bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection and possible role of proteasomes in the bronchoalveolar space of the injured lung
Authors: Majetschak M , Sorell LT , Patricelli T , Seitz DH , Knöferl MW
Published: February 2021

Recent observations suggest the presence of 20S proteasomes
(20S) in the lung epithelial lining fluid. However, the physiological
relevance of 20S in the alveolar space and possible contribution
to disease processes are unknown. Thus, we evaluated whether
extracellular proteasomes could have a pathophysiological role in
the injured lung using a rat model of lung contusion (LC).
Bronchoalveolar lavage fluids (BALF) were obtained at various
time points for up to 168 h after LC or sham procedure. Enzyme
activities, ELISA and Western blots indicated enzymatically active
20S, the 19S subunit Rpt5 and ubiquitin in BALF. 20S and
ubiquitin increased significantly after LC, peaked at 24 h and
normalized within 168 h. Mg2+/ATP-dependent peptidase
activities were detectable 6-24 h after LC. BALF after LC also
contained ubiquitin-protein-ligase activity. Addition of Mg2+/ATP
to BALF after LC led to significant proteolysis and could be
prevented with epoxomicin and EDTA. These data suggest for
the first time that the Mg2+/ATP-dependent 26S proteasome
complex exists outside the cell, is released into the lung epithelial
lining fluid after LC and contributes to the proteolysis of the bulk
of protein in the alveolar space of the injured lung. We infer that
proteasome complexes may have a pathophysiological role
during lung edema clearance.
Plasma dependent and independent accumulation of betaine in male and female rat tissues
Authors: Slow S , Lever M , Chambers ST , George PM
Published: February 2021

Tissue betaine is an intracellular osmolyte that also provides a
store of labile methyl groups. Despite these important biological
roles, there are few data regarding tissue betaine content. We
measured the betaine concentration of plasma and various
tissues (brain, heart, lungs, liver, kidney, spleen, intestine,
reproductive tissues, skeletal muscle and skin) in male and
female rats and assessed whether there were any gender-specific
differences in betaine content or distribution and whether there
was any relationship between tissue accumulation and plasma
levels. Betaine was highest in the liver and kidney with values
ranging from 1.6 to 9.5 mmol/l and 2.0 to 5.4 mmol/l,
respectively. Plasma betaine concentrations were significantly
lower than tissue levels except in the brain (≈ 25 % of plasma)
and skeletal muscle (similar to plasma). Regression analysis of
the combined male and female data revealed a significant
plasma-related accumulation of betaine in the heart, skin and
skeletal muscle, while the lung, liver, kidney, spleen, and
intestine showed significant plasma-related and plasmaindependent accumulations of betaine. The betaine content of
the skin, liver and kidney was not significantly different between
males and females, but in plasma and all tissues analyzed it was
significantly higher in males (P<0.01).
A Database of Laboratory Analogue Models of Caldera Collapse Testing the Role of Inherited Structures
Authors: Maestrelli Daniele , Bonini Marco , Corti Giacomo , Del Ventisette Chiara , Moratti Giovanna , Montanari Domenico
Published: February 2021

Since caldera collapse deformation is extremely difficult to study in real time - due to the high deformation rates that characterize this process and the difficult access to the caldera structures-analogue modeling has been widely used during past decades to integrate field data and, more recently, remote-sensing data (e.g., InSAR). However, the relationships between caldera collapse and inherited discontinuities, such as inherited crustal faults, remain poorly investigated. We therefore provide a new dataset of analogue models that aims to specifically address this issue and that can be potentially compared with literature and natural case studies worldwide. We present a dataset of 13 analogue models of caldera collapse investigating the interactions between caldera collapse processes and inherited crustal discontinuities. The dataset is composed of raw data and elaborations that can be used to qualitatively visualize and/or quantitatively analyze model deformation through the use of top-view photos, digital elevation models (DEM) and digital particle image velocimetry (DPIV).
Comparison of the Efficacy of Glucagon-Like Peptide-1 Receptor Agonists in Patients With Metabolic Associated Fatty Liver Disease: Updated Systematic Review and Meta-Analysis
Authors: Dai Yuzhao , He He , Li Sheyu , Yang Lidan , Wang Xia , Liu Zhi , An Zhenmei
Published: February 2021

Aims

Metabolic associated fatty liver disease (MAFLD) is the most common cause of chronic liver disease and is a major health and economic burden in society. New drugs are urgently needed to treat MAFLD. This systematic review and meta-analysis was conducted to evaluate the efficacy of glucagon-like peptide-1 receptor agonists (GLP-1RAs) in patients with MAFLD.

Method

We searched PubMed, Embase, Cochrane Library database, and Web of Science since 1977. We selected all randomized controlled trials which met the inclusion and exclusion criteria and evaluated the quality of evidence. A random-effects meta-analysis was performed to assess all the primary and second outcomes.

Results

Eight randomized controlled trials, including 396 patients, of which 265 patients had type 2 diabetes mellitus, met the inclusion criteria. Compared with the placebo or active agents group, the GLP-RA group showed a significant reduction in the liver fat content [weight mean difference (WMD) -3.17%, 95%CI -5.30 to -1.03, P < 0.0001], body weight (WMD -4.58 kg, 95%CI -8.07 to -1.10, P = 0.010), waist circumference (WMD -3.74 cm, 95%CI -6.73 to -0.74, P = 0.010), alanine aminotransferase (WMD -10.73 U/L, 95%CI -20.94 to -0.52, P = 0.04), γ- glutamyl transferase (WMD -12.25 U/L,95% -18.85 to -5.66, P = 0.0003, with I²=23%), fasting blood glucose (MD, -0.36 mmol/L; 95%CI, -0.69 to -0.03, P = 0.030), and hemoglobin A1c (WMD -0.36%, 95%CI -0.52 to -0.19, P < 0.0001). The reported adverse events were gastrointestinal complications with no serious adverse events, and most symptoms were relieved within 1–2 weeks after dose titration.

Conclusion

GLP-RAs may improve liver injury and metabolic disorder in patients with MAFLD, regardless of the presence of type 2 diabetes mellitus. The benefits of GLP-RAs treatment outweigh the adverse effects of drugs in patients with MAFLD.
RETRACTED: Optimization of Pyrolysis Parameters for Production of Biochar From Banana Peels: Evaluation of Biochar Application on the Growth of Ipomoea aquatica
Authors: Te Wei Zun , Muhanin Kavinesh Nair Manor , Chu Yu-Ming , Selvarajoo Anurita , Singh Ajit , Ahmed Shams Forruque , Vo Dai-Viet N. , Show Pau Loke
Published: February 2021

Banana peels waste can be utilized to produce high quality biochar that can be incorporated into the soil for sustainable production of crops. This research analyzed several properties of the biochar produced from the banana peel at different temperatures, residence times and heating rates. This study focuses on the biochar yield and the EDX analysis of the biochar produced. Response surface methodology using central composite design (CCD) was used to optimize these parameters in the batch reactor pyrolysis system. These factors were operated in different ranges for banana peels, in which pyrolysis temperature (200 to 600°C), residence time (60 to 180 min) and heating rate (5 to 15°C·min−1) were varied using 20 experiments respectively. Quality of the biochar was determined based on the biochar yield and O/C ratio. The optimum biochar chosen from the CCD model was applied to several pots of Ipomoea aquatica in different biochar dosage levels of 0, 3, 9 and 15 g (0, 1, 3 and 5 wt% of soil) respectively. Pot experiment was conducted with completely randomized design (CRD) of one factor with five replications to correlate the average plant heights with the biochar dosage levels. Results showed that biochar dosage of 1% yields the highest average final Ipomoea aquatica plant height of 37.04 cm.
Construction of Circular RNA–MicroRNA–Messenger RNA Regulatory Network of Recurrent Implantation Failure to Explore Its Potential Pathogenesis
Authors: Luo Jiahuan , Zhu Li , Zhou Ning , Zhang Yuanyuan , Zhang Lirong , Zhang Ruopeng
Published: February 2021

Background: Many studies on circular RNAs (circRNAs) have recently been published. However, the function of circRNAs in recurrent implantation failure (RIF) is unknown and remains to be explored. This study aims to determine the regulatory mechanisms of circRNAs in RIF.

Methods: Microarray data of RIF circRNA (GSE147442), microRNA (miRNA; GSE71332), and messenger RNA (mRNA; GSE103465) were downloaded from the Gene Expression Omnibus (GEO) database to identify differentially expressed circRNA, miRNA, and mRNA. The circRNA–miRNA–mRNA network was constructed by Cytoscape 3.8.0 software, then the protein–protein interaction (PPI) network was constructed by STRING database, and the hub genes were identified by cytoHubba plug-in. The circRNA–miRNA–hub gene regulatory subnetwork was formed to understand the regulatory axis of hub genes in RIF. Finally, the Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the hub genes were performed by clusterProfiler package of Rstudio software, and Reactome Functional Interaction (FI) plug-in was used for reactome analysis to comprehensively analyze the mechanism of hub genes in RIF.

Results: A total of eight upregulated differentially expressed circRNAs (DECs), five downregulated DECs, 56 downregulated differentially expressed miRNAs (DEmiRs), 104 upregulated DEmiRs, 429 upregulated differentially expressed genes (DEGs), and 1,067 downregulated DEGs were identified regarding RIF. The miRNA response elements of 13 DECs were then predicted. Seven overlapping miRNAs were obtained by intersecting the predicted miRNA and DEmiRs. Then, 56 overlapping mRNAs were obtained by intersecting the predicted target mRNAs of seven miRNAs with 1,496 DEGs. The circRNA–miRNA–mRNA network and PPI network were constructed through six circRNAs, seven miRNAs, and 56 mRNAs; and four hub genes (YWHAZ, JAK2, MYH9, and RAP2C) were identified. The circRNA–miRNA–hub gene regulatory subnetwork with nine regulatory axes was formed in RIF. Functional enrichment analysis and reactome analysis showed that these four hub genes were closely related to the biological functions and pathways of RIF.

Conclusion: The results of this study provide further understanding of the potential pathogenesis from the perspective of circRNA-related competitive endogenous RNA network in RIF.
Identification of Predictor Genes for Feed Efficiency in Beef Cattle by Applying Machine Learning Methods to Multi-Tissue Transcriptome Data
Authors: Chen Weihao , Alexandre Pâmela A. , Ribeiro Gabriela , Fukumasu Heidge , Sun Wei , Reverter Antonio , Li Yutao
Published: February 2021

Machine learning (ML) methods have shown promising results in identifying genes when applied to large transcriptome datasets. However, no attempt has been made to compare the performance of combining different ML methods together in the prediction of high feed efficiency (HFE) and low feed efficiency (LFE) animals. In this study, using RNA sequencing data of five tissues (adrenal gland, hypothalamus, liver, skeletal muscle, and pituitary) from nine HFE and nine LFE Nellore bulls, we evaluated the prediction accuracies of five analytical methods in classifying FE animals. These included two conventional methods for differential gene expression (DGE) analysis (t-test and edgeR) as benchmarks, and three ML methods: Random Forests (RFs), Extreme Gradient Boosting (XGBoost), and combination of both RF and XGBoost (RX). Utility of a subset of candidate genes selected from each method for classification of FE animals was assessed by support vector machine (SVM). Among all methods, the smallest subsets of genes (117) identified by RX outperformed those chosen by t-test, edgeR, RF, or XGBoost in classification accuracy of animals. Gene co-expression network analysis confirmed the interactivity existing among these genes and their relevance within the network related to their prediction ranking based on ML. The results demonstrate a great potential for applying a combination of ML methods to large transcriptome datasets to identify biologically important genes for accurately classifying FE animals.
Lymph Node Stromal Cells From Different Draining Areas Distinctly Regulate the Development of Chronic Intestinal Inflammation
Authors: Basic Marijana , Peppermüller Pia Pascale , Bolsega Silvia , Bleich André , Bornemann Melanie , Bode Ulrike , Buettner Manuela
Published: February 2021

The balance between the responsiveness of the intestinal immune system and the gut environment is fundamental for the maintenance of intestinal homeostasis, which is required for an adequate recognition of entering antigens. The disruption of this homeostasis by exaggerated immune response to harmless antigens can lead to the development of intestinal disorders such as inflammatory bowel disease. Stromal cells are sessile non-hematopoietic cells that build the backbone of the lymph node, an important site for the immune response induction, but also contribute to immune response and tolerance induction. However, the knowledge about the role of stromal cells in the regulation of inflammatory responses is still limited. Therefore, in this study we analyzed the influence of stromal cells on the development of chronic intestinal inflammation. Here, we show that intestinal inflammation alters the immune activation of the mesenteric lymph node-derived stromal cells. Podoplanin+and CD21/35+stromal cells showed increased expression of MHC class II molecules, but CD106 expression on CD21/35+cells was reduced. Stromal cells secreted cytokines and chemokines such as CCL7 and CXCL16 influenced the gut-homing phenotype and proliferation of CD4+and CD8+T cells. Furthermore, stromal cells of peripheral lymph nodes transplanted into the mesentery attenuated colitis severity in B6-Il10-/-mice. The reduced colitis severity in these mice was associated with increased expression of IL4 and distinct activation pattern of stromal cells derived from transplanted peripheral lymph nodes. Altogether, our results demonstrate that lymph node stromal cells impact development of chronic colitis via T cell induction. Moreover, lymph node stromal cells from different draining area due to neonatally imprinted processes distinctly regulate the induction of immune responses.
Temporal Dynamics of Chronic Inflammation on the Cecal Microbiota in IL-10-/- Mice
Authors: Overstreet Anne-Marie C. , Ramer-Tait Amanda E. , Suchodolski Jan S. , Hostetter Jesse M. , Wang Chong , Jergens Albert E. , Phillips Gregory J. , Wannemuehler Michael J.
Published: February 2021

The intestinal microbiota is a critical component of mucosal health as evidenced by the fact that alterations in the taxonomic composition of the gastrointestinal microbiota are associated with inflammatory bowel diseases. To better understand how the progression of inflammation impacts the composition of the gastrointestinal microbiota, we used culture independent taxonomic profiling to identify temporal changes in the cecal microbiota of C3Bir IL-10-/- mice concomitantly with the onset and progression of colitis. This analysis revealed that IL-10-/- mice displayed a biphasic progression in disease severity, as evidenced by histopathological scores and cytokine production. Beginning at 4 weeks of age, pro-inflammatory cytokines including TNF-α, IFN-γ, IL-6, G-CSF, and IL-1α as well as chemokines including RANTES and MIP-1α were elevated in the serum of IL-10-/- mice. By 19 weeks of age, the mice developed clinical signs of disease as evidenced by weight loss, which was accompanied by a significant increase in serum levels of KC and IL-17. While the overall diversity of the microbiota of both wild type and IL-10-/- were similar in young mice, the latter failed to increase in complexity as the mice matured and experienced changes in abundance of specific bacterial taxa that are associated with inflammatory bowel disease in humans. Collectively, these results reveal that there is a critical time in young mice between four to six weeks of age when inflammation and the associated immune responses adversely affect maturation of the microbiota.
Systemic and Mucosal B and T Cell Responses Upon Mucosal Vaccination of Teleost Fish
Authors: Muñoz-Atienza Estefanía , Díaz-Rosales Patricia , Tafalla Carolina
Published: February 2021

The development of mucosal vaccines against pathogens is currently a highly explored area of research in both humans and animals. This is due to the fact that mucosal vaccines have the potential to best elicit protective responses at these mucosal surfaces, which represent the frontline of host defense, thus blocking the pathogen at its initial replication sites. However, in order to provide an efficient long-lasting protection, these mucosal vaccines have to be capable of eliciting an adequate systemic immune response in addition to local responses. In aquaculture, the need for mucosal vaccines has further practical implications, as these vaccines would avoid the individual manipulation of fish out of the water, being beneficial from both an economic and animal welfare point of view. However, how B and T cells are organized in teleost fish within these mucosal sites and how they respond to mucosally delivered antigens varies greatly when compared to mammals. For this reason, it is important to establish which mucosally delivered antigens have the capacity to induce strong and long-lasting B and T cell responses. Hence, in this review, we have summarized what is currently known regarding the adaptive immune mechanisms that are induced both locally and systemically in fish after mucosal immunization through different routes of administration including oral and nasal vaccination, anal intubation and immersion vaccination. Finally, based on the data presented, we discuss how mucosal vaccination strategies could be improved to reach significant protection levels in these species.
Bone Marrow Mesenchymal Stem Cells Ameliorate Cisplatin-Induced Renal Fibrosis via miR-146a-5p/Tfdp2 Axis in Renal Tubular Epithelial Cells
Authors: Wu Lei , Rong Chao , Zhou Qing , Zhao Xin , Zhuansun Xue-Mei , Wan Shan , Sun Mao-Min , Wang Shou-Li
Published: February 2021

Mesenchymal stem cells (MSCs) have regenerative properties in acute kidney injury (AKI). However, the potential function of MSCs in chronic kidney disease remains elusive. Renal fibrosis is the common endpoint of chronic progressive kidney diseases and causes a considerable health burden worldwide. In this study, the protective effects of bone marrow mesenchymal stem cells (BM-MSCs) were assessed in repeated administration of low-dose cisplatin-induced renal fibrosis mouse model in vivo as well as a TGF-β1-induced fibrotic model in vitro. Differentially expressed miRNAs in mouse renal tubular epithelial cells (mRTECs) regulated by BM-MSCs were screened by high-throughput sequencing. We found microRNA (miR)-146a-5p was the most significant up-regulated miRNA in mRTECs. In addition, the gene Tfdp2 was identified as one target gene of miR-146a-5p by bioinformatics analysis. The expression of Tfdp2 in the treatment of BM-MSCs on cisplatin-induced renal injury was evaluated by immunohistochemistry analysis. Our results indicate that BM-MSC attenuates cisplatin-induced renal fibrosis by regulating the miR-146a-5p/Tfdp2 axis in mRTECs.
Wnt5A-Mediated Actin Organization Regulates Host Response to Bacterial Pathogens and Non-Pathogens
Authors: Jati Suborno , Sengupta Soham , Sen Malini
Published: February 2021

Wnt5A signaling facilitates the killing of several bacterial pathogens, but not the non-pathogen E. coli DH5α. The basis of such pathogen vs. non-pathogen distinction is unclear. Accordingly, we analyzed the influence of Wnt5A signaling on pathogenic E. coli K1 in relation to non-pathogenic E. coli K12-MG1655 and E. coli DH5α eliminating interspecies variability from our study. Whereas cell internalized E. coli K1 disrupted cytoskeletal actin organization and multiplied during Wnt5A depletion, rWnt5A mediated activation revived cytoskeletal actin assembly facilitating K1 eradication. Cell internalized E. coli K12-MG1655 and E. coli DH5α, which did not perturb actin assembly appreciably, remained unaffected by rWnt5A treatment. Phagosomes prepared separately from Wnt5A conditioned medium treated K1 and K12-MG1655 infected macrophages revealed differences in the relative levels of actin and actin network promoting proteins, upholding that the Wnt5A-Actin axis operates differently for internalized pathogen and non-pathogen. Interestingly, exposure of rWnt5A treated K1 and K12-MG1655/DH5α infected macrophages to actin assembly inhibitors reversed the scenario, blocking killing of K1, yet promoting killing of both K12-MG1655 and DH5α. Taken together, our study illustrates that the state of activation of the Wnt5A/Actin axis in the context of the incumbent bacteria is crucial for directing host response to infection.
Impact of an Intervention to Control Imipenem-Resistant Acinetobacter baumannii and Its Resistance Mechanisms: An 8-Year Survey
Authors: Chen Lida , Tan Pinghai , Zeng Jianming , Yu Xuegao , Cai Yimei , Liao Kang , Guo Penghao , Chen Yili , Wu Zongwen , Qu Pinghua , Cai Renxin , Chen Cha , Huang Bin
Published: February 2021

Background

This study aimed to examine the impact of an intervention carried out in 2011 to combat multi-drug resistance and outbreaks of imipenem-resistantAcinetobacter baumannii(IRAB), and to explore its resistance mechanism.

Methods

A total of 2572 isolates ofA. baumannii, including 1673 IRAB isolates, were collected between 2007 and 2014. An intervention was implemented to controlA. baumanniiresistance and outbreaks. Antimicrobial susceptibility was tested by calculating minimal inhibitory concentrations (MICs), and outbreaks were typed using pulsed-field gel electrophoresis (PFGE). Resistance mechanisms were explored by polymerase chain reaction (PCR) and whole genome sequencing (WGS).

Results

Following the intervention in 2011, the resistance rates ofA. baumanniito almost all tested antibiotics decreased, from 85.3 to 72.6% for imipenem, 100 to 80.8% for ceftriaxone, and 45.0 to 6.9% for tigecycline. The intervention resulted in a decrease in the number (seven to five), duration (8–3 months), and departments (five to three) affected by outbreaks; no outbreaks occurred in 2011. After the intervention, onlyblaAMPC(76.47 to 100%) andblaTEM–1(75.74 to 96.92%) increased (P< 0.0001); whereasblaGES–1(32.35 to 3.07%),blaPER–1(21.32 to 1.54%),blaOXA–58(60.29 to 1.54%),carO(37.50 to 7.69%), andadeB(9.56 to 3.08%) decreased (P< 0.0001). Interestingly, the frequency of class B β-lactamase genes decreased from 91.18% (blaSPM–1) and 61.03% (blaIMP–1) to 0%, while that of class DblaOXA–23increased to 96.92% (P< 0.0001). WGS showed that the major PFGE types causing outbreaks each year (type 01, 11, 18, 23, 26, and 31) carried the same resistance genes (blaKPC–1,blaADC–25,blaOXA–66, andadeABC), AdeR-S mutations (G186V and A136V), and a partially blocked porin channel CarO. Meanwhile, plasmids harboringblaOXA–23were found after the intervention.

Conclusion

The intervention was highly effective in reducing multi-drug resistance ofA. baumanniiand IRAB outbreaks in the long term. The resistance mechanisms of IRAB may involve genes encoding β-lactamases, efflux pump overexpression, outer membrane porin blockade, and plasmids; in particular, clonal spread ofblaOXA–23was the major cause of outbreaks. Similar interventions may also help reduce bacterial resistance rates and outbreaks in other hospitals.
Starvation Alters Gut Microbiome in Black Soldier Fly (Diptera: Stratiomyidae) Larvae
Authors: Yang Fengchun , Tomberlin Jeffery K. , Jordan Heather R.
Published: February 2021

Unlike for vertebrates, the impact of starvation on the gut microbiome of invertebrates is poorly studied. Deciphering shifts in metabolically active associated bacterial communities in vertebrates has led to determining the role of the associated microbiome in the sensation of hunger and discoveries of associated regulatory mechanisms. From an invertebrate perspective, such as the black soldier fly, such information could lead to enhanced processes for optimized biomass production and waste conversion. Bacteria associated with food substrates of black soldier fly are known to impact corresponding larval life-history traits (e.g., larval development); however, whether black soldier fly larval host state (i.e., starved) impacts the gut microbiome is not known. In this study, we measured microbial community structural and functional shifts due to black soldier fly larvae starvation. Data generated demonstrate such a physiological state (i.e., starvation) does in fact impact both aspects of the microbiome. At the phylum level, community diversity decreased significantly during black soldier fly larval starvation (p= 0.0025). Genus level DESeq2 analysis identified five genera with significantly different relative abundance (q< 0.05) across the 24 and 48 H post initiation of starvation:Actinomyces,Microbacterium,Enterococcus,Sphingobacterium, andLeucobacter. Finally, we inferred potential gene function and significantly predicted functional KEGG Orthology (KO) abundance. We demonstrated the metabolically active microbial community structure and function could be influenced by host-feeding status. Such perturbations, even when short in duration (e.g., 24 H) could stunt larval growth and waste conversion due to lacking a full complement of bacteria and associated functions.
Escherichia coli Exopolysaccharides Induced by Ceftriaxone Regulated Human Gut Microbiota in vitro
Authors: Li Baiyuan , Chen Huahai , Cao Linyan , Hu Yunfei , Chen Dan , Yin Yeshi
Published: February 2021

A stable intestinal microflora is an essential prerequisite for human health. This study investigated the interaction between Escherichia coli exopolysaccharides (named EPS-m2) and the human gut microbiota (HGM) in vitro. The EPS-m2 was produced by E. coli WM3064 when treated with ceftriaxone. The monosaccharide composition analysis revealed that EPS-m2 is composed of glucuronic acid, glucose, fucose, galactose/N-acetyl glucosamine, arabinose, xylose, and ribose with a molar ratio of approximately 77:44:29:28:2:1:1. The carbohydrates, protein, and uronic acids contents in EPS-m2 was 78.6 ± 0.1%, 4.38 ± 0.11%, and 3.86 ± 0.09%, respectively. In vitro batch fermentation experiments showed that 77% of EPS-m2 could be degraded by human fecal microbiota after 72 h of fermentation. In reverse, 16S rRNA gene sequencing analysis showed that EPS-m2 increased the abundance of Alistipes, Acinetobacter, Alloprevotella, Howardella, and Oxalobacter; GC detection illustrated that EPS-m2 enhanced the production of SCFAs. These findings indicated that EPS-m2 supplementation could regulate the HGM and might facilitate modulation of human health.
Measurement of Protein Mobility in Listeria monocytogenes Reveals a Unique Tolerance to Osmotic Stress and Temperature Dependence of Diffusion
Authors: Tran Buu Minh , Prabha Haritha , Iyer Aditya , O’Byrne Conor , Abee Tjakko , Poolman Bert
Published: February 2021

Protein mobility in the cytoplasm is essential for cellular functions, and slow diffusion may limit the rates of biochemical reactions in the living cell. Here, we determined the apparent lateral diffusion coefficient (DL) of GFP in Listeria monocytogenes as a function of osmotic stress, temperature, and media composition. We find that DL is much less affected by hyperosmotic stress in L. monocytogenes than under similar conditions in Lactococcus lactis and Escherichia coli. We find a temperature optimum for protein diffusion in L. monocytogenes at 30°C, which deviates from predicted trends from the generalized Stokes-Einstein equation under dilute conditions and suggests that the structure of the cytoplasm and macromolecular crowding vary as a function of temperature. The turgor pressure of L. monocytogenes is comparable to other Gram-positive bacteria like Bacillus subtilis and L. lactis but higher in a knockout strain lacking the stress-inducible sigma factor SigB. We discuss these findings in the context of how L. monocytogenes survives during environmental transmission and interaction with the human host.
A Combined Metagenomics and Metatranscriptomics Approach to Unravel Costa Rican Cocoa Box Fermentation Processes Reveals Yet Unreported Microbial Species and Functionalities
Authors: Verce Marko , Schoonejans Jorn , Hernandez Aguirre Carlos , Molina-Bravo Ramón , De Vuyst Luc , Weckx Stefan
Published: February 2021

Cocoa fermentation is the first step in the post-harvest processing chain of cocoa and is important for the removal of the cocoa pulp surrounding the beans and the development of flavor and color precursors. In the present study, metagenomic and metatranscriptomic sequencing were applied to Costa Rican cocoa fermentation processes to unravel the microbial diversity and assess the function and transcription of their genes, thereby increasing the knowledge of this spontaneous fermentation process. Among 97 genera found in these fermentation processes, the major ones were Acetobacter, Komagataeibacter, Limosilactobacillus, Liquorilactobacillus, Lactiplantibacillus, Leuconostoc, Paucilactobacillus, Hanseniaspora, and Saccharomyces. The most prominent species were Limosilactobacillus fermentum, Liquorilactobacillus cacaonum, and Lactiplantibacillus plantarum among the LAB, Acetobacter pasteurianus and Acetobacter ghanensis among the AAB, and Hanseniaspora opuntiae and Saccharomyces cerevisiae among the yeasts. Consumption of glucose, fructose, and citric acid, and the production of ethanol, lactic acid, acetic acid, and mannitol were linked to the major species through metagenomic binning and the application of metatranscriptomic sequencing. By using this approach, it was also found that Lacp. plantarum consumed mannitol and oxidized lactic acid, that A. pasteurianus degraded oxalate, and that species such as Cellvibrio sp., Pectobacterium spp., and Paucilactobacillus vaccinostercus could contribute to pectin degradation. The data generated and results presented in this study could enhance the ability to select and develop appropriate starter cultures to steer the cocoa fermentation process toward a desired course.
Beta2 Oscillations in Hippocampal-Cortical Circuits During Novelty Detection
Authors: França Arthur S. C. , Borgesius Nils Z. , Souza Bryan C. , Cohen Michael X.
Published: February 2021

Novelty detection is a core feature of behavioral adaptation and involves cascades of neuronal responses—from initial evaluation of the stimulus to the encoding of new representations—resulting in the behavioral ability to respond to unexpected inputs. In the past decade, a new important novelty detection feature, beta2 (~20–30 Hz) oscillations, has been described in the hippocampus (HC). However, the interactions between beta2 and the hippocampal network are unknown, as well as the role—or even the presence—of beta2 in other areas involved with novelty detection. In this work, we combined multisite local field potential (LFP) recordings with novelty-related behavioral tasks in mice to describe the oscillatory dynamics associated with novelty detection in the CA1 region of the HC, parietal cortex, and mid-prefrontal cortex. We found that transient beta2 power increases were observed only during interaction with novel contexts and objects, but not with familiar contexts and objects. Also, robust theta-gamma phase-amplitude coupling was observed during the exploration of novel environments. Surprisingly, bursts of beta2 power had strong coupling with the phase of delta-range oscillations. Finally, the parietal and mid-frontal cortices had strong coherence with the HC in both theta and beta2. These results highlight the importance of beta2 oscillations in a larger hippocampal-cortical circuit, suggesting that beta2 plays a role in the mechanism for detecting and modulating behavioral adaptation to novelty.
The tRNA-Derived Fragment-3017A Promotes Metastasis by Inhibiting NELL2 in Human Gastric Cancer
Authors: Tong Linhao , Zhang Weixu , Qu Bicheng , Zhang Fei , Wu Zhonghua , Shi Jinxin , Chen Xiaowan , Song Yongxi , Wang Zhenning
Published: February 2021

tRNA-derived fragments (tRFs) are a new classification of small non-coding RNAs (sncRNAs) derived from the specific cleavage of precursors and mature tRNAs. Accumulating recent evidence has shown that tRFs are frequently abnormal in several cancers. Nevertheless, the role of tRFs in gastric cancer and its mechanism remain unclear. In this study, we found abnormal expression of tRF-3017A (derived from tRNA-Val-TAC) in gastric cancer tissues and cell lines and confirmed its effect on promoting the invasion and migration of gastric cancer cells through functional experiments in vitro. Analysis of clinicopathologic data showed patients with higher tRF-3017A were associated with significantly higher lymph node metastasis. Mechanistic investigation implies that tRF-3017A regulates the tumor suppressor gene NELL2 through forming the RNA-induced silencing complex (RISC) with Argonaute (AGO) proteins. In this study, we found that higher tRF-3017A were associated with significantly higher lymph node metastasis in gastric cancer patients and the tRF-3017A may play a role in promoting the migration and invasion of gastric cancer cells by silencing tumor suppressor NELL2.
Wilms’ Tumor 1-Associated Protein Contributes to Chemo-Resistance to Cisplatin Through the Wnt/β-Catenin Pathway in Endometrial Cancer
Authors: Xie Wenli , Liu Naifu , Wang Xiangyu , Wei Ling , Xie Wenyan , Sheng Xiugui
Published: February 2021

Background

Cisplatin remains the mainstay of endometrial cancer (EC) chemotherapy. Wilms’ tumor 1-associated protein (WTAP), playing a critical role in transcriptional and post-transcriptional regulation, has been reported as an oncogene, and its expression is elevated in multiple types of human tumors. Recent evidence has shown that the increased expression of WTAP is also closely related to chemo-resistance. However, its specific role in the susceptibility of human EC cells to cisplatin remains largely unexplored.

Methods

WTAP over-expression and WTAP depletion cell lines as well as their corresponding controls were constructed by transfection with lentivirus. Western blotting analysis and quantitative real-time polymerase chain reaction (qRT-PCR) were employed to detect the expression of WTAP. Cell proliferation assay, colony formation assay, cell cycle assay, and apoptosis analysis were adopted to evaluate the effect of WTAP on the chemo-sensitivity of EC cells to cisplatin as well as its underlying mechanism. Immunofluorescence staining was used to assess the translocation of β-catenin. Moreover, a subcutaneous xenograft tumor model was established to assess the effect of WTAP on tumor growth after cisplatin treatment.

Results

Depletion of WTAP in RL95-2 cells significantly enhanced the chemo-susceptibility of cells to cisplatin and increased the cell apoptosis, while WTAP over-expression in ARK-2 cells exhibited the opposite effects. Additionally, WTAP depletion significantly suppressed xenograft-tumor growth and enhanced sensitivity and apoptosis of tumor cells in vivo. Mechanistic analysis exhibited that WTAP over-expression facilitated the cytoplasm-to-nucleus translocation of β-catenin and enhanced the GSK3β phosphorylation at Ser9, while WTAP depletion revealed the opposite results, indicating that WTAP rendered chemo-resistance of EC cells to cisplatin by promoting the Wnt/β-catenin pathway.

Conclusions

WTAP might promote the chemo-resistance of EC cells to cisplatin through activating the Wnt/β-catenin pathway. Collectively, our findings offered novel insights into EC treatment.
Chronic Metformin Therapy is Associated with a Lower Risk of Hemorrhoid in Patients with Type 2 Diabetes Mellitus
Authors: Tseng Chin-Hsiao
Published: February 2021

Background: Metformin has anti-inflammatory property and reduces the risk of varicose vein in our previous study.

Aim: To investigate the risk of hemorrhoid, another common disease involving the hemorrhoidal venous plexus, in ever vs. never users of metformin in patients with type 2 diabetes mellitus.

Methods: This is a population-based retrospective cohort study. Patients with new-onset type 2 diabetes mellitus during 1999–2005 were enrolled from Taiwan’s National Health Insurance. All patients who were alive on January 1, 2006 were followed up until December 31, 2011. Analyses were conducted in both an unmatched cohort of 152,347 ever users and 19,523 never users and in 19,498 propensity score (PS)-matched pairs of ever and never users. Traditional Cox regression and Cox regression incorporated with the inverse probability of treatment weighting (IPTW) using the PS were used to estimate hazard ratios.

Results: New-onset hemorrhoid was diagnosed in 8,211 ever users and 2025 never users in the unmatched cohort and in 1,089 ever users and 2022 never users in the matched cohort. The hazard ratio for ever vs. never users derived from the traditional Cox regression was 0.464 (95% confidence interval: 0.440–0.488) in the unmatched cohort; and was 0.488 (0.453–0.525) in the matched cohort. In the IPTW models, the hazard ratio was 0.464 (0.442–0.487) in the unmatched cohort and was 0.492 (0.457–0.530) in the matched cohort. A dose-response pattern was observed while comparing the tertiles of cumulative duration, cumulative dose and defined daily dose of metformin therapy to never users in all analyses. A risk reduction of approximately 40–50% was consistently observed in various sensitivity analyses.

Conclusion: Chronic therapy with metformin in patients with type 2 diabetes mellitus is associated with a lower risk of hemorrhoid.
Borders as Crossroads: The Diverging Routes of Herbal Knowledge of Romanians Living on the Romanian and Ukrainian Sides of Bukovina
Authors: Mattalia Giulia , Stryamets Nataliya , Grygorovych Anya , Pieroni Andrea , Sõukand Renata
Published: February 2021

Cross-border and cross-cultural ethnomedicine are novel ways to address the evolution of local ecological knowledge. As is widely acknowledged, ethnomedicinal knowledge is not static, but evolves according to several factors, including changes in ecological availability and socioeconomic conditions, and yet the effect of the political context on medicinal knowledge remains largely underexplored. Bukovina, a small region of Eastern Europe that has been divided by a border since the 1940s and is currently part of both Romania and Ukraine, represents a unique case study in which to address the impact of political contexts on ethnomedicinal knowledge. The aim of this study was to compare plant-based medicinal uses among Romanians living on the two sides of the Romanian–Ukrainian border. In addition, we performed cross-cultural and cross-border analysis with published data on the ethnomedicine of the neighboring ethnolinguistic group of Hutsuls. We conducted 59 semistructured interviews with conveniently selected Romanians living in both Romanian and Ukrainian Bukovina. We elicited preparations for treating different ailments and disorders by naming each part of the body. We also asked about the sources of this medicinal knowledge. We documented the medicinal use of 108 plant taxa belonging to 45 families. Fifty-four taxa were common to both Romanian communities; 20 were only found among Romanians living in Romania and 34 only among Romanians living in Ukraine. However, the number of recorded uses was higher among Romanians living in Romania, revealing that they make consistent use of local medicinal plants, and Romanians living in Ukrainian Bukovina use more taxa but less consistently. Comparison with the data published in our study on neighboring Hutsuls shows that medicinal knowledge is more homogeneous among Hutsuls and Romanians living in Ukraine, yet many similar uses were found among Romanian communities across the border. We argue that the 50 years during which Ukrainian Bukovina was part of the USSR resulted in the integration of standard pan-Soviet elements as evidenced by several plant uses common among the groups living in Ukraine yet not among Hutsuls and Romanians living in Romania.
First-Principles Investigation on Electrochemical Performance of Na-Doped LiNi1/3Co1/3Mn1/3O2
Authors: Gao Yumei , Shen Kaixiang , Liu Ping , Liu Liming , Chi Feng , Hou Xianhua , Yang Wenxin
Published: February 2021

The cathode material LiNi1/3Co1/3Mn1/3O2 for lithium-ion battery has a better electrochemical property than LiCoO2. In order to improve its electrochemical performance, Na-doped LiNi1/3Co1/3Mn1/3O2 is one of the effective modifications. In this article, based on the density functional theory of the first-principles, the conductivity and the potential energy of the Na-doped LiNi1/3Co1/3Mn1/3O2 are calculated with Materials Studio and Nanodcal, respectively. The calculation results of the band gap, partial density of states, formation energy of intercalation of Li+, electron density difference, and potential energy of electrons show that the new cathode material Li1−xNax Ni1/3Co1/3Mn1/3O2 has a better conductivity when the Na-doping amount is x = 0.05 mol. The 3D and 2D potential maps of Li1−xNaxNi1/3Co1/3Mn1/3O2 can be obtained from Nanodcal. The maps demonstrate that Na-doping can reduce the potential well and increase the removal rate of lithium-ion. The theoretical calculation results match well with experimental results. Our method and analysis can provide some theoretical proposals for the electrochemical performance study of doping. This method can also be applied to the performance study of new optoelectronic devices.
Hybrid Incompatibility of the Plant Immune System: An Opposite Force to Heterosis Equilibrating Hybrid Performances
Authors: Calvo-Baltanás Vanesa , Wang Jinge , Chae Eunyoung
Published: February 2021

Hybridization is a core element in modern rice breeding as beneficial combinations of two parental genomes often result in the expression of heterosis. On the contrary, genetic incompatibility between parents can manifest as hybrid necrosis, which leads to tissue necrosis accompanied by compromised growth and/or reduced reproductive success. Genetic and molecular studies of hybrid necrosis in numerous plant species revealed that such self-destructing symptoms in most cases are attributed to autoimmunity: plant immune responses are inadvertently activated in the absence of pathogenic invasion. Autoimmunity in hybrids predominantly occurs due to a conflict involving a member of the major plant immune receptor family, the nucleotide-binding domain and leucine-rich repeat containing protein (NLR; formerly known as NBS-LRR). NLR genes are associated with disease resistance traits, and recent population datasets reveal tremendous diversity in this class of immune receptors. Cases of hybrid necrosis involving highly polymorphic NLRs as major causes suggest that diversifiedRgene repertoires found in different lineages would require a compatible immune match for hybridization, which is a prerequisite to ensure increased fitness in the resulting hybrids. In this review, we overview recent genetic and molecular findings on hybrid necrosis in multiple plant species to provide an insight on how the trade-off between growth and immunity is equilibrated to affect hybrid performances. We also revisit the cases of hybrid weakness in which immune system components are found or implicated to play a causative role. Based on our understanding on the trade-off, we propose that the immune system incompatibility in plants might play an opposite force to restrict the expression of heterosis in hybrids. The antagonism is illustrated under the plant fitness equilibrium, in which the two extremes lead to either hybrid necrosis or heterosis. Practical proposition from the equilibrium model is that breeding efforts for combining enhanced disease resistance and high yield shall be achieved by balancing the two forces. Reverse breeding toward utilizing genomic data centered on immune components is proposed as a strategy to generate elite hybrids with balanced immunity and growth.
Molecular Mechanisms of Autophagy Regulation in Plants and Their Applications in Agriculture
Authors: Cao Jia-Jian , Liu Chen-Xu , Shao Shu-Jun , Zhou Jie
Published: February 2021

Autophagy is a highly conserved cellular process for the degradation and recycling of unnecessary cytoplasmic components in eukaryotes. Various studies have shown that autophagy plays a crucial role in plant growth, productivity, and survival. The extensive functions of plant autophagy have been revealed in numerous frontier studies, particularly those regarding growth adjustment, stress tolerance, the identification of related genes, and the involvement of metabolic pathways. However, elucidation of the molecular regulation of plant autophagy, particularly the upstream signaling elements, is still lagging. In this review, we summarize recent progress in research on the molecular mechanisms of autophagy regulation, including the roles of protein kinases, phytohormones, second messengers, and transcriptional and epigenetic control, as well as the relationship between autophagy and the 26S proteasome in model plants and crop species. We also discuss future research directions for the potential application of autophagy in agriculture.
High Throughput Field Phenotyping for Plant Height Using UAV-Based RGB Imagery in Wheat Breeding Lines: Feasibility and Validation
Authors: Volpato Leonardo , Pinto Francisco , González-Pérez Lorena , Thompson Iyotirindranath Gilberto , Borém Aluízio , Reynolds Matthew , Gérard Bruno , Molero Gemma , Rodrigues Francelino Augusto
Published: February 2021

Plant height (PH) is an essential trait in the screening of most crops. While in crops such as wheat, medium stature helps reduce lodging, tall plants are preferred to increase total above-ground biomass. PH is an easy trait to measure manually, although it can be labor-intense depending on the number of plots. There is an increasing demand for alternative approaches to estimate PH in a higher throughput mode. Crop surface models (CSMs) derived from dense point clouds generated via aerial imagery could be used to estimate PH. This study evaluates PH estimation at different phenological stages using plot-level information from aerial imaging-derived 3D CSM in wheat inbred lines during two consecutive years. Multi-temporal and high spatial resolution images were collected by fixed-wing (PlatFW) and multi-rotor (PlatMR) unmanned aerial vehicle (UAV) platforms over two wheat populations (50 and 150 lines). The PH was measured and compared at four growth stages (GS) using ground-truth measurements (PHground) and UAV-based estimates (PHaerial). The CSMs generated from the aerial imagery were validated using ground control points (GCPs) as fixed reference targets at different heights. The results show that PH estimations using PlatFW were consistent with those obtained from PlatMR, showing some slight differences due to image processing settings. The GCPs heights derived from CSM showed a high correlation and low error compared to their actual heights (R2 ≥ 0.90, RMSE ≤ 4 cm). The coefficient of determination (R2) between PHground and PHaerial at different GS ranged from 0.35 to 0.88, and the root mean square error (RMSE) from 0.39 to 4.02 cm for both platforms. In general, similar and higher heritability was obtained using PHaerial across different GS and years and ranged according to the variability, and environmental error of the PHground observed (0.06–0.97). Finally, we also observed high Spearman rank correlations (0.47–0.91) and R2 (0.63–0.95) of PHaerial adjusted and predicted values against PHground values. This study provides an example of the use of UAV-based high-resolution RGB imagery to obtain time-series estimates of PH, scalable to tens-of-thousands of plots, and thus suitable to be applied in plant wheat breeding trials.