairly reliable for predicting co-crystallization outcomes; however, it is crucial to also consider factors such as molecular flexibility. Finally, halogen-bond donors are capable of competing for acceptor sites, even in the presence of strong hydrogen-bond donors.
Synthesis and Characterization of Preacinetobactin and 5-Phenyl Preacinetobactin
Authors: Bray Jean M. , Pierce Scott , Angeles-Boza Alfredo M. , Peczuh Mark W.
Published: June 2022

We report the first total synthesis of 5-phenyl preacinetobactin and its characterization. The route was developed for the synthesis of preacinetobactin, the siderophore critical to the Gram-negative pathogen A. baumannii. It leverages a C5-substituted benzaldehyde as a key starting material and should enable the synthesis of similar analogs. 5-Phenyl preacinetobactin binds iron in a manner analogous to the natural siderophore, but it did not rescue growth in a strain of A. baumannii unable to produce preacinetobactin.
Theoretical Studies on the Structure and Intramolecular Interactions of Fagopyrins—Natural Photosensitizers of Fagopyrum
Authors: Szymański Sebastian , Majerz Irena
Published: June 2022

Compounds characterized by a double-anthrone moiety are found in many plant species. One of them are fagopyrins—naturally occurring photosensitizers of Fagopyrum. The photosensitizing properties of fagopyrins are related to the selective absorption of light, which is a direct result of their spatial and electronic structure and many intramolecular interactions. The nature of the interactions varies in different parts of the molecule. The aim of this study is to determine the structure and intramolecular interactions of fagopyrin molecules. For this purpose, in silico calculations were used to perform geometry optimization in the gas phase. QTAIM and NCI analysis suggest the formation of the possible conformers in the fagopyrin molecules. The presence of a strong OHO hydrogen bond was shown in the anthrone moiety of fagopyrin. The minimum energy difference for selected conformers of fagopyrins was 1.1 kcal∙mol−1, which suggested that the fagopyrin structure may exist in a different conformation in plant material. Similar interactions were observed in previously studied structures of hypericin and sennidin; however, only fagopyrin showed the possibility of brake the strong OHO hydrogen bond in favor of forming a new OHN hydrogen bond.