bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic Dissection of the Regulatory Mechanisms of Ace2 in the Infected Mouse Lung
Authors: Xu Fuyi , Gao Jun , Bergmann Silke , Sims Amy C. , Ashbrook David G. , Baric Ralph S. , Cui Yan , Jonsson Colleen B. , Li Kui , Williams Robert W. , Schughart Klaus , Lu Lu
Published: January 2021

Acute lung injury (ALI) is an important cause of morbidity and mortality after viral infections, including influenza A virus H1N1, SARS-CoV, MERS-CoV, and SARS-CoV-2. The angiotensin I converting enzyme 2 (ACE2) is a key host membrane-bound protein that modulates ALI induced by viral infection, pulmonary acid aspiration, and sepsis. However, the contributions of ACE2 sequence variants to individual differences in disease risk and severity after viral infection are not understood. In this study, we quantified H1N1 influenza-infected lung transcriptomes across a family of 41 BXD recombinant inbred strains of mice and both parents—C57BL/6J and DBA/2J. In response to infection Ace2 mRNA levels decreased significantly for both parental strains and the expression levels was associated with disease severity (body weight loss) and viral load (expression levels of viral NA segment) across the BXD family members. Pulmonary RNA-seq for 43 lines was analyzed using weighted gene co-expression network analysis (WGCNA) and Bayesian network approaches. Ace2 not only participated in virus-induced ALI by interacting with TNF, MAPK, and NOTCH signaling pathways, but was also linked with high confidence to gene products that have important functions in the pulmonary epithelium, including Rnf128, Muc5b, and Tmprss2. Comparable sets of transcripts were also highlighted in parallel studies of human SARS-CoV-infected primary human airway epithelial cells. Using conventional mapping methods, we determined that weight loss at two and three days after viral infection maps to chromosome X—the location of Ace2. This finding motivated the hierarchical Bayesian network analysis, which defined molecular endophenotypes of lung infection linked to Ace2 expression and to a key disease outcome. Core members of this Bayesian network include Ace2, Atf4, Csf2, Cxcl2, Lif, Maml3, Muc5b, Reg3g, Ripk3, and Traf3. Collectively, these findings define a causally-rooted Ace2 modulatory network relevant to host response to viral infection and identify potential therapeutic targets for virus-induced respiratory diseases, including those caused by influenza and coronaviruses.
LAG3’s Enigmatic Mechanism of Action
Authors: Graydon Colin G. , Mohideen Shifa , Fowke Keith R.
Published: January 2021

LAG3 is an important immune checkpoint with relevance in cancer, infectious disease and autoimmunity. However, despite LAG3’s role in immune exhaustion and the great potential of LAG3 inhibition as treatment, much remains unknown about its biology, particularly its mechanism of action. This review describes the knowns, unknowns and controversies surrounding LAG3. This includes examination of how LAG3 is regulated transcriptionally and post-translationally by endocytosis and proteolytic cleavage. We also discuss the interactions of LAG3 with its ligands and the purpose thereof. Finally, we review LAG3’s mechanism of action, including the roles of LAG3 intracellular motifs and the lack of a role for CD4 competition. Overall, understanding the biology of LAG3 can provide greater insight on LAG3 function, which may broaden the appreciation for LAG3’s role in disease and potentially aid in the development of targeted therapies.
Applications and Prospects of Microfluidic Chips in Orthopaedic Diseases
Authors: Yang Xiran , Tang Qiangqiang , Lai Chen , Wu Kai , Shi Xuetao
Published: January 2021

With the advent of an ageing society, bone-related diseases such as osteoporosis have become a major human health issue, and osteolytic lesions caused by cancer bone metastasis have always had a poor prognosis. Researchers have studied the pathogenesis of these orthopaedic diseases to obtain efficacious treatments. Microfluidic chip technology is a popular technology developed in recent years. This technology can build an experimental platform for a bionic in vivo microenvironment in vitro, which has been favored by an increasing number of researchers. In this review, we will take osteoporosis and cancer bone metastasis as examples to illustrate the pathogenesis, introduce the latest progress in the research of orthopaedics-related diseases of the microfluidic model, and describe the current approaches and their limitations.
Is Community Relevance Enough? Civic and Science Identity Impact of Microbiology CUREs Focused on Community Environmental Justice
Authors: Adkins-Jablonsky Sarah J. , Akscyn Rob , Bennett Brad C. , Roberts Qutia , Morris J. Jeffrey
Published: January 2021

Course-based undergraduate research experiences (CUREs) often involve a component where the outcomes of student research are broadly relevant to outside stakeholders. We wanted to see if building courses around an environmental justice issue relevant to the local community would impact students’ sense of civic engagement and appreciation of the relevance of scientific research to the community. In this quasi-experimental study, we assessed civic engagement and scientific identity gains (N = 98) using pre- and post-semester surveys and open-ended interview responses in three different CUREs taught simultaneously at three different universities. All three CURES were focused on an environmental heavy metal pollution issue predominantly affecting African–Americans in Birmingham, Alabama. While we found increases in students’ sense of science efficacy and identity, our team was unable to detect meaningful changes in civic engagement levels, all of which were initially quite high. However, interviews suggested that students were motivated to do well in their research because the project was of interest to outside stakeholders. Our observations suggest that rather than directly influencing students’ civic engagement, the “broadly relevant” component of our CUREs engaged their pre-existing high levels of engagement to increase their engagement with the material, possibly influencing gains in science efficacy and science identity. Our observations are consistent with broader community relevance being an important component of CURE success, but do not support our initial hypothesis that CURE participation would influence students’ attitudes toward the civic importance of science.
Utilization of Phenol as Carbon Source by the Thermoacidophilic Archaeon Saccharolobus solfataricus P2 Is Limited by Oxygen Supply and the Cellular Stress Response
Authors: Wolf Jacqueline , Koblitz Julia , Albersmeier Andreas , Kalinowski Jörn , Siebers Bettina , Schomburg Dietmar , Neumann-Schaal Meina
Published: January 2021

Present in many industrial effluents and as common degradation product of organic matter, phenol is a widespread compound which may cause serious environmental problems, due to its toxicity to animals and humans. Degradation of phenol from the environment by mesophilic bacteria has been studied extensively over the past decades, but only little is known about phenol biodegradation at high temperatures or low pH. In this work we studied phenol degradation in the thermoacidophilic archaeonSaccharolobus solfataricusP2 (basonym:Sulfolobus solfataricus) under extreme conditions (80°C, pH 3.5). We combined metabolomics and transcriptomics together with metabolic modeling to elucidate the organism’s response to growth with phenol as sole carbon source. AlthoughS. solfataricusis able to utilize phenol for biomass production, the carbon source induces profound stress reactions, including genome rearrangement as well as a strong intracellular accumulation of polyamines. Furthermore, computational modeling revealed a 40% higher oxygen demand for substrate oxidation, compared to growth on glucose. However, only 16.5% of oxygen is used for oxidation of phenol to catechol, resulting in a less efficient integration of carbon into the biomass. Finally, our data underlines the importance of the phenolmeta-degradation pathway inS. solfataricusand enables us to predict enzyme candidates involved in the degradation processes downstream of 2-hydroxymucconic acid.
Effects of Dietary Isomaltooligosaccharide Levels on the Gut Microbiota, Immune Function of Sows, and the Diarrhea Rate of Their Offspring
Authors: Zhang Longlin , Gu Xueling , Wang Jie , Liao Shuang , Duan Yehui , Li Hao , Song Zehe , He Xi , Fan Zhiyong
Published: January 2021

To investigate the effects of dietary isomaltooligosaccharide (IMO) levels on the gut microbiota, immune function of sows, and the diarrhea rate of their offspring, 120 multiparous gestating pig improvement company (PIC) sows with similar body conditions were selected and fed 1 of 6 diets: a basal diet with no supplement (control, CON), or a diet supplemented with 2.5 g/kg, 5.0 g/kg, 10.0 g/kg, 20.0 g/kg, or 40.0 g/kg IMO (IMO1, IMO2, IMO3, IMO4, or IMO5 group, respectively). Results showed that dietary treatments did not affect the reproductive performance and colostrum composition of sows (P > 0.05). However, compared to the CON, IMO reduced the diarrhea rate of suckling piglets (P < 0.05) and improved the concentrations of colostrum IgA, IgG, and IgM (P < 0.05). Moreover, IMO decreased the concentrations of serum D-lactate (D-LA) and lipopolysaccharides (LPS) at farrowing and day 18 of lactation (L18) (P < 0.05). High-throughput pyrosequencing of the 16S rRNA demonstrated that IMO shaped the composition of gut microbiota in different reproductive stages (day 107 of gestation, G107; day 10 of lactation, L10) (P < 0.05). At the genus level, the relative abundance of g_Parabacteroides and g_Slackia in G107 and g_Unclassified_Peptostreptococcaceae, g_Turicibacter, g_Sarcina, and g_Coprococcus in L10 was increased in IMO groups but the g_YRC22 in G107 was decreased in IMO groups relative to the CON group (P < 0.05). Furthermore, the serum D-LA and LPS were negatively correlated with the genus g_Akkermansia and g_Parabacteroides but positively correlated with the genus g_YRC22 and g_Unclassified_Peptostreptococcaceae. Additionally, the colostrum IgA, IgG, and IgM of sows were positively correlated with the genus g_Parabacteroides, g_Sarcina, and g_Coprococcus but negatively correlated with the genus g_YRC22. These findings indicated that IMO could promote the immune activation and had a significant influence in sows’ gut microbiota during perinatal period, which may reduce the diarrhea rate of their offspring.
Isolation and Characterization of Enterococcus faecalis-Infecting Bacteriophages From Different Cheese Types
Authors: del Rio Beatriz , Sánchez-Llana Esther , Martínez Noelia , Fernández María , Ladero Victor , Alvarez Miguel A.
Published: January 2021

Enterococci are a diverse group of Gram-positive, lactic acid bacteria (LAB). They are found in many environments, including fermented foods, in which they could constitute a health threat since they produce biogenic amines, which consumption can lead to intoxication. Moreover, enterococci has also emerged as an important hospital-acquired pathogens via its acquisition of antimicrobial resistance. Bacteriophages possess features that make them optimal biotechnological weapons for controlling bacterial growth in disease and food spoilage contexts. However, no silver bullet bacteriophage exists that can eliminate all the undesirable bacteria in a complex environment. Rather, a combination of phages with different host ranges would be required which implies the need for large collections of diverse phages. This work reports the isolation of several Enterococcus faecalis-infecting bacteriophages from different types of cheese, along with the range of E. faecalis strains of diverse origin (from dairy to clinical environments) they are able to infect. The isolated phages showed a large diversity regarding the number and origin of strains they infect. Some of these phages were subjected to morphological and genomic characterization which confirmed their diversity and showed they belong to different families and genera. The present findings increase the potential arsenal for the bacteriophage-based biocontrol of harmful E. faecalis populations.
Peeling the Layers Away: The Genomic Characterization of Bacillus pumilus 64-1, an Isolate With Antimicrobial Activity From the Marine Sponge Plakina cyanorosea (Porifera, Homoscleromorpha)
Authors: Freitas-Silva Jéssyca , de Oliveira Bruno Francesco Rodrigues , Vigoder Felipe de Mello , Muricy Guilherme , Dobson Alan D. W. , Laport Marinella Silva
Published: January 2021

Bacillus pumilus64-1, a bacterial strain isolated from the marine spongePlakina cyanorosea, which exhibits antimicrobial activity against both pathogenic and drug-resistant Gram-positive and Gram-negative bacteria. This study aimed to conduct an in-depth genomic analysis of this bioactive sponge-derived strain. The nearly complete genome of strain 64-1 consists of 3.6 Mbp (41.5% GC), which includes 3,705 coding sequences (CDS). An open pangenome was observed when limiting to the type strains of theB. pumilusgroup and aquatic-derivedB. pumilusrepresentatives. The genome appears to encode for at least 12 potential biosynthetic gene clusters (BGCs), including both types I and III polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and one NRPS-T1PKS hybrid, among others. In particular, bacilysin and other bacteriocin-coding genes were found and may be associated with the detected antimicrobial activity. Strain 64-1 also appears to possess a broad repertoire of genes encoding for plant cell wall-degrading carbohydrate-active enzymes (CAZymes). A myriad of genes which may be involved in various process required by the strain in its marine habitat, such as those encoding for osmoprotectory transport systems and the biosynthesis of compatible solutes were also present. Several heavy metal tolerance genes are also present, together with various mobile elements including a region encoding for a type III-B Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, four prophage segments and transposase elements. This is the first report on the genomic characterization of a cultivable bacterial member of thePlakina cyanoroseaholobiont.
Distinct Microbial Communities in Adjacent Rock and Soil Substrates on a High Arctic Polar Desert
Authors: Choe Yong-Hoe , Kim Mincheol , Lee Yoo Kyung
Published: January 2021

Understanding microbial niche variability in polar regions can provide insights into the adaptive diversification of microbial lineages in extreme environments. Compositions of microbial communities in Arctic soils are well documented but a comprehensive multidomain diversity assessment of rocks remains insufficiently studied. In this study, we obtained two types of rocks (sandstone and limestone) and soils around the rocks in a high Arctic polar desert (Svalbard), and examined the compositions of archaeal, bacterial, fungal, and protistan communities in the rocks and soils. The microbial community structure differed significantly between rocks and soils across all microbial groups at higher taxonomic levels, indicating that Acidobacteria, Gemmatimonadetes, Latescibacteria, Rokubacteria, Leotiomycetes, Pezizomycetes, Mortierellomycetes, Sarcomonadea, and Spirotrichea were more abundant in soils, whereas Cyanobacteria, Deinococcus-Thermus, FBP, Lecanoromycetes, Eurotiomycetes, Trebouxiophyceae, and Ulvophyceae were more abundant in rocks. Interestingly, fungal communities differed markedly between two different rock types, which is likely to be ascribed to the predominance of distinct lichen-forming fungal taxa (Verrucariales in limestone, and Lecanorales in sandstone). This suggests that the physical or chemical properties of rocks could be a major determinant in the successful establishment of lichens in lithic environments. Furthermore, the biotic interactions among microorganisms based on co-occurrence network analysis revealed that Polyblastia and Verrucaria in limestone, and Atla, Porpidia, and Candelariella in sandstone play an important role as keystone taxa in the lithic communities. Our study shows that even in niches with the same climate regime and proximity to each other, heterogeneity of edaphic and lithic niches can affect microbial community assembly, which could be helpful in comprehensively understanding the effects of niche on microbial assembly in Arctic terrestrial ecosystems.
Three Novel Entomopathogenic Fungi From China and Thailand
Authors: Wei De-Ping , Wanasinghe Dhanushka N. , Xu Jian-Chu , To-anun Chaiwat , Mortimer Peter E. , Hyde Kevin D. , Elgorban Abdallah M. , Madawala Sumedha , Suwannarach Nakarin , Karunarathna Samantha C. , Tibpromma Saowaluck , Lumyong Saisamorn
Published: January 2021

Entomopathogenic fungi are ubiquitous in tropical rainforests and feature a high level of diversity. This group of fungi not only has important ecological value but also medicinal value. Nevertheless, they are often ignored, and many unknown species have yet to be discovered and described. The present study aims to contribute to the taxonomical and phylogenetic understanding of the genus Paraisaria by describing three new species collected from Guizhou and Yunnan Provinces in China and Krabi Province in Thailand. The three novel species named Paraisaria alba, P. arcta, and P. rosea share similar morphologies as those in the genus Paraisaria, containing solitary, simple, fleshy stroma, completely immersed perithecia and cylindrical asci with thickened caps and filiform ascospores that often disarticulate at maturity. Phylogenetic analyses of combined LSU, SSU, TEF1-α, RPB1, RPB2, and ITS sequence data confirm their placement in the genus Paraisaria. In this study, the three entomopathogenic taxa are comprehensively described with color photographs and phylogenetic analyses. A synopsis table and a key to all treated species of Paraisaria are also included.
Isolation and Genetic Identification of Endophytic Lactic Acid Bacteria From the Amazonian Açai Fruits: Probiotics Features of Selected Strains and Their Potential to Inhibit Pathogens
Authors: Abe Sato Suenne Taynah , Marques Joana Montezano , da Luz de Freitas André , Sanches Progênio Raphaela Cristina , Nunes Márcio Roberto Teixeira , Mota de Vasconcelos Massafra Janaína , Gomes Moura Fábio , Rogez Hervé
Published: January 2021

The açai palm (Euterpe oleracea) is native to the Amazon basin, a humid tropical forest. High levels of total mesophilic bacteria with high diversity have been consistently reported in açai fruits. As local consumers have few digestive problems, the results of the present study reveal the lactic acid bacteria (LAB) recovered from açai fruits with characteristics that suggest they are possible candidates for probiotics and antagonistic potential against pathogens for the first time. Açai fruits were sampled from five different locations in the Eastern Amazonia floodplains. Sixty-six isolates were recovered from fruits and tested for some probiotic characteristics following FAO/WHO guidelines. Approximately 65% of the isolates showed no catalase or oxidase activity, Gram-positive staining or cocci and bacilli cell morphology. Furthermore, 48% of the isolates demonstrated preliminary characteristics that suggest safety for use, as they presented no coagulase enzyme activity or gamma-hemolysis. These strains were identified as belonging to the genera Lactiplantibacillus and Pediococcus, and 32 strains also presented resistance to vancomycin, ciprofloxacin and streptomycin. In addition, 28 isolates showed a survival rate, expressed as log cycle reduction, higher than 0.9 under gastric conditions (pH 2). All strains tested positive in bile salts deconjugation tests and showed a survival rate higher than 0.8 in the presence of this salt. Regarding antimicrobial activity against pathogens, all strains were able to inhibit Salmonella Typhimurium (ATCC® 14028TM) and 97% were capable of inhibiting Escherichia coli (ATCC® 25922TM). Concerning the results of in vitro antagonistic assays, three isolates (B125, B135, and Z183 strains) were selected for antagonistic tests using açai juice contaminated with these two pathogens. All tested LAB strains were able to inhibit pathogen growth in açai juice. In summary, açai fruits are a potential source of LAB isolates to be investigated as probiotics.
Functional Characteristics of Lactobacillus and Yeast Single Starter Cultures in the Ripening Process of Dry Fermented Sausage
Authors: Liu Yingli , Wan Zhen , Yohannes Kalekristos Woldemariam , Yu Qinglin , Yang Ziyan , Li Hongyan , Liu Jie , Wang Jing
Published: January 2021

Dry fermented sausage is popular among the world because of its rich nutrition and unique flavor. Starter cultures play an important role in the quality of dry fermented sausage. In this study, probiotics lactic acid bacteria Lactobacillus delbrueckii N102, Latilactobacillus sakei H1-5, Debaryomyces hansenii Y4-1, and Wickerhamomyces anomalus Y12-3 were isolated from food-borne materials. The physicochemical properties, microbial populations, TBARS, lipolysis, proteolysis, and volatile flavor compounds of dry fermented sausages with different starter cultures were evaluated comparatively during the ripening process. The results showed that both L. delbrueckii N102 and L. sakei H1-5 grow well and could rapidly reduce the pH value of the products. At the same time, they could significantly reduce the number of Enterobacter putrefaciens, so as to ensure the safety of the products. In addition, the strains N102 promoted the formation of flavor compounds 2,3-butanedione, 3-hydroxy-2-butanone, and carnosine, whereas taurine content of batch H1-5 was significantly increased, while yeast y4-1 and y12-3 could also grow faster in sausage and promoted the esters and alcohols formation such as ethyl acetate and linalool, with the formation of γ-aminobutyric acid by y4-1. Compared with lactic acid bacteria, yeasts showed to contribute more in flavor formation and effective inhibition of lipid oxidation. The starter cultures played different roles in flavor contribution and had obvious differentiation in the ripening process of dry fermented sausage.
Rigorous Plasma Microbiome Analysis Method Enables Disease Association Discovery in Clinic
Authors: Luo Zhenwu , Alekseyenko Alexander V. , Ogunrinde Elizabeth , Li Min , Li Quan-Zhen , Huang Lei , Tsao Betty P. , Kamen Diane L. , Oates Jim C. , Li Zihai , Gilkeson Gary S. , Jiang Wei
Published: January 2021

Blood microbiome is important to investigate microbial-host interactions and the effects on systemic immune perturbations. However, this effort has met with major challenges due to low microbial biomass and background artifacts. In the current study, microbial 16S DNA sequencing was applied to analyze plasma microbiome. We have developed a quality-filtering strategy to evaluate and exclude low levels of microbial sequences, potential contaminations, and artifacts from plasma microbial 16S DNA sequencing analyses. Furthermore, we have applied our technique in three cohorts, including tobacco-smokers, HIV-infected individuals, and individuals with systemic lupus erythematosus (SLE), as well as corresponding controls. More than 97% of total sequence data was removed using stringent quality-filtering strategy analyses; those removed amplicon sequence variants (ASVs) were low levels of microbial sequences, contaminations, and artifacts. The specifically enriched pathobiont bacterial ASVs have been identified in plasmas from tobacco-smokers, HIV-infected individuals, and individuals with SLE but not from control subjects. The associations between these ASVs and disease pathogenesis were demonstrated. The pathologic activities of some identified bacteria were further verifiedin vitro. We present a quality-filtering strategy to identify pathogenesis-associated plasma microbiome. Our approach provides a method for studying the diagnosis of subclinical microbial infection as well as for understanding the roles of microbiome-host interaction in disease pathogenesis.
The Ribosome as a Switchboard for Bacterial Stress Response
Authors: Cheng-Guang He , Gualerzi Claudio Orlando
Published: January 2021

As free-living organisms, bacteria are subject to continuous, numerous and occasionally drastic environmental changes to which they respond with various mechanisms which enable them to adapt to the new conditions so as to survive. Here we describe three situations in which the ribosome and its functions represent the sensor or the target of the stress and play a key role in the subsequent cellular response. The three stress conditions which are described are those ensuing upon: a) zinc starvation; b) nutritional deprivation, and c) temperature downshift.
A Novel Iflavirus Was Discovered in Green Rice Leafhopper Nephotettix cincticeps and Its Proliferation Was Inhibited by Infection of Rice Dwarf Virus
Authors: Jia Wenxi , Wang Fei , Li Jingjing , Chang Xuefei , Yang Yi , Yao Hongwei , Bao Yanyuan , Song Qisheng , Ye Gongyin
Published: January 2021

The green rice leafhopper, Nephotettix cincticeps (Hemiptera: Cicadellidae), is a key insect vector transmitting rice dwarf virus (RDV) that causes rice dwarf disease. We discovered a novel iflavirus from the transcriptomes of N. cincticeps and named it as Nephotettix cincticeps positive-stranded RNA virus-1 (NcPSRV-1). The viral genome consists of 10,524 nucleotides excluding the poly(A) tail and contains one predicted open reading frame encoding a polyprotein of 3,192 amino acids, flanked by 5' and 3' untranslated regions. NcPSRV-1 has a typical iflavirus genome arrangement and is clustered with the members of the family Iflaviridae in the phylogenetic analysis. NcPSRV-1 was detected in all tested tissues and life stages of N. cincticeps and could be transmitted horizontally and vertically. Moreover, NcPSRV-1 had high prevalence in the laboratory populations and was widely spread in field populations of N. cincticeps. NcPSRV-1 could also infect the two-striped leafhopper, Nephotettix apicalis, at a 3.33% infection rate, but was absent in the zigzag leafhopper, Recilia dorsalis, and rice Oryza sativa variety TN1. The infection of RDV altered the viral load and infection rate of NcPSRV-1 in N. cincticeps, for which it seems that RDV has an antagonistic effect on NcPSRV-1 infection in the host.
Optimization of CRISPR/Cas System for Improving Genome Editing Efficiency in Plasmodium falciparum
Authors: Zhao Yuemeng , Wang Fei , Wang Changhong , Zhang Xiaobai , Jiang Cizhong , Ding Feng , Shen Li , Zhang Qingfeng
Published: January 2021

Studies of molecular mechanisms and related gene functions have long been restricted by limited genome editing technologies in malaria parasites. Recently, a simple and effective genome editing technology, the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) system, has greatly facilitated these studies in many organisms, including malaria parasites. However, due to the special genome feature of malaria parasites, the manipulation and gene editing efficacy of the CRISPR/Cas system in this pathogen need to be improved, particularly in the human malaria parasite, Plasmodium falciparum. Herein, based on the CRISPR/Cas9 system, we developed an integrating strategy to generate a Cas9i system, which significantly shortened the time for generation of transgenic strains in P. falciparum. Moreover, with this Cas9i system, we have successfully achieved multiplexed genome editing (mutating or tagging) by a single-round transfection in P. falciparum. In addition, we for the first time adapted AsCpf1 (Acidaminococcus sp. Cpf1), an alternative to Cas9, into P. falciparum parasites and examined it for gene editing. These optimizations of the CRISPR/Cas system will further facilitate the mechanistic research of malaria parasites and contribute to eliminating malaria in the future.
Rapid Detection of Hepatitis B Virus in Blood Samples Using a Combination of Polymerase Spiral Reaction With Nanoparticles Lateral-Flow Biosensor
Authors: Lin Lin , Guo Jinshuai , Liu Haiyang , Jiang Xiaofeng
Published: January 2021

A rapid, highly sensitive, and robust diagnostic technique for point-of-care (PoC) testing can be developed using the combination of the nanoparticle-based lateral flow biosensors (LFB) and isothermal nucleic acid amplification technology. Here, we developed a polymerase spiral reaction (PSR) containing FITC-labeled DNA probes coupled with the nanoparticle-based LFB assay (PSR-LFB) to detect the amplified products to detect HBV visually. Under the optimized conditions, the PSR assay involved incubation of the reaction mixture for 20 min at 63°C, followed by visual detection of positive amplicons using LFB, which would generate a red test line based on the biotin/streptavidin interaction and immunoreactions, within 5 min. A cross-reactivity test revealed that the developed PSR-LFB assay showed good specificity for HBV and could distinguish HBV from other pathogenic microorganisms. For the analytical sensitivity, the limit of detection (LoD) of PSR-LFB assay was recorded as 5.4 copies/mL of HBV genomic DNA, which was ten-times more sensitive than qPCR and loop-mediated isothermal amplification (LAMP). Additionally, all the HBV-positive (29/82) samples, identified using ELISA, were also successfully detected by the PSR-LFB assay. We found that the true positive rate of the PSR-LFB assay was higher than that of qPCR (100 vs. 89.66%, respectively), as well as the LAMP assay (100 vs. 96.55%, respectively). Furthermore, the integrated procedure could be completed in 60 min, including the processing of the blood samples (30 min), an isothermal reaction (20 min), and result visualization (5 min). Thus, this PSR-LFB assay could be a potentially useful technique for PoC diagnosis of HBV in resource-limited countries.
Striatal Transcriptome Reveals Differences Between Cognitively Impaired and Unimpaired Aged Male Rats
Authors: Korz Volker , Kremslehner Christopher , Maliković Jovana , Hussein Ahmed , Feyissa Daniel Daba , Nagelreiter Ionela-Mariana , Smidak Roman , Plasenzotti Roberto , Gruber Florian , Lubec Gert
Published: January 2021

Cognitive processes require striatal activity. The underlying molecular mechanisms are widely unknown. For this reason the striatal transcriptome of young (YM), aged cognitively impaired (OMB), and unimpaired (OMG) male rats was analyzed. The global comparison of transcripts reveal a higher number of differences between OMG and YM as compared to OMB and YM. Hierarchical clustering detects differences in up- and down-regulated gene clusters in OMG and OMB when compared to YM. In OMG we found more single genes to be specifically regulated in this group than in OMB when compared to young. These genes were considered as cognition specific, whereas genes shared in OMG and OMB were considered as age specific. OMB specific up-regulated genes are related to negative control of cell differentiation and transcription (Hopx), to phagocytosis (Cd202) and cell adhesion (Pcdhb21), whereas down-regulated genes are related to associative learning, behavioral fear response and synaptic transmission (Gabra5). OMG specific up-regulated genes are in the context of maintenance of transcription and estrogen receptor signaling (Padi2, Anxa3), signal transduction [Rassf4, Dock8)], sterol regulation (Srebf1), and complement activity (C4a, C4b). Down-regulated genes are related to lipid oxidation reduction processes (Far2) and positive regulation of axon extension (Islr2). These relations were supported by pathway analysis, which reveals cholesterol metabolism processes in both aged group and cholesterol biosynthesis specifically in OMG; adipogenesis and focal adhesion in OMB. In OMG glucuronidation, estrogen metabolism, inflammatory responses and TGF beta signaling where detected as specific for this group. Signal transduction of the sphingosine-1-phospate-receptor (S1P) receptor was the main pathway difference in the comparison of OMB and OMG with downregulated genes in the first group. This difference could also be observed in the OMB vs. YM comparison but not in the OMG vs. YM analysis. Thus, an up-regulation of cognition related genes could be observed in OMG compared to OMB rats. The S1P pathway discriminated between OMB and OMG as well as between OMB and OMG. Since this pathway has been described as essential for cognitive processes in the striatum of mice, it may, among steroid hormone signaling, significantly contribute to the maintenance of cognitive processes in OMG.
Binary and Hybrid Work-Condition Maps for Interactive Exploration of Ergonomic Human Arm Postures
Authors: Peternel Luka , Schøn Daniel Tofte , Fang Cheng
Published: January 2021

Ergonomics of human workers is one of the key elements in design and evaluation of production processes. Human ergonomics have a major impact on productivity as well as chronic health risks incurred by inappropriate working postures and conditions. In this paper we propose a novel method for estimating and communicating the ergonomic work condition called Binary Work-Condition Map, which provides a visualized feedback about work conditions of different configurations of an arm. The map is of binary nature and is derived by imposing the desired thresholds on considered ergonomic and safety related criteria. Therefore, the suggested arm postures in the map guarantee that all considered criteria are satisfied. This eliminates the ambiguity compared to state-of-the-art maps that uses continuous scales derived from weighted sum of multiple ergonomics criteria. In addition, to combine the advantages of both the binary map and the continuous map, we additionally propose a Hybrid Work-Condition Map that rules out unsuitable workspace with the binary map approach and renders the suitable workspace with the continuous map approach. The proposed approach was tested in simulation for various tasks and conditions. In addition, we conducted subjective evaluation experiments to compare the proposed methods with the state-of-the art method regarding the usability. The results indicated that the binary map is simpler to use, while the hybrid map is a good tradeoff between the binary and the continuous map. In selecting the map, strong points of each map should be considered with respect to the requirements of a specific application and task.
One-Shot Multi-Path Planning Using Fully Convolutional Networks in a Comparison to Other Algorithms
Authors: Kulvicius Tomas , Herzog Sebastian , Lüddecke Timo , Tamosiunaite Minija , Wörgötter Florentin
Published: January 2021

Path planning plays a crucial role in many applications in robotics for example for planning an arm movement or for navigation. Most of the existing approaches to solve this problem are iterative, where a path is generated by prediction of the next state from the current state. Moreover, in case of multi-agent systems, paths are usually planned for each agent separately (decentralized approach). In case of centralized approaches, paths are computed for each agent simultaneously by solving a complex optimization problem, which does not scale well when the number of agents increases. In contrast to this, we propose a novel method, using a homogeneous, convolutional neural network, which allows generation of complete paths, even for more than one agent, in one-shot, i.e., with a single prediction step. First we consider single path planning in 2D and 3D mazes. Here, we show that our method is able to successfully generate optimal or close to optimal (in most of the cases <10% longer) paths in more than 99.5% of the cases. Next we analyze multi-paths either from a single source to multiple end-points or vice versa. Although the model has never been trained on multiple paths, it is also able to generate optimal or near-optimal (<22% longer) paths in 96.4 and 83.9% of the cases when generating two and three paths, respectively. Performance is then also compared to several state of the art algorithms.
The Association of Early Electrocardiographic Abnormalities With Brain Injury Severity and Outcome in Severe Traumatic Brain Injury
Authors: Lenstra Jelmer-Joost , Kuznecova-Keppel Hesselink Lidija , la Bastide-van Gemert Sacha , Jacobs Bram , Nijsten Maarten Willem Nicolaas , van der Horst Iwan Cornelis Clemens , van der Naalt Joukje
Published: January 2021

The aim of this study was to evaluate the frequency of electrocardiographic (ECG) abnormalities in the acute phase of severe traumatic brain injury (TBI) and the association with brain injury severity and outcome. In contrast to neurovascular diseases, sparse information is available on this issue. Data of adult patients with severe TBI admitted to the Intensive Care Unit (ICU) for intracranial pressure monitoring of a level-1 trauma center from 2002 till 2018 were analyzed. Patients with a cardiac history were excluded. An ECG recording was obtained within 24 h after ICU admission. Admission brain computerized tomography (CT)-scans were categorized by Marshall-criteria (diffuse vs. mass lesions) and for location of traumatic lesions. CT-characteristics and maximum Therapy Intensity Level (TILmax) were used as indicators for brain injury severity. We analyzed data of 198 patients, mean (SD) age of 40 ± 19 years, median GCS score 3 [interquartile range (IQR) 3–6], and 105 patients (53%) had thoracic injury. In-hospital mortality was 30%, with sudden death by cardiac arrest in four patients. The incidence of ECG abnormalities was 88% comprising ventricular repolarization disorders (57%) mostly with ST-segment abnormalities, conduction disorders (45%) mostly with QTc-prolongation, and arrhythmias (38%) mostly of supraventricular origin. More cardiac arrhythmias were observed with increased grading of diffuse brain injury (p = 0.042) or in patients treated with hyperosmolar therapy (TILmax) (65%, p = 0.022). No association was found between ECG abnormalities and location of brain lesions nor with thoracic injury. Multivariate analysis with baseline outcome predictors showed that cardiac arrhythmias were not independently associated with in-hospital mortality (p = 0.097). Only hypotension (p = 0.029) and diffuse brain injury (p = 0.017) were associated with in-hospital mortality. In conclusion, a high incidence of ECG abnormalities was observed in patients with severe TBI in the acute phase after injury. No association between ECG abnormalities and location of brain lesions or presence of thoracic injury was present. Cardiac arrhythmias were indicative for brain injury severity but not independently associated with in-hospital mortality. Therefore, our findings likely suggest that ECG abnormalities should be considered as cardiac mimicry representing the secondary effect of traumatic brain injury allowing for a more rationale use of neuroprotective measures.
Pallidal Deep Brain Stimulation for Monogenic Dystonia: The Effect of Gene on Outcome
Authors: Tisch Stephen , Kumar Kishore Raj
Published: January 2021

Globus pallidus internus deep brain stimulation (GPi DBS) is the most effective intervention for medically refractory segmental and generalized dystonia in both children and adults. Predictive factors for the degree of improvement after GPi DBS include shorter disease duration and dystonia subtype with idiopathic isolated dystonia usually responding better than acquired combined dystonias. Other factors contributing to variability in outcome may include body distribution, pattern of dystonia and DBS related factors such as lead placement and stimulation parameters. The responsiveness to DBS appears to vary between different monogenic forms of dystonia, with some improving more than others. The first observation in this regard was reports of superior DBS outcomes in DYT-TOR1A (DYT1) dystonia, although other studies have found no difference. Recently a subgroup with young onset DYT-TOR1A, more rapid progression and secondary worsening after effective GPi DBS, has been described. Myoclonus dystonia due to DYT-SCGE (DYT11) usually responds well to GPi DBS. Good outcomes following GPi DBS have also been documented in X-linked dystonia Parkinsonism (DYT3). In contrast, poorer, more variable DBS outcomes have been reported in DYT-THAP1 (DYT6) including a recent larger series. The outcome of GPi DBS in other monogenic isolated and combined dystonias including DYT-GNAL (DYT25), DYT-KMT2B (DYT28), DYT-ATP1A3 (DYT12), and DYT-ANO3 (DYT24) have been reported with varying results in smaller numbers of patients. In this article the available evidence for long term GPi DBS outcome between different genetic dystonias is reviewed to reappraise popular perceptions of expected outcomes and revisit whether genetic diagnosis may assist in predicting DBS outcome.
Drug Repositioning Screen on a New Primary Cell Line Identifies Potent Therapeutics for Glioblastoma
Authors: Senbabaoglu Filiz , Aksu Ali Cenk , Cingoz Ahmet , Seker-Polat Fidan , Borklu-Yucel Esra , Solaroglu İhsan , Bagci-Onder Tugba
Published: January 2021

Glioblastoma is a malignant brain cancer with limited treatment options and high mortality rate. While established glioblastoma cell line models provide valuable information, they ultimately lose most primary characteristics of tumors under long-term serum culture conditions. Therefore, established cell lines do not necessarily recapitulate genetic and morphological characteristics of real tumors. In this study, in line with the growing interest in using primary cell line models derived from patient tissue, we generated a primary glioblastoma cell line, KUGBM8 and characterized its genetic alterations, long term growth ability, tumor formation capacity and its response to Temozolomide, the front-line chemotherapy utilized clinically. In addition, we performed a drug repurposing screen on the KUGBM8 cell line to identify FDA-approved agents that can be incorporated into glioblastoma treatment regimen and identified Topotecan as a lead drug among 1,200 drugs. We showed Topotecan can induce cell death in KUGBM8 and other primary cell lines and cooperate with Temozolomide in low dosage combinations. Together, our study provides a new primary cell line model that can be suitable for both in vitro and in vivo studies and suggests that Topotecan can offer promise as a therapeutic approach for glioblastoma.
Unraveling the Nanoscopic Organization and Function of Central Mammalian Presynapses With Super-Resolution Microscopy
Authors: Carvalhais Lia G. , Martinho Vera C. , Ferreiro Elisabete , Pinheiro Paulo S.
Published: January 2021

The complex, nanoscopic scale of neuronal function, taking place at dendritic spines, axon terminals, and other minuscule structures, cannot be adequately resolved using standard, diffraction-limited imaging techniques. The last couple of decades saw a rapid evolution of imaging methods that overcome the diffraction limit imposed by Abbe’s principle. These techniques, including structured illumination microscopy (SIM), stimulated emission depletion (STED), photo-activated localization microscopy (PALM), and stochastic optical reconstruction microscopy (STORM), among others, have revolutionized our understanding of synapse biology. By exploiting the stochastic nature of fluorophore light/dark states or non-linearities in the interaction of fluorophores with light, by using modified illumination strategies that limit the excitation area, these methods can achieve spatial resolutions down to just a few tens of nm or less. Here, we review how these advanced imaging techniques have contributed to unprecedented insight into the nanoscopic organization and function of mammalian neuronal presynapses, revealing new organizational principles or lending support to existing views, while raising many important new questions. We further discuss recent technical refinements and newly developed tools that will continue to expand our ability to delve deeper into how synaptic function is orchestrated at the nanoscopic level.
E2F7 Transcriptionally Inhibits MicroRNA-199b Expression to Promote USP47, Thereby Enhancing Colon Cancer Tumor Stem Cell Activity and Promoting the Occurrence of Colon Cancer
Authors: Guo Xiong , Liu Ling , Zhang Qi , Yang Weiming , Zhang Yang
Published: January 2021

microRNAs (miRNAs) can modulate the expression level of genes in a post-transcription manner, which are closely related to growth and metastasis of colon cancer. Herein, we aimed to explore how miR-199b influences colon cancer and to characterize its underlying molecular mechanism associating with E2F transcription factor 7 (E2F7). Assays of RT-qPCR, Western blot, and immunohistochemistry were utilized to detect the expression of E2F7 in the tissue samples collected from 30 patients diagnosed with colon cancer. Flow analysis was utilized to detect the ratio of ALDH1+ and CD133+ colon cancer stem cells. The interaction between E2F7, miR-199b, USP47, and MAPK was identified by ChIP-Seq analysis, luciferase reporter, RNA pull-down, co-immunoprecipitation, as well as glutathione-S-transferase (GST) pull-down experiments. Based on the gain- and loss-of-function approaches, the cellular functions of colon cancer cells by the E2F7-regulated miR-199b/USP47/MAPK axis were assessed. It was identified that E2F7 are expressed highly in the collected colon cancer tissues. E2F7 silencing reduced the production of ALDH1+ and CD133+ colon cancer stem cells and antagonized the effects of 5-fluorouracil (5-FU) treatment. Besides, the silencing of E2F7 was observed to suppress the oxidative stress, proliferation, migration, as well as invasion of ALDH1+ cells in vitro and tumorigenesis of colon cancer cells in vivo. Our findings reveal the pro-oncogenic effect of E2F7 on colon cancer development, highlighting E2F7 as a novel target for therapeutic strategy for colon cancer.
Analysis of the Prognosis and Therapeutic Value of the CXC Chemokine Family in Head and Neck Squamous Cell Carcinoma
Authors: Li Yongchao , Wu Tinghui , Gong Shujuan , Zhou Hangzheng , Yu Lufei , Liang Meiyan , Shi Ruijun , Wu Zhenhui , Zhang Jinpei , Li Shuwei
Published: January 2021

The CXC chemokines belong to a family which includes 17 different CXC members. Accumulating evidence suggests that CXC chemokines regulate tumor cell proliferation, invasion, and metastasis in various types of cancers by influencing the tumor microenvironment. The different expression profiles and specific function of each CXC chemokine in head and neck squamous cell carcinoma (HNSCC) are not yet clarified. In our work, we analyzed the altered expression, interaction network, and clinical data of CXC chemokines in patients with HNSCC by using the following: the Oncomine dataset, cBioPortal, Metascape, String analysis, GEPIA, and the Kaplan–Meier plotter. The transcriptional level analysis suggested that the mRNA levels of CXCL1, CXCL2, CXCL3, CXCL5, CXCL6, CXCL8, CXCL9, CXCL10, CXCL11, and CXCL13 increased in HNSCC tissue samples when compared to the control tissue samples. The expression levels of CXCL9, CXCL10, CXCL11, CXCL12, and CXCL14 were associated with various tumor stages in HNSCC. Clinical data analysis showed that high transcription levels of CXCL2, CXCL3, and CXCL12, were linked with low relapse-free survival (RFS) in HNSCC patients. On the other hand, high CXCL14 levels predicted high RFS outcomes in HNSCC patients. Meanwhile, increased gene transcription levels of CXCL9, CXCL10, CXCL13, CXCL14, and CXCL17 were associated with a higher overall survival (OS) advantage in HNSCC patients, while high levels of CXCL1, and CXCL8 were associated with poor OS in all HNSCC patients. This study implied that CXCL1, CXCL2, CXCL3, CXCL8, and CXCL12 could be used as prognosis markers to identify low survival rate subgroups of patients with HNSCC as well as be potential suitable therapeutic targets for HNSCC patients. Additionally, CXCL9, CXCL10, CXCL13, CXCL14, and CXCL17 could be used as functional prognosis biomarkers to identify better survival rate subgroups of patients with HNSCC.