bluuebunny/crossref_metadata_2025 huggingface dataset:
Deciphering the Immune Complexity in Esophageal Adenocarcinoma and Pre-Cancerous Lesions With Sequential Multiplex Immunohistochemistry and Sparse Subspace Clustering Approach
Authors: Sundaram Srinand , Kim Eun Na , Jones Georgina M. , Sivagnanam Shamilene , Tripathi Monika , Miremadi Ahmad , Di Pietro Massimiliano , Coussens Lisa M. , Fitzgerald Rebecca C. , Chang Young Hwan , Zhuang Lizhe
Published: May 2022

Esophageal adenocarcinoma (EAC) develops from a chronic inflammatory environment across four stages: intestinal metaplasia, known as Barrett’s esophagus, low- and high-grade dysplasia, and adenocarcinoma. Although the genomic characteristics of this progression have been well defined via large-scale DNA sequencing, the dynamics of various immune cell subsets and their spatial interactions in their tumor microenvironment remain unclear. Here, we applied a sequential multiplex immunohistochemistry (mIHC) platform with computational image analysis pipelines that allow for the detection of 10 biomarkers in one formalin-fixed paraffin-embedded (FFPE) tissue section. Using this platform and quantitative image analytics, we studied changes in the immune landscape during disease progression based on 40 normal and diseased areas from endoscopic mucosal resection specimens of chemotherapy treatment- naïve patients, including normal esophagus, metaplasia, low- and high-grade dysplasia, and adenocarcinoma. The results revealed a steady increase of FOXP3+ T regulatory cells and a CD163+ myelomonocytic cell subset. In parallel to the manual gating strategy applied for cell phenotyping, we also adopted a sparse subspace clustering (SSC) algorithm allowing the automated cell phenotyping of mIHC-based single-cell data. The algorithm successfully identified comparable cell types, along with significantly enriched FOXP3 T regulatory cells and CD163+ myelomonocytic cells as found in manual gating. In addition, SCC identified a new CSF1R+CD1C+ myeloid lineage, which not only was previously unknown in this disease but also increases with advancing disease stages. This study revealed immune dynamics in EAC progression and highlighted the potential application of a new multiplex imaging platform, combined with computational image analysis on routine clinical FFPE sections, to investigate complex immune populations in tumor ecosystems.
Nitracentric/Hydrographic Classification and Prediction of Nitrate Profiles for Oceanographic Stations Under the Influence of Mesoscale Eddies in the Gulf of Mexico
Authors: Velásquez-Aristizábal Jorge A. , Camacho-Ibar Víctor F. , Durazo Reginaldo , Valencia-Gasti José A. , Lee-Sánchez Erika , Trasviña-Castro Armando
Published: May 2022

In the ocean, nitrogen availability is an important control of primary production and influences the amount of energy flowing through food webs. Mesoscale eddies play important roles in modulating the spatial distributions of physical and biogeochemical properties in the Gulf of Mexico (GM), including the availability of nitrate + nitrite (NN). In this study, we explore an oceanographic station classification based on the integrated NN stock that we have named the “nitracentric classification” and a classification based on hydrographic variables that we call the Best Fit Variables (BFVs), such as the depth of the 20°C isotherm and the depth of the 26 kg m-3 isopycnal, to identify stations under the influence of mesoscale eddies. We analyzed hydrographic profiles of CTD data and the NN concentrations in discrete samples collected in June 2016 during the oceanographic campaign XIXIMI-5, which was conducted in the deep-water region of the GM. The best station separation was produced when the NN concentration was integrated between the surface and 200 m depth, which was supported by the station classification based on the BFVs. Our classification system produces a better separation between station groups when compared to other classifications that rely on the use of altimetric variables and hydrographic criteria that have been previously employed to study biogeochemical and physical processes in the GM. We obtained parameterizations that accurately predicted the NN profiles between 100–500 m of stations sampled under stratified conditions in two other XIXIMI cruises in the gulf, although the parameterization has to be adapted to obtain accurate predictions under winter mixing conditions. Our results can be used to predict nitrate stocks and profiles based on a single BFV value obtained from the existing hydrographic databases of the GM as well as from CTD data at the time of sampling. The analysis of the CLIVAR Section A22 in the Caribbean Sea indicates that the nitracentric and hydrographic classification methodology developed in this study can also be applied to other oligotrophic basins where mesoscale eddies play important roles in controlling the distributions of hydrographic and biogeochemical properties.
The Potential of Kelp Saccharina japonica in Shielding Pacific Oyster Crassostrea gigas From Elevated Seawater pCO2 Stress
Authors: Jiang Zengjie , Jiang Weiwei , Rastrick Samuel P. S. , Wang Xiaoqin , Fang Jinghui , Du Meirong , Gao Yaping , Mao Yuze , Strand Øivind , Fang Jianguang
Published: May 2022

Ocean acidification (OA) caused by elevated atmospheric CO2 concentration is predicted to have negative impacts on marine bivalves in aquaculture. However, to date, most of our knowledge is derived from short-term laboratory-based experiments, which are difficult to scale to real-world production. Therefore, field experiments, such as this study, are critical for improving ecological relevance. Due to the ability of seaweed to absorb dissolved carbon dioxide from the surrounding seawater through photosynthesis, seaweed has gained theoretical attention as a potential partner of bivalves in integrated aquaculture to help mitigate the adverse effects of OA. Consequently, this study investigates the impact of elevated pCO2 on the physiological responses of the Pacific oyster Crassostrea gigas in the presence and absence of kelp (Saccharina japonica) using in situ mesocosms. For 30 days, mesocosms were exposed to six treatments, consisting of two pCO2 treatments (500 and 900 μatm) combined with three biotic treatments (oyster alone, kelp alone, and integrated kelp and oyster aquaculture). Results showed that the clearance rate (CR) and scope for growth (SfG) of C. gigas were significantly reduced by elevated pCO2, whereas respiration rates (MO2) and ammonium excretion rates (ER) were significantly increased. However, food absorption efficiency (AE) was not significantly affected by elevated pCO2. The presence of S. japonica changed the daytime pHNBS of experimental units by ~0.16 units in the elevated pCO2 treatment. As a consequence, CR and SfG significantly increased and MO2 and ER decreased compared to C. gigas exposed to elevated pCO2 without S. japonica. These findings indicate that the presence of S. japonica in integrated aquaculture may help shield C. gigas from the negative effects of elevated seawater pCO2.
Declining Population Sizes and Loss of Genetic Diversity in Commercial Fishes: A Simple Method for a First Diagnostic
Authors: Petit-Marty Natalia , Liu Min , Tan Iris Ziying , Chung Arthur , Terrasa Bàrbara , Guijarro Beatriz , Ordines Francesc , Ramírez-Amaro Sergio , Massutí Enric , Schunter Celia
Published: May 2022

Exploited fish species may have or are experiencing declines in population sizes coupled with changes in their environmental conditions owing to global change. Declining populations might lead to a decrease in genetic diversity, which in turn may produce losses of adaptive potential to face current and future environmental changes. Thus, this study aims to answer a simple, even naive question, given the complexity of the subject: Could we use a simple method to obtain information on the loss of genetic diversity in exploited fish species? We investigated the use of the levels of genetic diversity in the widely used genetic marker Cytochrome C Oxidase subunit I (COI) mitochondrial gene. Estimates of genetic diversity in COI were obtained for populations of seven fish species with different commercial importance from the East China Sea. These estimates were contrasted against large datasets of genetic diversity in COI for fish species (East-Asian N=118, and worldwide N=1425), and six control species with known biology and history. We found that estimates of genetic diversity in COI match the expectations from theoretical predictions and known declines by fishing pressures. Thus, the answer to our question is affirmative and we conclude that estimates of genetic diversity in COI provide an effective first diagnostic of the conservation status of exploited fish species.
Ternary Logics Based on 2D Ferroelectric-Incorporated 2D Semiconductor Field Effect Transistors
Authors: Zhao Guangchao , Wang Xingli , Yip Weng Hou , Vinh Huy Nguyen To , Coquet Philippe , Huang Mingqiang , Tay Beng Kang
Published: May 2022

Ternary logic has been proven to carry an information ratio 1.58 times that of binary logic and is capable to reduce circuit interconnections and complexity of operations. However, the excessive transistor count of ternary logic gates has impeded their industry applications for decades. With the modulation of the ferroelectric negative capacitance (NC) properties on the channel potential, MOSFETs show many novel features including steep subthreshold swing and non-saturation output characteristics, based on which an ultra-compact ternary inverter can be achieved. Compared with traditional bulk materials, layered 2D materials and 2D ferroelectrics provide a clean interface and better electrostatic control and reliability. Even though ultra-low SS (∼10 mV/dec) has been experimentally demonstrated in ferroelectric-negative capacitance-incorporated 2D semiconductor (NC2D) FETs, the available models are still rare for large-scale circuit simulations. In this study, the superb electrical properties of pure 2D material stack-based NC2D FETs (layered CuInP2S6 adopted as the 2D ferroelectric layer) are investigated through device modeling based on the Landau–Khalatnikov (LK) equations in HSPICE. We managed to realize an ultra-compact ternary inverter with one NC2D-PMOS (WSe2) and one NC2D-NMOS (MoS2) in HSPICE simulations, whose transistor count is significantly reduced compared with other counterparts. We also proposed a novel input waveform scheme to solve the hysteresis problem caused by ferroelectric modulation to avoid logic confusion. Additionally, the power consumption and propagation delay of the NC2D-based ternary inverter are also investigated. This work may provide some insights into the design and applications of ferroelectric-incorporated 2D semiconductor devices.
Corrosion Behavior of Aluminum-Forming Alloy 310S for Application in Molten Chloride Salt CSP Thermal Storage Tank
Authors: Wei Ying , La Peiqing , Jin Jing , Du Mingchen , Zheng Yuehong , Zhan Faqi , Sheng Jie , Yu Haicun , Zhu Min
Published: May 2022

The key to the new generation of solar thermal power plants is to increase the operating temperature of molten salt to 800°C, and change the heat transfer medium from nitric acid mixed salt to chlorine mixed salt, so as to significantly reduce the cost of power generation. Therefore, the alloy material’s resistance to high temperatures and fusible chloride salt is one of the core technologies for the successful implementation of concentrated solar power (CSP) technology. In this study, the aluminum-forming alloy (AFA) 310S for the heat storage tank was prepared by the aluminum-thermal reaction casting method. The hot corrosion behavior and mechanism of AFA 310S in chloride molten salt at 800°C were studied by static immersion etching for 600 h. AFA 310S exhibits good thermal corrosion properties in KCl 20.4 wt% + MgCl2-55.1 wt% + NaCl 24.5 wt%. The results indicate that compared with commercial 310S, AFA 310S has better oxidation resistance at 800°C. At the initial stage of corrosion, dense Cr2O3 and continuous Al2O3 passivation films are formed. At the same time, MgO-rich oxidation products were produced in the outermost layers of the two alloys during the 600 h process. Over time, however, the damage caused by chlorine became more apparent, mainly due to the “oxidation-chlorination” process of the metal. A large number of cavities and cracks on the surface are formed, and the oxide layer has obvious spalling. When the Al element was added into the alloy, the dense passivation film could be formed after 120 h of corrosion with the stronger corrosion resistance. The experiment simulated the corrosion behavior in the worst environment, such as air, unoxidized alloy, molten salt without corrosion inhibitor, etc. By weight loss calculation, commercial 310S plate is completely unsuitable for CSP plant. The corrosion rates of the two alloys are compared as follows: commercial 310S > AFA 310S. To sum up, AFA 310S has a good application prospect in concentrated solar power.
Prediction of Red Blood Cell Demand for Pediatric Patients Using a Time-Series Model: A Single-Center Study in China
Authors: Guo Kai , Song Shanshan , Qiu Lijuan , Wang Xiaohuan , Ma Shuxuan
Published: May 2022

Background

Red blood cells (RBCs) are an essential factor to consider for modern medicine, but planning the future collection of RBCs and supply efforts for coping with fluctuating demands is still a major challenge.

Objectives

This study aimed to explore the feasibility of the time-series model in predicting the clinical demand of RBCs for pediatric patients each month.

Methods

Our study collected clinical RBC transfusion data from years 2014 to 2019 in the National Center for Children's Health (Beijing) in China, with the goal of constructing a time-series, autoregressive integrated moving average (ARIMA) model by fitting the monthly usage of RBCs from 2014 to 2018. Furthermore, the optimal model was used to forecast the monthly usage of RBCs in 2019, and we subsequently compared the data with actual values to verify the validity of the model.

Results

The seasonal multiplicative model SARIMA (0, 1, 1) (1, 1, 0)12 (normalized BIC = 8.740, R2 = 0.730) was the best prediction model and could better fit and predict the monthly usage of RBCs for pediatric patients in this medical center in 2019. The model residual sequence was white noise (Ljung-Box Q(18) = 15.127, P > 0.05), and its autocorrelation function (ACF) and partial autocorrelation function (PACF) coefficients also fell within the 95% confidence intervals (CIs). The parameter test results were statistically significant (P < 0.05). 91.67% of the actual values were within the 95% CIs of the forecasted values of the model, and the average relative error of the forecasted and actual values was 6.44%, within 10%.

Conclusions

The SARIMA model can simulate the changing trend in monthly usage of RBCs of pediatric patients in a time-series aspect, which represents a short-term prediction model with high accuracy. The continuously revised SARIMA model may better serve the clinical environments and aid with planning for RBC demand. A clinical study including more data on blood use should be conducted in the future to confirm these results.
Dual Inhibitory Activity of Petroselinic Acid Enriched in Fennel Against Porphyromonas gingivalis
Authors: Yoshino Nanami , Ikeda Tsuyoshi , Nakao Ryoma
Published: May 2022

Increasing evidence has shown that a major periodontal pathobiont, Porphyromonas gingivalis, triggers oral dysbiosis leading to deterioration not only of periodontal health, but also of several systemic conditions. In the present study we identified remarkable anti-P. gingivalis activity of Foeniculum vulgare (fennel), an herbal plant used in Asian cuisine as well as in traditional medicine, by screening of 92 extracts prepared from 23 edible plants. The n-hexane-extracted fennel (HEF) showed a rapid lethal action toward P. gingivalis, while it was rather ineffective with a wide range of other oral commensal bacterial species. Morphological analysis using both high-speed atomic force microscopy and field emission scanning electron microscopy revealed that a low concentration of HEF (8 μg/mL) resulted in formation of protruding nanostructures composed of outer membrane vesicle (OMV)-like particles, while a high concentration of HEF (64 μg/mL) induced bacteriolysis with overproduction of OMVs with unusual surface properties. Interestingly, HEF treatment resulted in deprivation of two outer membrane transporter proteins, RagA and RagB, which is essential for nutrient acquisition in P. gingivalis, by extracellularly releasing RagA/RagB-enriched OMVs. Furthermore, HEF showed gingipain-inhibitory activity toward both arginine-specific (Rgps) and lysine-specific (Kgp) gingipains, resulting in blocking oral epithelial cell rounding and the subsequent detachment from culture dishes. Finally, we isolated petroselinic acid as a major bactericide as well as a gingipain inhibitor through a bioassay-guided fractionation of HEF. Taken together, our findings suggest clinical applicability of HEF and petroselinic acid for periodontitis therapy to eliminate P. gingivalis and its major virulence factors on the basis of the dual anti-P. gingivalis activity, i.e., rapid bacteriolysis and gingipain inhibition.
SymbiQuant: A Machine Learning Object Detection Tool for Polyploid Independent Estimates of Endosymbiont Population Size
Authors: James Edward B. , Pan Xu , Schwartz Odelia , Wilson Alex C. C.
Published: May 2022

Quantifying the size of endosymbiont populations is challenging because endosymbionts are typically difficult or impossible to culture and commonly polyploid. Current approaches to estimating endosymbiont population sizes include quantitative PCR (qPCR) targeting endosymbiont genomic DNA and flow-cytometry. While qPCR captures genome copy number data, it does not capture the number of bacterial cells in polyploid endosymbiont populations. In contrast, flow cytometry can capture accurate estimates of whole host-level endosymbiont population size, but it is not readily able to capture data at the level of endosymbiotic host cells. To complement these existing approaches for estimating endosymbiont population size, we designed and implemented an object detection/segmentation tool for counting the number of endosymbiont cells in micrographs of host tissues. The tool, called SymbiQuant, which makes use of recent advances in deep neural networks includes a graphic user interface that allows for human curation of tool output. We trained SymbiQuant for use in the model aphid/Buchnera endosymbiosis and studied Buchnera population dynamics and phenotype over aphid postembryonic development. We show that SymbiQuant returns accurate counts of endosymbionts, and readily captures Buchnera phenotype. By replacing our training data with data composed of annotated microscopy images from other models of endosymbiosis, SymbiQuant has the potential for broad application. Our tool, which is available on GitHub, adds to the repertoire of methods researchers can use to study endosymbiosis at the organismal, genome, and now endosymbiotic host tissue or cell levels.
A Comparison of the Adaptive Response of Staphylococcus aureus vs. Streptococcus mutans and the Development of Chlorhexidine Resistance
Authors: van de Lagemaat Marieke , Stockbroekx Valerie , Geertsema-Doornbusch Gésinda I. , Dijk Melissa , Carniello Vera , Woudstra Willem , van der Mei Henny C. , Busscher Henk J. , Ren Yijin
Published: May 2022

Antimicrobials with nonselective antibacterial efficacy such as chlorhexidine can be effective in reducing biofilm, but bear the risk of inducing resistance in specific bacteria. In clinical practice, bacteria such as Staphylococcus aureus have been found resistant to chlorhexidine, but other bacteria, including Streptococcus mutans, have largely remained susceptible to chlorhexidine despite its widespread use in oral healthcare. Here, we aim to forward a possible reason as to why S. aureus can acquire resistance against chlorhexidine, while S. mutans remains susceptible to chlorhexidine. Measurement of surface-enhanced fluorescence indicated that chlorhexidine caused gradual, but irreversible deformation to adhering green fluorescent S. aureus due to irreparable damage to the cell wall. Concurrently, the metabolic activity of adhering staphylococci was higher than of planktonic bacteria, suggesting efflux mechanisms may have been activated upon cell wall deformation, impeding the buildup of a high chlorhexidine concentration in the cytoplasm and therewith stimulating the development of chlorhexidine resistance in S. aureus. Exposure of S. mutans to chlorhexidine caused immediate, but reversible deformation in adhering streptococci, indicative of rapid self-repair of cell wall damage done by chlorhexidine. Due to cell wall self-repair, S. mutans will be unable to effectively reduce the chlorhexidine concentration in the cytoplasm causing solidification of the cytoplasm. In line, no increased metabolic activity was observed in S. mutans during exposure to chlorhexidine. Therewith, self-repair is suicidal and prevents the development of a chlorhexidine-resistant progeny in S. mutans.
Evidence for an Independent Hydrogenosome-to-Mitosome Transition in the CL3 Lineage of Fornicates
Authors: Vargová Romana , Hanousková Pavla , Salamonová Jana , Žihala David , Silberman Jeffrey D. , Eliáš Marek , Čepička Ivan
Published: May 2022

Fornicata, a lineage of a broader and ancient anaerobic eukaryotic clade Metamonada, contains diverse taxa that are ideally suited for evolutionary studies addressing various fundamental biological questions, such as the evolutionary trajectory of mitochondrion-related organelles (MROs), the transition between free-living and endobiotic lifestyles, and the derivation of alternative genetic codes. To this end, we conducted detailed microscopic and transcriptome analyses in a poorly documented strain of an anaerobic free-living marine flagellate, PCS, in the so-called CL3 fornicate lineage. Fortuitously, we discovered that the original culture contained two morphologically similar and closely related CL3 representatives, which doubles the taxon representation within this lineage. We obtained a monoeukaryotic culture of one of them and formally describe it as a new member of the family Caviomonadidae, Euthynema mutabile gen. et sp. nov. In contrast to previously studied caviomonads, the endobiotic Caviomonas mobilis and Iotanema spirale, E. mutabile possesses an ultrastructurally discernible MRO. We sequenced and assembled the transcriptome of E. mutabile, and by sequence subtraction, obtained transcriptome data from the other CL3 clade representative present in the original PCS culture, denoted PCS-ghost. Transcriptome analyses showed that the reassignment of only one of the UAR stop codons to encode Gln previously reported from I. spirale does not extend to its free-living relatives and is likely due to a unique amino acid substitution in I. spirale’s eRF1 protein domain responsible for termination codon recognition. The backbone fornicate phylogeny was robustly resolved in a phylogenomic analysis, with the CL3 clade amongst the earliest branching lineages. Metabolic and MRO functional reconstructions of CL3 clade members revealed that all three, including I. spirale, encode homologs of key components of the mitochondrial protein import apparatus and the ISC pathway, indicating the presence of a MRO in all of them. In silico evidence indicates that the organelles of E. mutabile and PCS-ghost host ATP and H2 production, unlike the cryptic MRO of I. spirale. These data suggest that the CL3 clade has experienced a hydrogenosome-to-mitosome transition independent from that previously documented for the lineage leading to Giardia.
Metagenomic Mining for Esterases in the Microbial Community of Los Rueldos Acid Mine Drainage Formation
Authors: Vidal Paula , Martínez-Martínez Mónica , Fernandez-Lopez Laura , Roda Sergi , Méndez-García Celia , Golyshina Olga V. , Guallar Víctor , Peláez Ana I. , Ferrer Manuel
Published: May 2022

Acid mine drainage (AMD) systems are extremely acidic and are metal-rich formations inhabited by relatively low-complexity communities of acidophiles whose enzymes remain mostly uncharacterized. Indeed, enzymes from only a few AMD sites have been studied. The low number of available cultured representatives and genome sequences of acidophiles inhabiting AMDs makes it difficult to assess the potential of these environments for enzyme bioprospecting. In this study, using naïve and in silico metagenomic approaches, we retrieved 16 esterases from the α/β-hydrolase fold superfamily with the closest match from uncultured acidophilic Acidobacteria, Actinobacteria (Acidithrix, Acidimicrobium, and Ferrimicrobium), Acidiphilium, and other Proteobacteria inhabiting the Los Rueldos site, which is a unique AMD formation in northwestern Spain with a pH of ∼2. Within this set, only two polypeptides showed high homology (99.4%), while for the rest, the pairwise identities ranged between 4 and 44.9%, suggesting that the diversity of active polypeptides was dominated not by a particular type of protein or highly similar clusters of proteins, but by diverse non-redundant sequences. The enzymes exhibited amino acid sequence identities ranging from 39 to 99% relative to homologous proteins in public databases, including those from other AMDs, thus indicating the potential novelty of proteins associated with a specialized acidophilic community. Ten of the 16 hydrolases were successfully expressed in Escherichia coli. The pH for optimal activity ranged from 7.0 to 9.0, with the enzymes retaining 33–68% of their activities at pH 5.5, which was consistent with the relative frequencies of acid residues (from 54 to 67%). The enzymes were the most active at 30–65°C, retaining 20–61% of their activity under the thermal conditions characterizing Los Rueldos (13.8 ± 0.6°C). The analysis of the substrate specificity revealed the capacity of six hydrolases to efficiently degrade (up to 1,652 ± 75 U/g at pH 8.0 and 30°C) acrylic- and terephthalic-like [including bis(2-hydroxyethyl)-terephthalate, BHET] esters, and these enzymes could potentially be of use for developing plastic degradation strategies yet to be explored. Our assessment uncovers the novelty and potential biotechnological interest of enzymes present in the microbial populations that inhibit the Los Rueldos AMD system.
Identification of Promoter Region Markers Associated With Altered Expression of Resistance-Nodulation-Division Antibiotic Efflux Pumps in Acinetobacter baumannii
Authors: López-Siles Mireia , McConnell Michael J. , Martín-Galiano Antonio J.
Published: May 2022

Genetic alterations leading to the constitutive upregulation of specific efflux pumps contribute to antibacterial resistance in multidrug resistant bacteria. The identification of such resistance markers remains one of the most challenging tasks of genome-level resistance predictors. In this study, 487 non-redundant genetic events were identified in upstream zones of three operons coding for resistance-nodulation-division (RND) efflux pumps of 4,130 Acinetobacter baumannii isolates. These events included insertion sequences, small indels, and single nucleotide polymorphisms. In some cases, alterations explicitly modified the expression motifs described for these operons, such as the promoter boxes, operators, and Shine-Dalgarno sequences. In addition, changes in DNA curvature and mRNA secondary structures, which are structural elements that regulate expression, were also calculated. According to their influence on RND upregulation, the catalog of upstream modifications were associated with “experimentally verified,” “presumed,” and “probably irrelevant” degrees of certainty. For experimental verification, DNA of upstream sequences independently carrying selected markers, three for each RND operon, were fused to a luciferase reporter plasmid system. Five out of the nine selected markers tested showed significant increases in expression with respect to the wild-type sequence control. In particular, a 25-fold expression increase was observed with the ISAba1 insertion sequence upstream the adeABC pump. Next, overexpression of each of the three multi-specific RND pumps was linked to their respective antibacterial substrates by a deep A. baumannii literature screen. Consequently, a data flow framework was then developed to link genomic upregulatory RND determinants to potential antibiotic resistance. Assignment of potential increases in minimal inhibitory concentrations at the “experimentally verified” level was permitted for 42 isolates to 7–8 unrelated antibacterial agents including tigecycline, which is overlooked by conventional resistome predictors. Thus, our protocol may represent a time-saving filter step prior to laborious confirmation experiments for efflux-driven resistance. Altogether, a computational-experimental pipeline containing all components required for identifying the upstream regulatory resistome is proposed. This schema may provide the foundational stone for the elaboration of tools approaching antibiotic efflux that complement routine resistome predictors for preventing antimicrobial therapy failure against difficult-to-threat bacteria.
Antimicrobial Peptides Controlling Resistant Bacteria in Animal Production
Authors: Rodrigues Gisele , Souza Santos Lucas , Franco Octávio Luiz
Published: May 2022

In the last few decades, antimicrobial resistance (AMR) has been a worldwide concern. The excessive use of antibiotics affects animal and human health. In the last few years, livestock production has used antibiotics as food supplementation. This massive use can be considered a principal factor in the accelerated development of genetic modifications in bacteria. These modifications are responsible for AMR and can be widespread to pathogenic and commensal bacteria. In addition, these antibiotic residues can be dispersed by water and sewer water systems, the contamination of soil and, water and plants, in addition, can be stocked in tissues such as muscle, milk, eggs, fat, and others. These residues can be spread to humans by the consumption of water or contaminated food. In addition, studies have demonstrated that antimicrobial resistance may be developed by vertical and horizontal gene transfer, producing a risk to public health. Hence, the World Health Organization in 2000 forbid the use of antibiotics for feed supplementation in livestock. In this context, to obtain safe food production, one of the potential substitutes for traditional antibiotics is the use of antimicrobial peptides (AMPs). In general, AMPs present anti-infective activity, and in some cases immune response. A limited number of AMP-based drugs are now available for use in animals and humans. This use is still not widespread due to a few problems like in-vivo effectiveness, stability, and high cost of production. This review will elucidate the different AMPs applications in animal diets, in an effort to generate safe food and control AMR.
Polyphosphate Dynamics in Cable Bacteria
Authors: Geerlings Nicole M. J. , Kienhuis Michiel V. M. , Hidalgo-Martinez Silvia , Hageman Renee , Vasquez-Cardenas Diana , Middelburg Jack J. , Meysman Filip J. R. , Polerecky Lubos
Published: May 2022

Cable bacteria are multicellular sulfide oxidizing bacteria that display a unique metabolism based on long-distance electron transport. Cells in deeper sediment layers perform the sulfide oxidizing half-reaction whereas cells in the surface layers of the sediment perform the oxygen-reducing half-reaction. These half-reactions are coupled via electron transport through a conductive fiber network that runs along the shared cell envelope. Remarkably, only the sulfide oxidizing half-reaction is coupled to biosynthesis and growth whereas the oxygen reducing half-reaction serves to rapidly remove electrons from the conductive fiber network and is not coupled to energy generation and growth. Cells residing in the oxic zone are believed to (temporarily) rely on storage compounds of which polyphosphate (poly-P) is prominently present in cable bacteria. Here we investigate the role of poly-P in the metabolism of cable bacteria within the different redox environments. To this end, we combined nanoscale secondary ion mass spectrometry with dual-stable isotope probing (13C-DIC and 18O-H2O) to visualize the relationship between growth in the cytoplasm (13C-enrichment) and poly-P activity (18O-enrichment). We found that poly-P was synthesized in almost all cells, as indicated by 18O enrichment of poly-P granules. Hence, poly-P must have an important function in the metabolism of cable bacteria. Within the oxic zone of the sediment, where little growth is observed, 18O enrichment in poly-P granules was significantly lower than in the suboxic zone. Thus, both growth and poly-P metabolism appear to be correlated to the redox environment. However, the poly-P metabolism is not coupled to growth in cable bacteria, as many filaments from the suboxic zone showed poly-P activity but did not grow. We hypothesize that within the oxic zone, poly-P is used to protect the cells against oxidative stress and/or as a resource to support motility, while within the suboxic zone, poly-P is involved in the metabolic regulation before cells enter a non-growing stage.
Effect of Ultraviolet-C Light-Emitting Diode Treatment on Disinfection of Norovirus in Processing Water for Reuse of Brine Water
Authors: Yoon So-Ra , Ha Sanghyun , Park Boyeon , Yang Ji-Su , Dang Yun-Mi , Ha Ji-Hyoung
Published: May 2022

Processes in the food industry that use large amounts of water have been an important cause of waterborne disease outbreaks, as they expose individuals to risks for waterborne disease transmission. Developing technologies to ensure the hygiene and safety of food-processing steps is an urgent concern from an economic perspective. Furthermore, economic benefits can be derived if the processed water can be reused under microbiologically safe conditions. Among the major manufacturing processes in the kimchi industry, the brining process for salted kimchi cabbages requires a considerable amount of brine (approximately 2,000–2,500 l/1,000 kg of raw cabbage). The aim of this study was to establish virucidal conditions with ultraviolet-C light-emitting diodes (UVC LEDs) that can ensure the microbiological safety of brine water samples with various turbidities for reuse after disinfection. For quantitative analysis, first of all, magnetic bead separation (MBS) technique was used to capture and recover the human norovirus (HuNoV) virus particles; propidium monoazide (PMA) combined with RT-qPCR (PMA-RT-qPCR) was subsequently used to selectively detect infectious norovirus. Overall, as the turbidity of the brine water samples increased, the reduction in the HuNoV genogroup II genotype 4 (HuNoV GII.4) levels by UVC LED disinfection decreased. The derived inactivation rate constant (kinac) and inactivation curves (calculated using the log-linear model) were studied as a function of turbidity based on the exponential one-phase inactivation kinetics of HuNoV. Using an impeller system set at 100 rotations/min (rpm) with an eight-nephelometric turbidity unit (NTU) sample (the lowest turbidity studied), the kinact based on the levels of viral genomic RNA concentrations was approximately 2.15-fold higher than that observed without rotation (0 rpm). Moreover, the kinact increased 1.69-fold with a 56-NTU sample (the highest turbidity studied) when the impeller system was set at 100 rpm. UVC LED treatment decreased the HuNoV GII.4 population more effectively in conjunction with the impeller system (100 rpm) than without the impeller system. Our novel findings and model provide fundamental and scientific data that may help reuse brine water and ensure its microbiological safety through disinfection. Our study highlights the benefits of UVC LED treatment in successfully eliminating waterborne viruses in a prompt, resistance-reducing, and energy-efficient approach at the laboratory scale, which lays the foundation for future plant-scale studies of UVC LED-disinfection systems.
Cytokinin Production by Azospirillum brasilense Contributes to Increase in Growth, Yield, Antioxidant, and Physiological Systems of Wheat (Triticum aestivum L.)
Authors: Zaheer Muhammad Saqlain , Ali Hafiz Haider , Iqbal Muhammad Arslan , Erinle Kehinde O. , Javed Talha , Iqbal Javaid , Hashmi Makhdoom Ibad Ullah , Mumtaz Muhammad Zahid , Salama Ehab A. A. , Kalaji Hazem M. , Wróbel Jacek , Dessoky Eldessoky S.
Published: May 2022

Plant growth-promoting rhizobacteria are known to associate with several cereal crops. The rhizobacterium exerts its function by synthesizing diverse arrays of phytohormones, such as cytokinin (Ck). However, it is difficult to determine the plant growth promotion when a bacterium produces many different kinds of phytohormones. Therefore, to assess the involvement of Ck in growth promotion and activation of antioxidant and physiological systems, we set up this experiment. Wheat seeds (Triticum aestivum L.) were inoculated with Azospirillum brasilense RA−17 (which produces zeatin type Ck) and RA−18 (which failed to produce Ck). Results showed that seed inoculation with RA−17 significantly improved growth and yield-related parameters compared with RA−18. The activity of enzymes, proline contents, and endogenous hormonal levels in wheat kernels were improved considerably with RA−17 than with RA−18. Strain RA−17 enhanced grain assimilation more than strain RA−18 resulting in a higher crop yield. These results suggest that microbial Ck production may be necessary for stimulating plant growth promotion and activating antioxidant and physiological systems in wheat.
Expression and Purification of BsaXI Restriction Endonuclease and Engineering New Specificity From BsaXI Specificity Subunit
Authors: Gidwani Sonal , Heiter Daniel , Xu Shuang-yong
Published: May 2022

It is stated that BsaXI is a Type IIB restriction endonuclease (REase) that cleaves both sides of its recognition sequence 5′↓N9 AC N5 CTCC N10↓ 3′ (complement strand 5′ ↓N7 GGAG N5 GT N12↓ 3′), creating 3-base 3′ overhangs. Here we report the cloning and expression of bsaXIS and bsaXIRM genes in Escherichia coli. The BsaXI activity was successfully reconstituted by mixing the BsaXI RM fusion subunit with the BsaXI S subunit and the enzyme complex further purified by chromatography over 6 columns. As expected, the S subunit consisted of two subdomains encoding TRD1-CR1 [target recognition domain (TRD), conserved region (CR)] for 5′ AC 3′, and TRD2-CR2 presumably specifying 5′ CTCC 3′. TRD1-CR1 (TRD2-CR2 deletion) or duplication of TRD1 (TRD1-CR1-TRD1-CR2) both generated a new specificity 5′ AC N5 GT 3′ when the S variants were complexed with the RM subunits. The circular permutation of TRD1 and TRD2, i.e., the relocation of TRD2-CR2 to the N-terminus and TRD1-CR1 to the C-terminus generated the same specificity with the RM subunits, although some wobble cleavage was detected. The TRD2 domain in the BsaXI S subunit can be substituted by a close homolog (∼59% sequence identity) and generated the same specificity. However, TRD2-CR2 domain alone failed to express in E. coli, but CR1-TRD2-CR2 protein could be expressed and purified which showed partial nicking activity with the RM subunits. This work demonstrated that like Type I restriction systems, the S subunit of a Type IIB system could also be manipulated to create new specificities. The genome mining of BsaXI TRD2 homologs in GenBank found more than 36 orphan TRD2 homologs, implying that quite a few orphan TRD2s are present in microbial genomes that may be potentially paired with other TRDs to create new restriction specificities.
The Putative Endonuclease Activity of MutL Is Required for the Segmental Gene Conversion Events That Drive Antigenic Variation of the Lyme Disease Spirochete
Authors: Castellanos Mildred , Verhey Theodore B. , Goldstein Madeleine , Chaconas George
Published: May 2022

The Lyme disease spirochete Borrelia burgdorferi, encodes an elaborate antigenic variation system that promotes the ongoing variation of a major surface lipoprotein, VlsE. Changes in VlsE are continual and always one step ahead of the host acquired immune system, which requires 1–2 weeks to generate specific antibodies. By the time this happens, new VlsE variants have arisen that escape immunosurveillance, providing an avenue for persistent infection. This antigenic variation system is driven by segmental gene conversion events that transfer information from a series of silent cassettes (vls2-16) to the expression locus, vlsE. The molecular details of this process remain elusive. Recombinational switching at vlsE is RecA-independent and the only required factor identified to date is the RuvAB branch migrase. In this work we have used next generation long-read sequencing to analyze the effect of several DNA replication/recombination/repair gene disruptions on the frequency of gene conversions at vlsE and report a requirement for the mismatch repair protein MutL. Site directed mutagenesis of mutL suggests that the putative MutL endonuclease activity is required for recombinational switching at vlsE. This is the first report of an unexpected essential role for MutL in a bacterial recombination system and expands the known function of this protein as well as our knowledge of the details of the novel recombinational switching mechanism for vlsE variation.
A Mutant Era GTPase Suppresses Phenotypes Caused by Loss of Highly Conserved YbeY Protein in Escherichia coli
Authors: Babu Vignesh M. P. , Sankari Siva , Ghosal Anubrata , Walker Graham C.
Published: May 2022

Ribosome assembly is a complex fundamental cellular process that involves assembling multiple ribosomal proteins and several ribosomal RNA species in a highly coordinated yet flexible and resilient manner. The highly conserved YbeY protein is a single-strand specific endoribonuclease, important for ribosome assembly, 16S rRNA processing, and ribosome quality control. In Escherichia coli, ybeY deletion results in pleiotropic phenotypes including slow growth, temperature sensitivity, accumulation of precursors of 16S rRNA, and impaired formation of fully assembled 70S subunits. Era, an essential highly conserved GTPase protein, interacts with many ribosomal proteins, and its depletion results in ribosome assembly defects. YbeY has been shown to interact with Era together with ribosomal protein S11. In this study, we have analyzed a suppressor mutation, era(T99I), that can partially suppress a subset of the multiple phenotypes of ybeY deletion. The era(T99I) allele was able to improve 16S rRNA processing and ribosome assembly at 37°C. However, it failed to suppress the temperature sensitivity and did not improve 16S rRNA stability. The era(T99I) allele was also unable to improve the 16S rRNA processing defects caused by the loss of ribosome maturation factors. We also show that era(T99I) increases the GroEL levels in the 30S ribosome fractions independent of YbeY. We propose that the mechanism of suppression is that the changes in Era’s structure caused by the era(T99I) mutation affect its GTP/GDP cycle in a way that increases the half-life of RNA binding to Era, thereby facilitating alternative processing of the 16S RNA precursor. Taken together, this study offers insights into the role of Era and YbeY in ribosome assembly and 16S rRNA processing events.
Molecular and Clinical Investigation of COVID-19: From Pathogenesis and Immune Responses to Novel Diagnosis and Treatment
Authors: Kashani Narjes Riahi , Azadbakht Javid , Ehteram Hassan , Kashani Hamed Haddad , Rajabi-Moghadam Hassan , Ahmad Ejaz , Nikzad Hossein , Hosseini Elahe Seyed
Published: May 2022

The coronavirus-related severe acute respiratory syndrome (SARS-CoV) in 2002/2003, the Middle East respiratory syndrome (MERS-CoV) in 2012/2013, and especially the current 2019/2021 severe acute respiratory syndrome-2 (SARS-CoV-2) negatively affected the national health systems worldwide. Different SARS-CoV-2 variants, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and recently Omicron (B.1.1.529), have emerged resulting from the high rate of genetic recombination and S1-RBD/S2 mutation/deletion in the spike protein that has an impact on the virus activity. Furthermore, genetic variability in certain genes involved in the immune system might impact the level of SARS-CoV-2 recognition and immune response against the virus among different populations. Understanding the molecular mechanism and function of SARS-CoV-2 variants and their different epidemiological outcomes is a key step for effective COVID-19 treatment strategies, including antiviral drug development and vaccine designs, which can immunize people with genetic variabilities against various strains of SARS-CoV-2. In this review, we center our focus on the recent and up-to-date knowledge on SARS-CoV-2 (Alpha to Omicron) origin and evolution, structure, genetic diversity, route of transmission, pathogenesis, new diagnostic, and treatment strategies, as well as the psychological and economic impact of COVID-19 pandemic on individuals and their lives around the world.
Mapping the O-GlcNAc Modified Proteome: Applications for Health and Disease
Authors: Burt Rajan A. , Alghusen Ibtihal M. , John Ephrame Sophiya , Villar Maria T. , Artigues Antonio , Slawson Chad
Published: May 2022

O-GlcNAc is a pleotropic, enigmatic post-translational modification (PTM). This PTM modifies thousands of proteins differentially across tissue types and regulates diverse cellular signaling processes. O-GlcNAc is implicated in numerous diseases, and the advent of O-GlcNAc perturbation as a novel class of therapeutic underscores the importance of identifying and quantifying the O-GlcNAc modified proteome. Here, we review recent advances in mass spectrometry-based proteomics that will be critical in elucidating the role of this unique glycosylation system in health and disease.
Multi-Scale Feature Fusion Convolutional Neural Network for Indoor Small Target Detection
Authors: Huang Li , Chen Cheng , Yun Juntong , Sun Ying , Tian Jinrong , Hao Zhiqiang , Yu Hui , Ma Hongjie
Published: May 2022

The development of object detection technology makes it possible for robots to interact with people and the environment, but the changeable application scenarios make the detection accuracy of small and medium objects in the practical application of object detection technology low. In this paper, based on multi-scale feature fusion of indoor small target detection method, using the device to collect different indoor images with angle, light, and shade conditions, and use the image enhancement technology to set up and amplify a date set, with indoor scenarios and the SSD algorithm in target detection layer and its adjacent features fusion. The Faster R-CNN, YOLOv5, SSD, and SSD target detection models based on multi-scale feature fusion were trained on an indoor scene data set based on transfer learning. The experimental results show that multi-scale feature fusion can improve the detection accuracy of all kinds of objects, especially for objects with a relatively small scale. In addition, although the detection speed of the improved SSD algorithm decreases, it is faster than the Faster R-CNN, which better achieves the balance between target detection accuracy and speed.