bluuebunny/crossref_metadata_2025 huggingface dataset:
New High-Resolution Modeling of the 2018 Palu Tsunami, Based on Supershear Earthquake Mechanisms and Mapped Coastal Landslides, Supports a Dual Source
Authors: Schambach Lauren , Grilli Stephan T. , Tappin David R.
Published: January 2021

The Mw 7.5 earthquake that struck Central Sulawesi, Indonesia, on September 28, 2018, was rapidly followed by coastal landslides and destructive tsunami waves within Palu Bay. Here, we present new tsunami modeling that supports a dual source mechanism from the supershear strike-slip earthquake and coastal landslides. Up until now the tsunami mechanism: earthquake, coastal landslides, or a combination of both, has remained controversial, because published research has been inconclusive; with some studies explaining most observations from the earthquake and others the landslides. Major challenges are the numerous different earthquake source models used in tsunami modeling, and that landslide mechanisms have been hypothetical. Here, we simulate tsunami generation using three published earthquake models, alone and in combination with seven coastal landslides identified in earlier work and confirmed by field and bathymetric evidence which, from video evidence, produced significant waves. To generate and propagate the tsunamis, we use a combination of two wave models, the 3D non-hydrostatic model NHWAVE and the 2D Boussinesq model FUNWAVE-TVD. Both models are nonlinear and address the physics of wave frequency dispersion critical in modeling tsunamis from landslides, which here, in NHWAVE are modeled as granular material. Our combined, earthquake and coastal landslide, simulations recreate all observed tsunami runups, except those in the southeast of Palu Bay where they were most elevated (10.5 m), as well as observations made in video recordings and at the Pantoloan Port tide gauge located within Palu Bay. With regard to the timing of tsunami impact on the coast, results from the dual landslide/earthquake sources, particularly those using the supershear earthquake models are in good agreement with reconstructed time series at most locations. Our new work shows that an additional tsunami mechanism is also necessary to explain the elevated tsunami observations in the southeast of Palu Bay. Using partial information from bathymetric surveys in this area we show that an additional, submarine landslide here, when simulated with the other coastal slides, and the supershear earthquake mechanism better explains the observations. This supports the need for future marine geology work in this area.
Drift Characteristics of DONET Pressure Sensors Determined From In-Situ and Experimental Measurements
Authors: Matsumoto Hiroyuki , Araki Eiichiro
Published: January 2021

DONET, the dense ocean-floor network system for earthquakes and tsunamis, began operations in the Nankai Trough, SW Japan, in 2010. The present study focuses on pressure sensors that are being used as tsunami meters to measure changes in hydraulic pressure. Pressure sensors typically show a drift in their readings over their operational lifespan. DONET pressure sensors can act as geodetic sensors measuring vertical crustal deformation change over time if the sensor drift can be accurately corrected. Monitoring crustal deformation before the occurrence of megathrust earthquakes is performed by discriminating between the vertical crustal deformation and the sensor drift of the pressure sensors. Therefore, in this study, we evaluated the sensor drift shown by the DONET pressure sensors since their deployment into the deep-sea, by removing the tidal component and confirming the occurrence of sensor drift. We evaluated the initial behavior of pressure sensors before deep-sea deployment using our own high-accuracy pressure standard. Our experiment involved 20-MPa pressurization for the pressure sensors under an ambient temperature of 2°C for a duration of 1 month. Some sensor drifts in our experiment correspond in rate and direction to those from the in-situ measurements determined to be in the initial stage. Our experiment suggests that the pre-deployment pressurization of pressure sensors can be an effective procedure to determine the sensor drift after sensor deployment into the deep-sea.
Opportunistic Osteoporosis Screening Reveals Low Bone Density in Patients With Screw Loosening After Lumbar Semi-Rigid Instrumentation: A Case-Control Study
Authors: Löffler Maximilian T. , Sollmann Nico , Burian Egon , Bayat Amirhossein , Aftahy Kaywan , Baum Thomas , Meyer Bernhard , Ryang Yu-Mi , Kirschke Jan S.
Published: January 2021

Objective

Decreased bone mineral density (BMD) impairs screw purchase in trabecular bone and can cause screw loosening following spinal instrumentation. Existing computed tomography (CT) scans could be used for opportunistic osteoporosis screening for decreased BMD. Purpose of this case-control study was to investigate the association of opportunistically assessed BMD with the outcome after spinal surgery with semi-rigid instrumentation for lumbar degenerative instability.

Methods

We reviewed consecutive patients that had primary surgery with semi-rigid instrumentation in our hospital. Patients that showed screw loosening in follow-up imaging qualified as cases. Patients that did not show screw loosening or—if no follow-up imaging was available (n = 8)—reported benefit from surgery ≥ 6 months after primary surgery qualified as controls. Matching criteria were sex, age, and surgical construct. Opportunistic BMD screening was performed at L1 to L4 in perioperative CT scans by automatic spine segmentation and using asynchronous calibration. Processing steps of this deep learning-driven approach can be reproduced using the freely available online-tool Anduin (https://anduin.bonescreen.de). Area under the curve (AUC) was calculated for BMD as a predictor of screw loosening.

Results

Forty-six elderly patients (69.9 ± 9.1 years)—23 cases and 23 controls—were included. The majority of surgeries involved three spinal motion segments (n = 34). Twenty patients had low bone mass and 13 had osteoporotic BMD. Cases had significantly lower mean BMD (86.5 ± 29.5 mg/cm³) compared to controls (118.2 ± 32.9 mg/cm³, p = 0.001), i.e. patients with screw loosening showed reduced BMD. Screw loosening was best predicted by a BMD < 81.8 mg/cm³ (sensitivity = 91.3%, specificity = 56.5%, AUC = 0.769, p = 0.002).

Conclusion

Prevalence of osteoporosis or low bone mass (BMD ≤ 120 mg/cm³) was relatively high in this group of elderly patients undergoing spinal surgery. Screw loosening was associated with BMD close to the threshold for osteoporosis (< 80 mg/cm³). Opportunistic BMD screening is feasible using the presented approach and can guide the surgeon to take measures to prevent screw loosening and to increase favorable outcomes.
Carbon Emission and Optimization of Energy for Sustainable Development: Rethinking the Possibility
Authors: Idowu Samuel Sunday , Mustapa Siti Indati , Joshua Segun
Published: January 2021

The adverse effects of climatic change and environmental degradation associated with the fossil energy sources from crude oil, coal, and gas have been used as a sad commentary by some transnational organizations and multilateral concern. Thus, such campaigns, actions, and concerted efforts are geared towards making them redundant while canvassing for renewable energy sources as perfect alternatives. Although gas is characterized by lower carbon emission, it is somehow not considered as a source capable of being improved upon for a sustainable energy source. Hence, this research is undertaken to project the viability of gas energy with a minimum deleterious impact on nature and humanity. With secondary data sources, the study employed a descriptive research method and employed dynamic capabilities theory as a framework. It was discovered through the study that state politicking that surrounds the current moves to jettison the fossil energy, and the multilateral concern also backs the ploy towards its abandonment, resulting in the development of cold feet towards renewing interests in engaging science, technology, and innovation to further decarbonize the gas energy. The authors suggest, among others, the need for a deliberate engagement of a cutting-edge research and innovative technology through collaborations among countries and international organizations such as OPEC and oil firms. If this is done, it will enhance its relevance even without compromising the minimum biosafety and environmental standards.
Epigenetic Alterations in Renal Cell Cancer With TKIs Resistance: From Mechanisms to Clinical Applications
Authors: Li Qinhan , Zhang Zhenan , Fan Yu , Zhang Qian
Published: January 2021

The appearance of tyrosine kinase inhibitors (TKIs) has been a major breakthrough in renal cell carcinoma (RCC) therapy. Unfortunately, a portion of patients with TKIs resistance experience disease progression after TKIs therapy. Epigenetic alterations play an important role in the development of TKIs resistance. Current evidence suggests that epigenetic alterations occur frequently in RCC patients with poor response to TKIs therapy, and modulation of them could enhance the cytotoxic effect of antitumor therapy. In this review, we summarize the currently known epigenetic alterations relating to TKIs resistance in RCC, focusing on DNA methylation, non-coding RNAs (ncRNAs), histone modifications, and their interactions with TKIs treatment. In addition, we discuss application of epigenetic alteration analyses in the clinical setting to predict prognosis of patients with TKIs treatment, and the potential use of epigenetics-based therapies to surmount TKIs resistance.
Bioinformatics Analysis Reveals MicroRNA-193a-3p Regulates ACTG2 to Control Phenotype Switch in Human Vascular Smooth Muscle Cells
Authors: Wang Weitie , Wang Yong , Piao Hulin , Li Bo , Zhu Zhicheng , Li Dan , Wang Tiance , Liu Kexiang
Published: January 2021

Aortic dissection (AD) is among the most fatal cardiovascular diseases. However, the pathogenesis of AD remains poorly understood. This study aims to integrate the microRNAs (miRNA) and mRNA profiles and use bioinformatics analyses with techniques in molecular biology to delineate the potential mechanisms involved in the development of AD. We used the human miRNA and mRNA microarray datasets GSE98770, GSE52093, and GEO2R, Venn diagram analysis, gene ontology, and protein–protein interaction networks to identify target miRNAs and mRNAs involved in AD. RNA interference, western blotting, and luciferase reporter assays were performed to validate the candidate miRNAs and mRNAs in AD tissues and human vascular smooth muscle cells (VSMCs). Furthermore, we studied vascular smooth muscle contraction in AD. In silico analyses revealed that miR-193a-3p and ACTG2 were key players in the pathogenesis of AD. miR-193a-3p was upregulated in the AD tissues. We also found that biomarkers for the contractile phenotype in VSMCs were downregulated in AD tissues. Overexpression and depletion of miR-193a-3p enhanced and suppressed VSMC proliferation and migration, respectively. Dual luciferase reporter assays confirmed that ACTG2 was a target of miR-193a-3p. ACTG2 was also downregulated in human AD tissues and VMSCs overexpressing miR-193a-3p. Taken together, miR-193a-3p may be a novel regulator of phenotypic switching in VSMCs and the miR-193a-3p/ACTG2 axis may serve as a promising diagnostic biomarker and therapeutic candidate for AD.
Dysregulated H3K27 Acetylation Is Implicated in Fatty Liver Hemorrhagic Syndrome in Chickens
Authors: Zhu Yaling , Zeng Qingjie , Li Fang , Fang Haoshu , Zhou Zhimin , Jiang Tao , Yin Chao , Wei Qing , Wang Yujie , Ruan Jiming , Huang Jianzhen
Published: January 2021

Epigenetic regulation of gene expression has been reported in the pathogenesis of metabolic disorders such as diabetes and liver steatosis in humans. However, the molecular mechanisms of fatty liver hemorrhagic syndrome (FLHS) in chickens have been rarely studied. H3K27ac chromatin immunoprecipitation coupled with high-throughput sequencing and high-throughput RNA sequencing was performed to compare genome-wide H3K27ac profiles and transcriptomes of liver tissue between healthy and FLHS chickens. In total, 1,321 differential H3K27ac regions and 443 differentially expressed genes were identified (| log2Fold change| ≥ 1 and P-value ≤ 0.05) between the two groups. Binding motifs for transcription factors involved in immune processes and metabolic homeostasis were enriched among those differential H3K27ac regions. Differential H3K27ac peaks were associated with multiple known FLHS risk genes, involved in lipid and energy metabolism (PCK1, APOA1, ANGPTL4, and FABP1) and the immune system (FGF7, PDGFRA, and KIT). Previous studies and our current results suggested that the high-energy, low-protein (HELP) diet might have an impact on histone modification and chromatin structure, leading to the dysregulation of candidate genes and the peroxisome proliferator-activated receptor (PPAR) signaling pathway, which causes excessive accumulation of fat in the liver tissue and induces the development of FLHS. These findings highlight that epigenetic modifications contribute to the regulation of gene expression and play a central regulatory role in FLHS. The PPAR signaling pathway and other genes implicated in FLHS are of great importance for the development of novel and specific therapies for FLHS-susceptible commercial laying hens.
Deciphering the Subtype Differentiation History of SARS-CoV-2 Based on a New Breadth-First Searching Optimized Alignment Method Over a Global Data Set of 24,768 Sequences
Authors: Lin Qianyu , Huang Yunchuanxiang , Jiang Ziyi , Wu Feng , Ma Lan
Published: January 2021

SARS-CoV-2 has caused a worldwide pandemic. Existing research on coronavirus mutations is based on small data sets, and multiple sequence alignment using a global-scale data set has yet to be conducted. Statistical analysis of integral mutations and global spread are necessary and could help improve primer design for nucleic acid diagnosis and vaccine development. Here, we optimized multiple sequence alignment using a conserved sequence search algorithm to align 24,768 sequences from the GISAID data set. A phylogenetic tree was constructed using the maximum likelihood (ML) method. Coronavirus subtypes were analyzed via t-SNE clustering. We performed haplotype network analysis and t-SNE clustering to analyze the coronavirus origin and spread. Overall, we identified 33 sense, 17 nonsense, 79 amino acid loss, and 4 amino acid insertion mutations in full-length open reading frames. Phylogenetic trees were successfully constructed and samples clustered into subtypes. The COVID-19 pandemic differed among countries and continents. Samples from the United States and western Europe were more diverse, and those from China and Asia mainly contained specific subtypes. Clades G/GH/GR are more likely to be the origin clades of SARS-CoV-2 compared with clades S/L/V. Conserved sequence searches can be used to segment long sequences, making large-scale multisequence alignment possible, facilitating more comprehensive gene mutation analysis. Mutation analysis of the SARS-CoV-2 can inform primer design for nucleic acid diagnosis to improve virus detection efficiency. In addition, research into the characteristics of viral spread and relationships among geographic regions can help formulate health policies and reduce the increase of imported cases.
Advances in mt-tRNA Mutation-Caused Mitochondrial Disease Modeling: Patients’ Brain in a Dish
Authors: Povea-Cabello Suleva , Villanueva-Paz Marina , Suárez-Rivero Juan M. , Álvarez-Córdoba Mónica , Villalón-García Irene , Talaverón-Rey Marta , Suárez-Carrillo Alejandra , Munuera-Cabeza Manuel , Sánchez-Alcázar José A.
Published: January 2021

Mitochondrial diseases are a heterogeneous group of rare genetic disorders that can be caused by mutations in nuclear (nDNA) or mitochondrial DNA (mtDNA). Mutations in mtDNA are associated with several maternally inherited genetic diseases, with mitochondrial dysfunction as a main pathological feature. These diseases, although frequently multisystemic, mainly affect organs that require large amounts of energy such as the brain and the skeletal muscle. In contrast to the difficulty of obtaining neuronal and muscle cell models, the development of induced pluripotent stem cells (iPSCs) has shed light on the study of mitochondrial diseases. However, it is still a challenge to obtain an appropriate cellular model in order to find new therapeutic options for people suffering from these diseases. In this review, we deepen the knowledge in the current models for the most studied mt-tRNA mutation-caused mitochondrial diseases, MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) and MERRF (myoclonic epilepsy with ragged red fibers) syndromes, and their therapeutic management. In particular, we will discuss the development of a novel model for mitochondrial disease research that consists of induced neurons (iNs) generated by direct reprogramming of fibroblasts derived from patients suffering from MERRF syndrome. We hypothesize that iNs will be helpful for mitochondrial disease modeling, since they could mimic patient’s neuron pathophysiology and give us the opportunity to correct the alterations in one of the most affected cellular types in these disorders.
Deregulation of a Cis-Acting lncRNA in Non-small Cell Lung Cancer May Control HMGA1 Expression
Authors: Stewart Greg L. , Sage Adam P. , Enfield Katey S. S. , Marshall Erin A. , Cohn David E. , Lam Wan L.
Published: January 2021

Background

Long non-coding RNAs (lncRNAs) have long been implicated in cancer-associated phenotypes. Recently, a class of lncRNAs, known as cis-acting, have been shown to regulate the expression of neighboring protein-coding genes and may represent undiscovered therapeutic action points. The chromatin architecture modification gene HMGA1 has recently been described to be aberrantly expressed in lung adenocarcinoma (LUAD). However, the mechanisms mediating the expression of HMGA1 in LUAD remain unknown. Here we investigate the deregulation of a putative cis-acting lncRNA in LUAD, and its effect on the oncogene HMGA1.

Methods

LncRNA expression was determined from RNA-sequencing data of tumor and matched non-malignant tissues from 36 LUAD patients. Transcripts with significantly deregulated expression were identified and validated in a secondary LUAD RNA-seq dataset (TCGA). SiRNA-mediated knockdown of a candidate cis-acting lncRNA was performed in BEAS-2B cells. Quantitative real-time PCR was used to observe the effects of lncRNA knockdown on the expression of HMGA1.

Results

We identified the lncRNA RP11.513I15.6, which we refer to as HMGA1-lnc, neighboring HMGA1 to be significantly downregulated in both LUAD cohorts. Conversely, we found HMGA1 significantly overexpressed in LUAD and anticorrelated with HMGA1-lnc. In vitro experiments demonstrated siRNA-mediated inhibition of HMGA1-lnc in immortalized non-malignant lung epithelial cells resulted in a significant increase in HMGA1 gene expression.

Conclusion

Our results suggest that HMGA1-lnc is a novel cis-acting lncRNA that negatively regulates HMGA1 gene expression in lung cells. Further characterization of this regulatory mechanism may advance our understanding of the maintenance of lung cancer phenotypes and uncover a novel therapeutic intervention point for tumors driven by HMGA1.
Predicting lincRNA-Disease Association in Heterogeneous Networks Using Co-regularized Non-negative Matrix Factorization
Authors: Lin Yong , Ma Xiaoke
Published: January 2021

Long intergenic non-coding ribonucleic acids (lincRNAs) are critical regulators for many complex diseases, and identification of disease-lincRNA association is both costly and time-consuming. Therefore, it is necessary to design computational approaches to predict the disease-lincRNA associations that shed light on the mechanisms of diseases. In this study, we develop a co-regularized non-negative matrix factorization (aka Cr-NMF) to identify potential disease-lincRNA associations by integrating the gene expression of lincRNAs, genetic interaction network for mRNA genes, gene-lincRNA associations, and disease-gene associations. The Cr-NMF algorithm factorizes the disease-lincRNA associations, while the other associations/interactions are integrated using regularization. Furthermore, the regularization does not only preserve the topological structure of the lincRNA co-expression network, but also maintains the links “lincRNA → gene → disease.” Experimental results demonstrate that the proposed algorithm outperforms state-of-the-art methods in terms of accuracy on predicting the disease-lincRNA associations. The model and algorithm provide an effective way to explore disease-lncRNA associations.
Vertical Migration of Pelagic and Mesopelagic Scatterers From ADCP Backscatter Data in the Southern Norwegian Sea
Authors: Cisewski Boris , Hátún Hjálmar , Kristiansen Inga , Hansen Bogi , Larsen Karin Margretha H. , Eliasen Sólvá Káradóttir , Jacobsen Jan Arge
Published: January 2021

Records of backscatter and vertical velocity obtained from moored Acoustic Doppler Current Profilers (ADCP) enabled new insights into the dynamics of deep scattering layers (DSLs) and diel vertical migration (DVM) of mesopelagic biomass between these deep layers and the near-surface photic zone in the southern Norwegian Sea. The DSL exhibits characteristic vertical movement on inter-monthly time scales, which is associated with undulations of the main pycnocline between the warm Atlantic water and the underlying colder water masses. Timing of the DVM is closely linked to the day-night light cycle—decent from the photic zone just before sunrise and ascent immediately after sunset. Seasonal variations are also evident, with the highest DVM activity and lowest depth averaged mean volume backscatter strength (MVBS) during spring. This suggests that both oceanographic and optical conditions are driving the complex dynamics of pelagic and mesopelagic activity in this region. We hypothesize that the increased abundance of calanoid copepods in the near-surface layer during spring increases the motivation for vertical migration of pelagic and mesopelagic species, which therefore can explain the increased DVM activity during this season.
The Fair Allocation of Scarce Medical Resources: A Comparative Study From Jordan
Authors: Yousef Muhannad H. , Alhalaseh Yazan N. , Mansour Razan , Sultan Hala , Alnadi Naseem , Maswadeh Ahmad , Al-Sheble Yasmeen M. , Sinokrot Raghda , Ammar Khawlah , Mansour Asem , Al-Hussaini Maysa
Published: January 2021

The allocation strategies during challenging situations among the different social groups is based on 9 principles which can be considered either individually: sickest first, waiting list, prognosis, youngest first, instrumental values, lottery, monetary contribution, reciprocity, and individual behavior, or in combination; youngest first and prognosis, for example. In this study, we aim to look into the most important prioritization principles amongst different groups in the Jordanian population, in order to facilitate the decision-making process for any potential medical crisis. We conducted an online survey that tackled how individuals would deal with three different scenarios of medical scarcity: (1) organ donation, (2) limited hospital beds during an influenza epidemic, and (3) allocation of novel therapeutics for lung cancer. In addition, a free-comment option was included at the end of the survey if respondents wished to contribute further. Seven hundred and fifty-four survey responses were gathered, including 372 males (49.3%), and 382 females (50.7%). Five groups of individuals were represented including religion scholars, physicians, medical students, allied health practitioners, and lay people. Of the five surveyed groups, four found “sickest-first” to be the most important prioritization principle in all three scenarios, and only the physicians group documented a disagreement. In the first scenario, physicians regarded “sickest-first” and “combined-criteria” to be of equal importance. In general, no differences were documented between the examined groups in comparison with lay people in the preference of options in all three scenarios; however, physicians were more likely to choose “combination” in both the second and third scenarios (OR 3.70, 95% CI 1.62–8.44, and 2.62, 95% CI 1.48–4.59; p < 0.01), and were less likely to choose “sickest-first” as the single most important prioritization principle (OR 0.57, CI 0.37–0.88, and 0.57; 95% CI 0.36–0.88; p < 0.01). Out of 100 free comments, 27 (27.0%) thought that the “social-value” of patients should also be considered, adding the 10th potential allocation principle. Our findings are concordant with literature in terms of allocating scarce medical resources. However, “social-value” appeared as an important principle that should be addressed when prioritizing scarce medical resources in Jordan.
Colonization With Staphylococcus aureus in Atopic Dermatitis Patients: Attempts to Reveal the Unknown
Authors: Ogonowska Patrycja , Gilaberte Yolanda , Barańska-Rybak Wioletta , Nakonieczna Joanna
Published: January 2021

Atopic dermatitis (AD) patients are massively colonized withStaphylococcus aureus(S. aureus) in lesional and non-lesional skin. A skin infection may become systemic if left untreated. Of interest, the incidence of multi-drug resistantS. aureus(MRSA) in AD patients is higher as compared to a healthy population, which makes treatment even more challenging. Information on the specific genetic background ofS. aureusaccompanying and/or causing AD flares would be of great importance in terms of possible treatment option development. In this review, we summarized the data on the prevalence ofS. aureusin general in AD skin, and the prevalence of specific clones that might be associated with flares of eczema. We put our special interest in the presence and role of staphylococcal enterotoxins as important virulence factors in the epidemiology of AD-derivedS. aureus. Also, we summarize the present and potentially useful future anti-staphylococcal treatment.
Phytophthora Root Rot Modifies the Composition of the Avocado Rhizosphere Microbiome and Increases the Abundance of Opportunistic Fungal Pathogens
Authors: Solís-García Itzel A. , Ceballos-Luna Oscar , Cortazar-Murillo Elvis Marian , Desgarennes Damaris , Garay-Serrano Edith , Patiño-Conde Violeta , Guevara-Avendaño Edgar , Méndez-Bravo Alfonso , Reverchon Frédérique
Published: January 2021

The structure and function of rhizosphere microbial communities are affected by the plant health status. In this study, we investigated the effect of root rot on the avocado rhizosphere microbiome, using 16S rDNA and ITS sequencing. Furthermore, we isolated potential fungal pathogens associated with root rot symptoms and assessed their pathogenic activity on avocado. We found that root rot did not affect species richness, diversity or community structure, but induced changes in the relative abundance of several microbial taxa. Root rot increased the proportion of Pseudomonadales and Burkholderiales in the rhizosphere but reduced that of Actinobacteria,Bacillusspp. and Rhizobiales. An increase in putative opportunistic fungal pathogens was also detected in the roots of symptomatic trees; the potential pathogenicity ofMortierellasp.,Fusariumspp.,Lasiodiplodiasp. andScytalidiumsp., is reported for the first time for the State of Veracruz, Mexico. Root rot also potentially modified the predicted functions carried out by rhizobacteria, reducing the proportion of categories linked with the lipid and amino-acid metabolisms whilst promoting those associated with quorum sensing, virulence, and antibiotic resistance. Altogether, our results could help identifying microbial taxa associated to the disease causal agents and direct the selection of plant growth-promoting bacteria for the development of biocontrol microbial consortia.
Inactivation of Hepatitis A Virus and Human Norovirus in Clams Subjected to Heat Treatment
Authors: Fuentes Cristina , Pérez-Rodríguez Francisco J. , Sabrià Aurora , Beguiristain Nerea , Pintó Rosa M. , Guix Susana , Bosch Albert
Published: January 2021

Bivalve mollusk contamination by enteric viruses, especially human noroviruses (HuNoV) and hepatitis A virus (HAV), is a problem with health and economic implications. The aim of the study was the evaluation of the effect of heat treatment in clams (Tawera gayi) experimentally contaminated with HuNoV using a PMA-viability RTqPCR assay to minimize measurement of non-infectious viruses, and used HAV as a model to estimate infectivity loss. Spiked clams were immersed in water at 90°C to ensure that internal meat temperature was maintained above 90°C for at least 5 min. The treatment resulted in >3.89 ± 0.24 log10TCID50/g reduction of infectious HAV, confirming inactivation. For HuNoV, RTqPCR assays showed log10reductions of 2.96 ± 0.79 and 2.56 ± 0.56, for GI and GII, respectively, and the use of PMA resulted in an additional log10reduction for GII, providing a better correlation with risk reduction. In the absence of a cell culture system which could be used to determine HuNoV infectivity reduction, a performance criteria based on PMA-RTqPCR log reduction could be used to evaluate food product safety. According to data from this study, heat treatments of clams which cause reductions >3.5 log10for GII as measured by PMA-RTqPCR assay may be regarded as an acceptable inactivation treatment, and could be set as a performance criterion to test the effectiveness of other time-temperature inactivation processes.
Substrate Pre-loading Influences Initial Colonization of GAC Biofilter Biofilms
Authors: Qin Wen , Hammes Frederik
Published: January 2021

Microbial community composition and stability affect pollutant removal for biological/granular activated carbon (BAC/GAC) processes. Here, we pre-loaded the organic carbon substrates sucrose, lactose, and Lysogeny Broth (LB) medium onto new GAC prior to use and then tested whether this substrate pre-loading promoted development of biofilms with high coverage that remained stable for prolonged operational periods. Temporal dynamics of the biomass and microbial community on the GAC were monitored via flow cytometry (FCM) and sequencing, respectively, in both batch and continuous-flow experiments. In comparison with the non-loaded GAC (control), the initial biofilm biomass on substrate-loaded GAC was 3–114 times higher, but the initial richness was considerably lower (only accounting for 13–28% of the control). The initial community compositions were significantly different between batch and continuous-flow column experiments, even when loaded with the same substrates. In the continuous-flow column experiments, both biomass and microbial community composition became remarkably similar to the control filters after 64 days of operation. From these findings, we conclude that substrate-loaded GAC could enhance initial colonization, affecting both biomass and microbial community composition. However, the biomass and composition did not remain stable during long-term operation due to continuous dispersal and competition from influent bacteria.
Characterization of Bacillus cereus Group Isolates From Human Bacteremia by Whole-Genome Sequencing
Authors: Bianco Angelica , Capozzi Loredana , Monno Maria Rosa , Del Sambro Laura , Manzulli Viviana , Pesole Graziano , Loconsole Daniela , Parisi Antonio
Published: January 2021

Members of the Bacillus cereus group are spore-forming organisms commonly associated with food poisoning and intestinal infections. Moreover, some strains of the group (i.e., B. cereus sensu stricto and Bacillus thuringiensis) can cause bacteremia in humans, mainly in immunocompromised individuals. Here we performed the genetic characterization of 17 human clinical strains belonging to B. cereus group isolated from blood culture. The whole-genome sequencing (WGS) revealed that the isolates were closely related to B. cereus sensu stricto and B. thuringiensis–type strain. Multilocus sequence typing analysis performed on the draft genome revealed the genetic diversity of our isolates, which were assigned to different sequence types. Based on panC nucleotide sequence, the isolates were grouped in the phylogenetic groups III and IV. The NHE, cer, and inhA gene cluster, entA, entFM, plcA, and plcB, were the most commonly detected virulence genes. Although we did not assess the ability to generate biofilm by phenotypic tests, we verified the prevalence of biofilm associated genes using an in silico approach. A high prevalence of pur gene cluster, xerC, clpY, codY, tasA, sipW, sinI, and sigB genes, was found. Genes related to the resistance to penicillin, trimethoprim, and ceftriaxone were identified in most of the isolates. Intriguingly, the majority of these virulence and AMR genes appeared to be evenly distributed among B. cereus s.s. isolates, as well as closely related to B. thuringiensis isolates. We showed the WGS represents a good approach to rapidly characterize B. cereus group strains, being able to give useful information about genetic epidemiology, the presence of virulence and antimicrobial genes, and finally about the potential hazard related to this underestimated risk.
Diazotrophic Bacteria Pantoea dispersa and Enterobacter asburiae Promote Sugarcane Growth by Inducing Nitrogen Uptake and Defense-Related Gene Expression
Authors: Singh Pratiksha , Singh Rajesh Kumar , Li Hai-Bi , Guo Dao-Jun , Sharma Anjney , Lakshmanan Prakash , Malviya Mukesh K. , Song Xiu-Peng , Solanki Manoj K. , Verma Krishan K. , Yang Li-Tao , Li Yang-Rui
Published: January 2021

Sugarcane is a major crop in tropical and subtropical regions of the world. In China, the application of large amounts of nitrogen (N) fertilizer to boost sugarcane yield is commonplace, but it causes substantial environmental damages, particularly soil, and water pollution. Certain rhizosphere microbes are known to be beneficial for sugarcane production, but much of the sugarcane rhizosphere microflora remains unknown. We have isolated several sugarcane rhizosphere bacteria, and 27 of them were examined for N-fixation, plant growth promotion, and antifungal activity. 16S rRNA gene sequencing was used to identify these strains. Among the isolates, several strains were found to have a relatively high activity of nitrogenase and ACC deaminase, the enzyme that reduces ethylene production in plants. These strains were found to possessnifHandacdSgenes associated with N-fixation and ethylene production, respectively. Two of these strains,Pantoea dispersa-AA7 andEnterobacter asburiae-BY4 showed maximum plant growth promotion (PGP) and nitrogenase activity, and thus they were selected for detailed analysis. The results show that they colonize different sugarcane tissues, use various growth substrates (carbon and nitrogen), and tolerate various stress conditions (pH and osmotic stress). The positive effect of AA7 and BY4 strains onnifHand stress-related gene (SuCAT,SuSOD,SuPAL,SuCHI, andSuGLU) expression and the induction of defense-related processes in two sugarcane varieties, GT11 and GXB9, showed their potential for stress amelioration and PGP. Both bacterial strains increased several sugarcane physiological parameters. i.e., plant height, shoot weight, root weight, leaf area, chlorophyll content, and photosynthesis, in plants grown under greenhouse conditions. The ability of rhizobacteria on N-fixing in sugarcane was also confirmed by a15N isotope-dilution study, and the estimate indicates a contribution of 21–35% of plant nitrogen by rhizobacterial biological N fixation (BNF). This is the first report of sugarcane growth promotion by N-fixing rhizobacteriaP. dispersaandE. asburiaestrains. Both strains could be used as biofertilizer for sugarcane to minimize nitrogen fertilizer use and better disease management.
Next-Generation Sequencing and the CRISPR-Cas Nexus: A Molecular Plant Virology Perspective
Authors: Shahid Muhammad Shafiq , Sattar Muhammad Naeem , Iqbal Zafar , Raza Amir , Al-Sadi Abdullah M.
Published: January 2021

In recent years, next-generation sequencing (NGS) and contemporary Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) technologies have revolutionized the life sciences and the field of plant virology. Both these technologies offer an unparalleled platform for sequencing and deciphering viral metagenomes promptly. Over the past two decades, NGS technologies have improved enormously and have impacted plant virology. NGS has enabled the detection of plant viruses that were previously undetectable by conventional approaches, such as quarantine and archeological plant samples, and has helped to track the evolutionary footprints of viral pathogens. The CRISPR-Cas-based genome editing (GE) and detection techniques have enabled the development of effective approaches to virus resistance. Different versions of CRISPR-Cas have been employed to successfully confer resistance against diverse plant viruses by directly targeting the virus genome or indirectly editing certain host susceptibility factors. Applications of CRISPR-Cas systems include targeted insertion and/or deletion, site-directed mutagenesis, induction/expression/repression of the gene(s), epigenome re-modeling, and SNPs detection. The CRISPR-Cas toolbox has been equipped with precision GE tools to engineer the target genome with and without double-stranded (ds) breaks or donor templates. This technique has also enabled the generation of transgene-free genetically engineered plants, DNA repair, base substitution, prime editing, detection of small molecules, and biosensing in plant virology. This review discusses the utilities, advantages, applications, bottlenecks of NGS, and CRISPR-Cas in plant virology.
SARS-CoV-2 Causes a Systemically Multiple Organs Damages and Dissemination in Hamsters
Authors: Song Zhiqi , Bao Linlin , Yu Pin , Qi Feifei , Gong Shuran , Wang Jie , Zhao Binbin , Liu Mingya , Han Yunlin , Deng Wei , Liu Jiangning , Wei Qiang , Xue Jing , Zhao Wenjie , Qin Chuan
Published: January 2021

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has spread across the world and impacted global healthcare systems. For clinical patients, COVID-19 not only induces pulmonary lesions but also affects extrapulmonary organs. An ideal animal model that mimics COVID-19 in humans in terms of the induced systematic lesions is urgently needed. Here, we report that Syrian hamster is highly permissive to SARS-CoV-2 and exhibit diffuse alveolar damage and induced extrapulmonary multi-organs damage, including spleen, lymph nodes, different segments of alimentary tract, kidney, adrenal gland, ovary, vesicular gland and prostate damage, at 3–7 days post inoculation (dpi), based on qRT-PCR,in situhybridization and immunohistochemistry detection. Notably, the adrenal gland is a novel target organ, with abundant viral RNA and antigen expression detected, accompanied by focal to diffuse inflammation. Additionally, viral RNA was also detected in the corpus luteum of the ovary, vesicular gland and prostate. Focal lesions in liver, gallbladder, myocardium, and lymph nodes were still present at 18 dpi, suggesting potential damage after disease. Our findings illustrate systemic histological observations and the viral RNA and antigen distribution in infected hamsters during disease and convalescence to recapitulate those observed in humans with COVID-19, providing helpful data to the pathophysiologic characterization of SARS-CoV-2-induced systemic disease and the development of effective treatment strategies.
Biocontrol Using Bacillus amyloliquefaciens PP19 Against Litchi Downy Blight Caused by Peronophythora litchii
Authors: Zheng Li , Huang Shilian , Hsiang Tom , Yu Guohui , Guo Dongliang , Jiang Zide , Li Jianguang
Published: January 2021

Bacillus amyloliquefaciens has been widely used in the agriculture, food, and medicine industries. Isolate PP19 was obtained from the litchi fruit carposphere and showed biocontrol efficacy against litchi downy blight (LDB) whether applied preharvest or postharvest. To further understand the underlying regulatory mechanisms, the genome of PP19 was sequenced and analyzed. The genome comprised a 3,847,565 bp circular chromosome containing 3990 protein-coding genes and 121 RNA genes. It has the smallest genome among 36 sequenced strains of B. amyloliquefaciens except for RD7-7. In whole genome phylogenetic analysis, PP19 was clustered into a group with known industrial applications, indicating that it may also produce high-yield metabolites that have yet to be identified. A large chromosome structural variation and large numbers of single nucleotide polymorphisms (SNPs) between PP19 (industrial strain) and UMAF6639 (plant-associated strain) were detected through comparative analysis, which may shed light on their functional differences. Preharvest treatment with PP19 enhanced resistance to LDB, by decreasing the plant H2O2 content and increasing the SOD activity. This is the first report of an industrial strain of B. amyloliquefaciens showing a plant-associated function and with major potential for the biocontrol of LDB.
Dual Functionality of HIV-1 Vif in APOBEC3 Counteraction and Cell Cycle Arrest
Authors: Salamango Daniel J. , Harris Reuben S.
Published: January 2021

Accessory proteins are a key feature that distinguishes primate immunodeficiency viruses such as human immunodeficiency virus type I (HIV-1) from other retroviruses. A prime example is the virion infectivity factor, Vif, which hijacks a cellular co-transcription factor (CBF-β) to recruit a ubiquitin ligase complex (CRL5) to bind and degrade antiviral APOBEC3 enzymes including APOBEC3D (A3D), APOBEC3F (A3F), APOBEC3G (A3G), and APOBEC3H (A3H). Although APOBEC3 antagonism is essential for viral pathogenesis, and a more than sufficient functional justification for Vif’s evolution, most viral proteins have evolved multiple functions. Indeed, Vif has long been known to trigger cell cycle arrest and recent studies have shed light on the underlying molecular mechanism. Vif accomplishes this function using the same CBF-β/CRL5 ubiquitin ligase complex to degrade a family of PPP2R5 phospho-regulatory proteins. These advances have helped usher in a new era of accessory protein research and fresh opportunities for drug development.
Rapid Production of a Novel Al(III) Dependent Bioflocculant Isolated From Raoultella ornithinolytica 160-1 and Its Application Combined With Inorganic Salts
Authors: Ding Rui , Luo Laipeng , Han Ruixiang , Zhang Meiling , Li Tingting , Tang Jihui , Huang Shenghai , Hong Jiong
Published: January 2021

An efficient bioflocculant-producing strain, Raoultella ornithinolytica 160-1, was identified by 16S rRNA and mass spectrometry analyses. Rapid production of bioflocculant EPS-160 was obtained with 10.01 g/(L⋅d) after optimized by response surface methodology. With the aid of Al(III), more than 90% flocculation activity of EPS-160 at 8 mg/L dosage was achieved in 5 min. Thus, this novel Al(III) dependent bioflocculant was used in combined with chemical coagulants AlCl3 to remove kaolin suspensions and wastewater treatment. The results indicated that the addition of EPS-160 in aggregation system not only largely improved the flocculation ability than the individual use of chemical flocculant (over 30 percent), but also overcome the decrease of flocculation activity due to the overdose of AlCl3 and maintained the optimum dosage of AlCl3 in a wide range (11–23 mg/L). The zeta potentials and EPS-160 structure indicated that both charge neutralization and bridging were the flocculation mechanism with kaolin. During the wastewater treatment, this composite flocculants consisted of EPS-160 and AlCl3 also had great performance for turbidity elimination. Moreover, with the properties of high flocculation activity, hyperthermal stability, pH tolerance and non-toxicity, EPS-160 shows great potential applications.
Targeting Unconventional Pathways in Pursuit of Novel Antifungals
Authors: Nguyen Stephanie , Truong Jia Q. , Bruning John B.
Published: January 2021

The impact of invasive fungal infections on human health is a serious, but largely overlooked, public health issue. Commonly affecting the immunocompromised community, fungal infections are predominantly caused by species ofCandida, Cryptococcus, andAspergillus. Treatments are reliant on the aggressive use of pre-existing antifungal drug classes that target the fungal cell wall and membrane. Despite their frequent use, these drugs are subject to unfavorable drug-drug interactions, can cause undesirable side-effects and have compromised efficacy due to the emergence of antifungal resistance. Hence, there is a clear need to develop novel classes of antifungal drugs. A promising approach involves exploiting the metabolic needs of fungi by targeted interruption of essential metabolic pathways. This review highlights potential antifungal targets including enolase, a component of the enolase-plasminogen complex, and enzymes from the mannitol biosynthesis and purine nucleotide biosynthesis pathways. There has been increased interest in the enzymes that comprise these particular pathways and further investigation into their merits as antifungal targets and roles in fungal survival and virulence are warranted. Disruption of these vital processes by targeting unconventional pathways with small molecules or antibodies may serve as a promising approach to discovering novel classes of antifungals.
The Neurocircuitry Underlying Additive Effects of Safety Instruction on Extinction Learning
Authors: Javanbakht Arash , Grasser Lana Ruvolo , Madaboosi Shantanu , Chowdury Asadur , Liberzon Israel , Diwadkar Vaibhav A.
Published: January 2021

Extinction learning is the dominant laboratory model for exposure therapy, a treatment involving both experience of safety near the feared object, and safety instructions relayed by a therapist. While the experiential aspect of extinction learning is well researched, less is known about instructed extinction learning and its neurocircuitry. Here, in 14 healthy participants we examined the neural correlates of, and the network interactions evoked by instructed extinction learning. Following fear conditioning to two CS+ stimuli, participants were instructed about the absence of the aversive unconditioned stimulus (US) for one of the CS+s (instructed CS; CS+I) but not the second CS+ (uninstructed CS+; CS+U). Early during extinction learning, greater activation was observed for the CS+I > CS+U contrast in regions including the vmPFC, dmPFC, vlPFC, and right parahippocampus. Subsequently, psychophysiological interaction (PPI) was applied to investigate functional connectivity of a seed in the vmPFC. This analyses revealed significant modulation of the dmPFC, parahippocampus, amygdala, and insula. Our findings suggest that the addition of cognitive instruction yields greater activation of emotion regulation and reappraisal networks during extinction learning. This work is a step in advancing laboratory paradigms that more accurately model exposure therapy and identifies regions which may be potential targets for neuromodulation to enhance psychotherapy effects.