bluuebunny/crossref_metadata_2025 huggingface dataset:
Benchmark for the ESA: Having a Backbone Is Good for Recovery
Authors: Haines Aaron M. , Leu Matthias , Costante Delaney M. , Treakle Tyler C. , Parenti Carli , Miller Jennifer R. B. , Malcom Jacob W.
Published: January 2021

To forestall the current rate of global extinction, we need to identify strategies that successfully recover species. In the last decade, the recovery record for the United States Endangered Species Act (ESA) has improved. Our aim was to review federal delisting documents for recovered species and quantify patterns in taxonomy, history of threats, policy, funding and actions that are associated with species recovery. In comparison to species still listed, the average recovered species was a vertebrate, had been listed longer under the ESA, was exposed to a lower number of threats at the time of listing, and received relatively higher levels of funding. Based on our review, we suggest the following strategies to improve species recovery: provide more time for ESA protection, allocate more funding for recovery, maintain environmental regulations that facilitate recovery, establish more private landowner agreements, and increase the area of protected lands.
Physicochemical Impacts of Dust Storms on Aerosol and Glacier Meltwater on the Northern Margin of the Taklimakan Desert
Authors: Zheng Cunying , Li Zhongqin , Zhou Ping , Zhang Xin , Zhou Xi , Ma Shan
Published: January 2021

To analyze the impacts of dust storms on the atmospheric and meltwater environment, intensive and simultaneous sampling for aerosols and meltwater on the terminal moraine (41°73′ N, 79°88′ E, 3,789 m a.s.l.) of Qingbingtan Glacier No. 72 (Glacier No. 72) on the northern margin of the Taklamakan Desert were conducted during the summer of 2008. Aerosol and meltwater chemistry (including the species of Na+, K+, Mg2+, Ca2+, NH4+, Cl−, SO42−, and NO3−) was analyzed by ion chromatography. The results indicated that the major anions and cations in the samples were SO42− and Ca2+, respectively. In the dust event, the average value of aerosol ions was 566.91 neq·m−3, which was nearly five times that under nondust conditions (115.58 neq·m−3). In addition, in the meltwater samples, the sum of ion concentrations ranged from 31.26 to 180.98 mg·L−1, with an average of 76.40 mg·L−1. When a dust storm occurred, the ion concentrations in these two media increased significantly and simultaneously, but with different trends due to the different influencing factors. That is, the atmospheric environment was significantly affected by the dust storm. According to the correlation analysis and principal component analysis, the water-soluble ions, such as SO42−, Cl−, Na+, K+, Mg2+, and Ca2+, originated from natural sources, while NH4+ and NO3− originated from anthropogenic sources. The results of the air mass trajectory suggested that the regional dust storms caused by the air masses originating from Eastern Europe and Siberia had a significant influence on the glacial environment.
10-year Characteristics of Moisture Source Regions and Their Potential Effect on Seasonal Isotopic Signatures of δ18O in Tropical Trees of Southern Ecuador
Authors: Landshuter Nadja , Mölg Thomas , Grießinger Jussi , Bräuning Achim , Peters Thorsten
Published: January 2021

Ratios of stable oxygen isotopes in tree rings (δ18O) are a valuable proxy for reconstructing past climates. Such reconstructions allow us to gain better knowledge of climate dynamics under different (eg warmer) environmental conditions, which also forms the basis for effective risk management. The latter aspect is particularly relevant for our study site on the western flanks of the Andes in Southern Ecuador, since the region is frequently affected by droughts and heavy precipitation events during the rainy season (January to April), leading to enormous social and economic losses. In particular, we focus on precipitation amounts and moisture source regions as they are known to influence the δ18O signature of tree rings. Moisture source regions are based on 240 h backward trajectories that were calculated with the trajectory model LAGRANTO for the rainy seasons 2008 to 2017. A moisture source diagnostic was applied to the air parcel pathways. The resulting moisture source regions were analyzed by calculating composites based on precipitation amounts, season, and calendar year. The precipitation amounts were derived from data of a local Automatic Weather Station (AWS). The analysis confirms that our study site receives its moisture both, from the Atlantic and the Pacific Oceans. Heavy precipitation events are linked to higher moisture contributions from the Pacific, and local SST anomalies along the coast of Ecuador are of higher importance than those off the coast toward the central Pacific. Moreover, we identified increasing moisture contributions from the Pacific over the course of the rainy season. This change and also rain amount effects are detectable in preliminary data of δ18O variations in tree rings of Bursera graveolens. These signatures can be a starting point for investigating atmospheric and hydroclimatic processes, which trigger δ18O variations in tree rings, more extensively in future studies.
Practical Volcano-Independent Recognition of Seismic Events: VULCAN.ears Project
Authors: Cortés Guillermo , Carniel Roberto , Lesage Philippe , Mendoza M. Ángeles , Della Lucia Ivo
Published: January 2021

Recognizing the mechanisms underlying seismic activity and tracking temporal and spatial patterns of earthquakes represent primary inputs to monitor active volcanoes and forecast eruptions. To quantify this seismicity, catalogs are established to summarize the history of the observed types and number of volcano-seismic events. In volcano observatories the detection and posterior classification or labeling of the events is manually performed by technicians, often suffering a lack of unified criteria and eventually resulting in poorly reliable labeled databases. State-of-the-art automatic Volcano-Seismic Recognition (VSR) systems allow real-time monitoring and consistent catalogs. VSR systems are generally designed to monitor one station of one volcano, decreasing their efficiency when used to recognize events from another station, in a different eruptive scenario or at different volcanoes. We propose a Volcano-Independent VSR (VI.VSR) solution for creating an exportable VSR system, whose aim is to generate labeled catalogs for observatories which do not have the resources for deploying their own systems. VI.VSR trains universal recognition models with data of several volcanoes to obtain portable and robust characteristics. We have designed the VULCAN.ears ecosystem to facilitate the VI.VSR application in observatories, including the pyVERSO tool to perform VSR tasks in an intuitive way, its graphical interface, geoStudio, and liveVSR for real-time monitoring. Case studies are presented at Deception, Colima, Popocatépetl and Arenal volcanoes testing VI.VSR models in challenging scenarios, obtaining encouraging recognition results in the 70–80% accuracy range. VI.VSR technology represents a major breakthrough to monitor volcanoes with minimal effort, providing reliable seismic catalogs to characterise real-time changes.
Generating Pennycress (Thlaspi arvense) Seed Triacylglycerols and Acetyl-Triacylglycerols Containing Medium-Chain Fatty Acids
Authors: Esfahanian Maliheh , Nazarenus Tara J. , Freund Meghan M. , McIntosh Gary , Phippen Winthrop B. , Phippen Mary E. , Durrett Timothy P. , Cahoon Edgar B. , Sedbrook John C.
Published: January 2021

Thlaspi arvense L. (pennycress) is a cold-tolerant Brassicaceae that produces large amounts of seeds rich in triacylglycerols and protein, making it an attractive target for domestication into an offseason oilseed cash cover crop. Pennycress is easily genetically transformed, enabling synthetic biology approaches to tailor oil properties for specific biofuel and industrial applications. To test the feasibility in pennycress of producing TAGs and acetyl-TAGs rich in medium-chain fatty acids (MCFAs; C6–C14) for industrial, biojet fuel and improved biodiesel applications, we generated transgenic lines with seed-specific expression of unique acyltransferase (LPAT and diacylglycerol acyltransferase) genes and thioesterase (FatB) genes isolated from Cuphea viscosissima, Cuphea avigera var. pulcherrima, Cuphea hookeriana, Coco nucifera, and Umbellularia californica. Wild-type pennycress seed TAGs accumulate no fatty acids shorter than 16C and less than 5 mol percent C16 as palmitic acid (16:0). Co-expressing UcFatB and CnLPAT produced up to 17 mol% accumulation of lauric acid (12:0) in seed TAGs, whereas CvFatB1 CvLPAT2 CpDGAT1 combinatorial expression produced up to 27 mol% medium chain FAs Medium Chain Fatty Acids mostly in the form of capric acid (10:0). CpFatB2 ChFatB2 combinatorial expression predominantly produced, in equal parts, up to 28 mol% myristic acid (14:0) and palmitic acid. Genetically crossing the combinatorial constructs into a fatty acid elongation1 (fae1) mutant that produced no 22:1 erucic acid, and with an Euonymus alatus diacylglycerol acetyltransferase (EaDAcT)-expressing line that produced 60 mol% acetyl-TAGs, had no or relatively minor effects on MCFAs accumulation, suggesting fluxes to MCFAs were largely unaltered. Seed germination assays revealed no or minor delays in seed germination for most lines, the exception being CpFatB2 ChFatB2-expressing lines, which had substantially slower seed germination rates. Taken together, these data show that pennycress can be engineered to produce seeds accumulating modest amounts of MCFAs of varying carbon-chain length in TAGs and acetyl-TAGs, with rates of seed germination being delayed in only some cases. We hypothesize that increasing MCFAs further may require functional reductions to endogenous transferases and/or other FA elongases.
A Systematic Review of Within-Population Variation in the Size of Home Range Across Ungulates: What Do We Know After 50 Years of Telemetry Studies?
Authors: Seigle-Ferrand Juliette , Atmeh Kamal , Gaillard Jean-Michel , Ronget Victor , Morellet Nicolas , Garel Mathieu , Loison Anne , Yannic Glenn
Published: January 2021

Studying the factors determining the sizes of home ranges, based on body mass, feeding style, and sociality level, is a long-standing goal at the intersection of ecology and evolution. Yet, how species-specific life history traits interact with different components of the landscape to shape differences in individual home ranges at within-population level has received much less attention. Here, we review the empirical literature on ungulates to map our knowledge of the relative effects of the key environmental drivers (resource availability, landscape heterogeneity, lethal and non-lethal risks) on the sizes of individual home ranges within a population and assess whether species' characteristics (body mass, diet, and social structure), account for observed variation in the responses of the sizes of individual home ranges to local environmental drivers. Estimating the sizes of home ranges and measuring environmental variables raise a number of methodological issues, which complicate the comparison of empirical studies. Still, from an ecological point of view, we showed that (1) a majority of papers (75%) supported the habitat productivity hypothesis, (2) the support for the influence of landscape heterogeneity was less pervasive across studies, (3) the response of cattle-type to variation in food availability was stronger than the response of moose-type, and (4) species-specific body mass or sociality level had no detectable effect on the level of support to the biological hypotheses. To our surprise, our systematic review revealed a dearth of studies focusing on the ecological drivers of the variation in the sizes of individual home ranges (only about 1% of articles that dealt with home ranges), especially in the later decade where more focus has been devoted to movement. We encourage researchers to continue providing such results with sufficient sample sizes and robust methodologies, as we still need to fully understand the link between environmental drivers and individual space use while accounting for life-history constraints.
Detection of Endangered Aquatic Plants in Rapid Streams Using Environmental DNA
Authors: Tsukamoto Yuta , Yonezawa Satoru , Katayama Natsu , Isagi Yuji
Published: January 2021

Podostemaceae are a eudicot family of plants that grow on rapid streams and waterfalls. Two genera and six species of this family are distributed in Japan, all of which are threatened with extinction. It is difficult to find these species from the river side and it takes much effort to investigate their distribution. In this study, we attempted to determine the presence and absence of the Podostemaceae species by environmental DNA (eDNA) metabarcoding. Four species of Podostemaceae were detected near four known habitats, and the detected species were in perfect agreement with the results of a past survey that was based on visual observation. The marker used in this study had sufficient resolution to distinguish all six Podostemaceae species distributed in Japan and detected multiple species growing in a site. These results show that eDNA metabarcoding can quickly detect rare aquatic plants that are difficult to find by visual observation and can provide important information regarding their conservation.
Genomic Insights Into the Molecular Basis of Sexual Selection in Birds
Authors: Jaiswal Shubham K. , Gupta Ankit , Shafer Aaron B. A. , P. K. Vishnu Prasoodanan , Vijay Nagarjun , Sharma Vineet K.
Published: January 2021

Sexual selection is a well-known biological process, yet the genomic basis and patterns of sexual selection are not fully understood. The extravagant ornamental plumage of peacock (Pavo cristatus) was instrumental in shaping Charles Darwin's theory of sexual selection and is considered to be an honest signal of its immunocompetence. Here, we used the recently generated draft genome sequence of peafowl (Pavo cristatus) and carried out a comparative analysis across 11 bird genomes that encompass a range of sexual selection and also had high-quality genomic and phenotypic data publically available to study the genomic basis of sexual selection. We found that varying degree of purifying selection was the predominant mechanism of action for sexual selection at the genome-wide scale and observed that sexual selection mostly influences genes regulating gene expression and protein processing. Specifically, the genome-wide phylogenetically corrected regression analysis supported the continuous or ongoing model of sexual selection. Genes involved in nucleic acid binding and gene expression regulation, including a specific regulator of sex-determination known as TRA2A to be under positive selection in the species with high post-copulatory sexual selection manifested as high sperm competition. We also detected specific feather-related and immune-related gene-pairs evolving under similar selection pressures across the 11 species, including peacock (Pavo cristatus), which is consistent with the Hamilton-Zuk hypothesis. The comparative genomics analysis of 11 avian taxa has provided new insights on the molecular underpinnings of sexual selection and identifies specific genomic regions for future in-depth analysis.
Characterization of Autozygosity in Pigs in Three-Way Crossbreeding
Authors: Ganteil Audrey , Rodriguez-Ramilo Silvia T. , Ligonesche Bruno , Larzul Catherine
Published: January 2021

Crossbreeding in livestock can be used to increase genetic diversity. The resulting increase in variability is related to the heterozygosity of the crossbred animal. The evolution of diversity during crossbreeding can be assessed using genomic data. The objective of this study was to describe patterns of runs of homozygosity (ROH) in animals resulting from three-way crossbreeding, from parental pure lines, and in their crossbred offspring. The crossbreeding scheme consisted of a first crossbreeding Pietrain boars and Large White sows, after which the offspring of the Pietrain × Large White were crossed with Duroc boars. The offspring of the second crossbreeding are called G0, the offspring of G0 boars and G0 sows are called G1. All the animals were genotyped using the Illumina SNP60 porcine chip. After filtering, analyses were performed with 2,336 animals and 48,579 autosomal single nucleotide polymorphism (SNP). The mean ROH-based inbreeding coefficients were shown to be 0.27 ± 0.05, 0.23 ± 0.04, and 0.26 ± 0.04 for Duroc, Large White, and Pietrain, respectively. ROH were detected in the Pietrain × Large White crossbred but the homozygous segments were fewer and smaller than in their parents. Similar results were obtained in the G0 crossbred. However, in the G1 crossbreds the number and the size of ROH were higher than in G0 parents. Similar ROH hotspots were detected on SSC1, SSC4, SSC7, SSC9, SSC13, SSC14, and SSC15 in both G0 and G1 animals. Long ROH (>16 Mb) were observed in G1 animals, suggesting regions with low recombination rates. The conservation of these homozygous segments in the three crossbred populations means that some haplotypes were shared between parental breeds. Gene annotation in ROH hotspots in G0 animals identified genes related to production traits including carcass composition and reproduction. These findings advance our understanding of how to manage genetic diversity in crossbred populations.
Breed Ancestry, Divergence, Admixture, and Selection Patterns of the Simbra Crossbreed
Authors: van der Nest Magriet A. , Hlongwane Nompilo , Hadebe Khanyisile , Chan Wai-Yin , van der Merwe Nicolaas A. , De Vos Lieschen , Greyling Ben , Kooverjee Bhaveni B. , Soma Pranisha , Dzomba Edgar F. , Bradfield Michael , Muchadeyi Farai C.
Published: January 2021

In this study, we evaluated an admixed South African Simbra crossbred population, as well as the Brahman (Indicine) and Simmental (Taurine) ancestor populations to understand their genetic architecture and detect genomic regions showing signatures of selection. Animals were genotyped using the Illumina BovineLD v2 BeadChip (7K). Genomic structure analysis confirmed that the South African Simbra cattle have an admixed genome, composed of 5/8 Taurine and 3/8 Indicine, ensuring that the Simbra genome maintains favorable traits from both breeds. Genomic regions that have been targeted by selection were detected using the linkage disequilibrium-based methods iHS and Rsb. These analyses identified 10 candidate regions that are potentially under strong positive selection, containing genes implicated in cattle health and production (e.g., TRIM63, KCNA10, NCAM1, SMIM5, MIER3, and SLC24A4). These adaptive alleles likely contribute to the biological and cellular functions determining phenotype in the Simbra hybrid cattle breed. Our data suggested that these alleles were introgressed from the breed's original indicine and taurine ancestors. The Simbra breed thus possesses derived parental alleles that combine the superior traits of the founder Brahman and Simmental breeds. These regions and genes might represent good targets for ad-hoc physiological studies, selection of breeding material and eventually even gene editing, for improved traits in modern cattle breeds. This study represents an important step toward developing and improving strategies for selection and population breeding to ultimately contribute meaningfully to the beef production industry.
Alpha-Enolase: Emerging Tumor-Associated Antigen, Cancer Biomarker, and Oncotherapeutic Target
Authors: Almaguel Frankis A. , Sanchez Tino W. , Ortiz-Hernandez Greisha L. , Casiano Carlos A.
Published: January 2021

Alpha-enolase, also known as enolase-1 (ENO1), is a glycolytic enzyme that “moonlights” as a plasminogen receptor in the cell surface, particularly in tumors, contributing to cancer cell proliferation, migration, invasion, and metastasis. ENO1 also promotes other oncogenic events, including protein-protein interactions that regulate glycolysis, activation of signaling pathways, and resistance to chemotherapy. ENO1 overexpression has been established in a broad range of human cancers and is often associated with poor prognosis. This increased expression is usually accompanied by the generation of anti-ENO1 autoantibodies in some cancer patients, making this protein a tumor associated antigen. These autoantibodies are common in patients with cancer associated retinopathy, where they exert pathogenic effects, and may be triggered by immunodominant peptides within the ENO1 sequence or by posttranslational modifications. ENO1 overexpression in multiple cancer types, localization in the tumor cell surface, and demonstrated targetability make this protein a promising cancer biomarker and therapeutic target. This mini-review summarizes our current knowledge of ENO1 functions in cancer and its growing potential as a cancer biomarker and guide for the development of novel anti-tumor treatments.
Comprehensive Analysis of Differentially Expressed lncRNA, circRNA and mRNA and Their ceRNA Networks in Mice With Severe Acute Pancreatitis
Authors: Wang Bing , Wu Jun , Huang Qilin , Yuan Xiaohui , Yang Yi , Jiang Wen , Wen Yi , Tang Lijun , Sun Hongyu
Published: January 2021

Severe acute pancreatitis (SAP) is an acute digestive system disease with high morbidity mortality and hospitalization rate worldwide, due to various causes and unknown pathogenesis. In recent years, a large number of studies have confirmed that non-coding RNAs (ncRNAs) play an important role in many cellular processes and disease occurrence. However, the underlying mechanisms based on the function of ncRNAs, including long noncoding RNA (lncRNA) and circular RNA (circRNA), in SAP remain unclear. In this study, we performed high-throughput sequencing on the pancreatic tissues of three normal mice and three SAP mice for the first time to describe and analyze the expression profiles of ncRNAs, including lncRNA and circRNA. Our results identified that 49 lncRNAs, 56 circRNAs and 1,194 mRNAs were differentially expressed in the SAP group, compared with the control group. Furthermore, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of differentially expressed lncRNAs and circRNAs, and found that the functions of the parental genes are enriched in the calcium-regulated signaling pathway, NF-κB signaling pathway, autophagy and protein digestion and absorption processes, which are closely related to the central events in pathogenesis of SAP. We also constructed lncRNA/circRNA-miRNA-mRNA networks to further explore their underlying mechanism and possible relationships in SAP. We found that in the competitive endogenous RNA (ceRNA) networks, differentially expressed lncRNAs and circRNAs are mainly involved in the apoptosis pathway and calcium signal transduction pathway. In conclusion, we found that lncRNAs and circRNAs play an important role in the pathogenesis of SAP, which may provide new insights in further exploring the pathogenesis of SAP and seek new targets for SAP.
Pregnancy-Induced Changes in microRNA Expression in Multiple Sclerosis
Authors: Søndergaard Helle Bach , Airas Laura , Christensen Jeppe Romme , Nielsen Birgitte Romme , Börnsen Lars , Oturai Annette , Sellebjerg Finn
Published: January 2021

Pregnancy affects the disease course in multiple sclerosis (MS), particularly in the third trimester, where the relapse rate is reduced by as much as two thirds. This study aimed at identifying changes in microRNA (miRNA) and immune cell phenotypes in pregnant MS patients. Discovery and validation studies to detect differentially expressed miRNAs were performed with quantitative real-time PCR on peripheral blood mononuclear cells (PBMC). Flow cytometry analysis was performed on PBMC stained with antibodies directed against surface markers of antigen presenting cells (APCs), NK-cells, NKT cells, CD4+ and CD8+ T cells and subsets of these cell types, including PDL1 and PDL2 expressing subsets. RNA was extracted from whole blood, monocytes, and NK-cells to investigate expression and correlation between regulated miRNAs and mRNAs. In total, 15 miRNAs were validated to be differentially expressed between third trimester pregnant and postpartum MS patients (Benjamini-Hochberg false discovery rate from p = 0.03–0.00004). Of these, 12 miRNAs were downregulated in pregnancy and 6 of the 15 miRNAs were altered by more than ±2-fold (+2.99- to -6.38-fold). Pregnant MS patients had a highly significant increase in the percentage of monocytes and a decrease of NK-cells and myeloid dendritic cells compared to non-pregnant MS patients. We confirm previous reports of a relative increase in CD56-bright NK-cells and a decrease in CD56-dim NK-cells in third trimester of pregnancy and report an increase in non-committed follicular helper cells.PDL1andPDL2expression was increased in pregnant patients together withIL10. Also, in monocytesIL10,PDL1, andPDL2were upregulated whereas miR-1, miR-20a, miR-28, miR-95, miR-146a, miR-335, and miR-625 were downregulated between pregnant and untreated MS patients.IL10,PDL1, andPDL2were predicted targets of MS pregnancy-changed miRNAs, further supported by their negative correlations. Additionally, previously identified pregnancy-regulated mRNAs were identified as predicted targets of the miRNAs. PDL1 and PDL2 bind PD-1 expressed on T cells with an inhibitory effect on T-cell proliferation and increase in IL10 production. These results indicate that some of the effects behind the disease-ameliorating third trimester of pregnancy might be caused by changed expression of miRNAs and immunoregulatory molecules in monocytes.
Acid-Sensing Ion Channel-1a in Articular Chondrocytes and Synovial Fibroblasts: A Novel Therapeutic Target for Rheumatoid Arthritis
Authors: Xu Yayun , Chen Feihu
Published: January 2021

Acid-sensing ion channel 1a (ASIC1a) is a member of the extracellular H+-activated cation channel family. Emerging evidence has suggested that ASIC1a plays a crucial role in the pathogenesis of rheumatoid arthritis (RA). Specifically, ASIC1a could promote inflammation, synovial hyperplasia, articular cartilage, and bone destruction; these lead to the progression of RA, a chronic autoimmune disease characterized by chronic synovial inflammation and extra-articular lesions. In this review, we provided a brief overview of the molecular properties of ASIC1a, including the basic biological characteristics, tissue and cell distribution, channel blocker, and factors influencing the expression and function, and focused on the potential therapeutic targets of ASIC1a in RA and possible mechanisms of blocking ASIC1a to improve RA symptoms, such as regulation of apoptosis, autophagy, pyroptosis, and necroptosis of articular cartilage, and synovial inflammation and invasion of fibroblast-like cells in synovial tissue.
Adipocytes Are the Control Tower That Manages Adipose Tissue Immunity by Regulating Lipid Metabolism
Authors: Park Jeu , Sohn Jee Hyung , Han Sang Mun , Park Yoon Jeong , Huh Jin Young , Choe Sung Sik , Kim Jae Bum
Published: January 2021

Accumulating evidence reveals that adipose tissue is an immunologically active organ that exerts multiple impacts on the regulation of systemic energy metabolism. Adipose tissue immunity is modulated by the interactions between adipocytes and various immune cells. Nevertheless, the underlying mechanisms that control inter-cellular interactions between adipocytes and immune cells in adipose tissue have not been thoroughly elucidated. Recently, it has been demonstrated that adipocytes utilize lipid metabolites as a key mediator to initiate and mediate diverse adipose tissue immune responses. Adipocytes present lipid antigens and secrete lipid metabolites to determine adipose immune tones. In addition, the interactions between adipocytes and adipose immune cells are engaged in the control of adipocyte fate and functions upon metabolic stimuli. In this review, we discuss an integrated view of how adipocytes communicate with adipose immune cells using lipid metabolites. Also, we briefly discuss the newly discovered roles of adipose stem cells in the regulation of adipose tissue immunity.
Self-Amplifying Pestivirus Replicon RNA Encoding Influenza Virus Nucleoprotein and Hemagglutinin Promote Humoral and Cellular Immune Responses in Pigs
Authors: Démoulins Thomas , Ruggli Nicolas , Gerber Markus , Thomann-Harwood Lisa J. , Ebensen Thomas , Schulze Kai , Guzmán Carlos A. , McCullough Kenneth C.
Published: January 2021

Self-amplifying replicon RNA (RepRNA) promotes expansion of mRNA templates encoding genes of interest through their replicative nature, thus providing increased antigen payloads. RepRNA derived from the non-cytopathogenic classical swine fever virus (CSFV) targets monocytes and dendritic cells (DCs), potentially promoting prolonged antigen expression in the DCs, contrasting with cytopathogenic RepRNA. We engineered pestivirus RepRNA constructs encoding influenza virus H5N1 (A/chicken/Yamaguchi/7/2004) nucleoprotein (Rep-NP) or hemagglutinin (Rep-HA). The inherent RNase-sensitivity of RepRNA had to be circumvented to ensure efficient delivery to DCs for intracellular release and RepRNA translation; we have reported how only particular synthetic delivery vehicle formulations are appropriate. The question remained concerning RepRNA packaged in virus replicon particles (VRPs); we have now compared an efficient polyethylenimine (PEI)-based formulation (polyplex) with VRP-delivery as well as naked RepRNA co-administered with the potent bis-(3’,5’)-cyclic dimeric adenosine monophosphate (c-di-AMP) adjuvant. All formulations contained a Rep-HA/Rep-NP mix, to assess the breadth of both humoral and cell-mediated defences against the influenza virus antigens. Assessment employed pigs for their close immunological relationship to humans, and as natural hosts for influenza virus. Animals receiving the VRPs, as well as PEI-delivered RepRNA, displayed strong humoral and cellular responses against both HA and NP, but with VRPs proving to be more efficacious. In contrast, naked RepRNA plus c-di-AMP could induce only low-level immune responses, in one out of five pigs. In conclusion, RepRNA encoding different influenza virus antigens are efficacious for inducing both humoral and cellular immune defences in pigs. Comparisons showed that packaging within VRP remains the most efficacious for delivery leading to induction of immune defences; however, this technology necessitates employment of expensive complementing cell cultures, and VRPs do not target human cells. Therefore, choosing the appropriate synthetic delivery vehicle still offers potential for rapid vaccine design, particularly in the context of the current coronavirus pandemic.
Elevated Circulating IL-10 Producing Breg, but Not Regulatory B Cell Levels, Restrain Antibody-Mediated Rejection After Kidney Transplantation
Authors: Luo Yongsheng , Luo Feifei , Zhang Kuanxin , Wang Shilei , Zhang Haojie , Yang Xianlei , Shang Wenjun , Wang Junxiang , Wang Zhigang , Pang Xinlu , Feng Yonghua , Liu Lei , Xie Hongchang , Feng Guiwen , Li Jinfeng
Published: January 2021

Background

Antibody-mediated rejection (AMR) occupies a major position for chronic rejection after kidney transplantation. Regulatory B cell (Breg) has been reported to have an inhibitory immune function, which contributes to the resistance for AMR.

Methods

A nested case–control study for nine healthy donors, 25 stable (ST) patients, and 18 AMR patients was performed to determine the type of Breg in maintaining immune tolerance and preventing AMR.

Results

Compared to the ST group, circulating interleukin (IL)-10+ Bregs, but not Bregs, significantly decreased. The receiver operating characteristic (ROC) curve analysis revealed that rather than the circulating Bregs, decreased circulating IL-10+ Breg levels were positively associated with AMR. However, kidney B cell and IL-10 infiltration was significantly increased in the AMR group with high expression of C-X-C motif chemokine 13 (CXCL13). In addition, circulating IL-10+ Bregs, rather than Bregs, remained higher than those at pre-operation, during the 90-day post-operation in immune homeostasis.

Conclusion

The circulating IL-10+ Breg levels are more appropriate measures for assessing the resistance of AMR after kidney transplantation.
Shining Light on Data-Poor Coastal Fisheries
Authors: Exeter Owen M. , Htut Thaung , Kerry Christopher R. , Kyi Maung Maung , Mizrahi Me'ira , Turner Rachel A. , Witt Matthew J. , Bicknell Anthony W. J.
Published: January 2021

Coastal fisheries provide livelihoods and sustenance for millions of people globally but are often poorly documented. Data scarcity, particularly relating to spatio-temporal trends in catch and effort, compounds wider issues of governance capacity. This can hinder the implementation and effectiveness of spatial tools for fisheries management or conservation. This issue is acute in developing and low-income regions with many small-scale inshore fisheries and high marine biodiversity, such as Southeast Asia. As a result, fleets often operate unmonitored with implications for target and non-target species populations and the wider marine ecosystem. Novel and cost-effective approaches to obtain fisheries data are required to monitor these activities and help inform sustainable fishery and marine ecosystem management. One such example is the detection and numeration of fishing vessels that use artificial light to attract catch with nighttime satellite imagery. Here we test the efficiency and application value of nighttime satellite imagery, in combination with landings data and GPS tracked vessels, to estimate the footprint and biomass removal of an inshore purse seine fishery operating within a region of high biodiversity in Myanmar. By quantifying the number of remotely sensed vessel detections per month, adjusted for error by the GPS tracked vessels, we can extrapolate data from fisher logbooks to provide fine-scale spatiotemporal estimates of the fishery's effort, value and biomass removal. Estimates reveal local landings of nearly 9,000 mt worth close to $4 million USD annually. This approach details how remote sensed and in situ collected data can be applied to other fleets using artificial light to attract catch, notably inshore fisheries of Southeast Asia, whilst also providing a much-needed baseline understanding of a data-poor fishery's spatiotemporal activity, biomass removal, catch composition and landing of vulnerable species.
MAC Project—Monitoring Anticoagulant Therapy Observational Study: Rationale and Protocol
Authors: Camporese Giuseppe , Bernardi Enrico , Bortoluzzi Cristiano , Noventa Franco , Hong Ngoc Vo , Callegari Elena , Villalta Sabina , Tonello Chiara , Nardin Michela , Campello Elena , Spiezia Luca , Simioni Paolo
Published: January 2021

Real-life studies complement data from registrative trials. Because of the delayed registration of direct oral anticoagulants in Italy, scarce real-life data on such treatments is available for the Italian population. The aim of the MAC project is to collect real-life clinical information in unselected patients given oral anticoagulants for venous thromboembolism, during a 5-year follow-up period. This is a prospective-cohort, multi-center, observational study performed in four Italian centers. The estimated samples size is 4,000 patients. The efficacy outcomes are: incidence of symptomatic recurrent venous thromboembolism and of post-thrombotic syndrome. The safety outcomes are: incidence of major bleeding, clinically relevant non-major bleeding, minor bleeding, serious adverse events, and mortality. The MAC project has the potential to improve our understanding of the epidemiology and of the therapeutic strategies adopted in Italian patients with venous thromboembolism.

Clinical Trial Registration: WWW.ClinicalTrials.Gov, identifier: NCT0432939.
Effect of Antibiotics on the Microbial Efficiency of Anaerobic Digestion of Wastewater: A Review
Authors: Xiao Leilei , Wang Yiping , Lichtfouse Eric , Li Zhenkai , Kumar P. Senthil , Liu Jian , Feng Dawei , Yang Qingli , Liu Fanghua
Published: January 2021

Recycling waste into new materials and energy is becoming a major challenge in the context of the future circular economy, calling for advanced methods of waste treatment. For instance, microbially-mediated anaerobic digestion is widely used for conversion of sewage sludge into biomethane, fertilizers and other products, yet the efficiency of microbial digestion is limited by the occurrence of antibiotics in sludges, originating from drug consumption for human and animal health. Here we present antibiotic levels in Chinese wastewater, then we review the effects of antibiotics on hydrolysis, acidogenesis and methanogenesis, with focus on macrolides, tetracyclines, β-lactams and antibiotic mixtures. We detail effects of antibiotics on fermentative bacteria and methanogenic archaea. Most results display adverse effects of antibiotics on anaerobic digestion, yet some antibiotics promote hydrolysis, acidogenesis and methanogenesis.
Forest Microhabitat Affects Succession of Fungal Communities on Decomposing Fine Tree Roots
Authors: Kohout Petr , Sudová Radka , Brabcová Vendula , Vosolsobě Stanislav , Baldrian Petr , Albrechtová Jana
Published: January 2021

Belowground litter derived from tree roots has been shown as a principal source of soil organic matter in coniferous forests. Fate of tree root necromass depends on fungal communities developing on the decaying roots. Local environmental conditions which affect composition of tree root mycobiome may also influence fungal communities developing on decaying tree roots. Here, we assessed fungal communities associated with decaying roots of Picea abies decomposing in three microhabitats: soil with no vegetation, soil with ericoid shrubs cover, and P. abies deadwood, for a 2-year period. Forest microhabitat showed stronger effect on structuring fungal communities associated with decaying roots compared to living roots. Some ericoid mycorrhizal fungi showed higher relative abundance on decaying roots in soils under ericoid shrub cover, while saprotrophic fungi had higher relative abundance in roots decomposing inside deadwood. Regardless of the studied microhabitat, we observed decline of ectomycorrhizal fungi and increase of endophytic fungi during root decomposition. Interestingly, we found substantially more fungal taxa with unknown ecology in late stages of root decomposition, indicating that highly decomposed roots may represent so far overlooked niche for soil fungi. Our study shows the importance of microhabitats on the fate of the decomposing spruce roots.
Trichoderma reesei Isolated From Austrian Soil With High Potential for Biotechnological Application
Authors: Hinterdobler Wolfgang , Li Guofen , Spiegel Katharina , Basyouni-Khamis Samira , Gorfer Markus , Schmoll Monika
Published: January 2021

Fungi of the genusTrichodermaare of high importance for biotechnological applications, in biocontrol and for production of homologous and heterologous proteins. However, sexual crossing under laboratory conditions has so far only been achieved with the speciesTrichoderma reesei, which was so far only isolated from tropical regions. Our isolation efforts aimed at the collection ofTrichodermastrains from Austrian soils surprisingly also yielded 12 strains of the speciesT. reesei, which was previously not known to occur in Europe. Their identity was confirmed withtef1- andrpb2-sequencing and phylogenetic analysis. They could clearly be distinguished from tropical strains including the common laboratory wildtypes by UP-PCR and genetic variations adjacent to the mating type locus. The strains readily mated with reference strains derived from CBS999.97. Secreted cellulase and xylanase levels of these isolates were up to six-fold higher than those of QM6a indicating a high potential for strain improvement. The strains showed different responses to injury in terms of induction of sporulation, but a correlation to alterations in thenox1-gene sequence was not detected. Several synonymous SNPs were found in the sequence of the regulator genenoxRof the soil isolates compared to QM6a. Only in one strain, non-synonymous SNPs were found which impact a PEST sequence of NoxR, suggesting altered protein stability. The availability of sexually fertile strains from middle Europe naturally producing decent amounts of plant cell wall degrading enzymes opens up novel perspectives for non-GMO strain improvement and biological pretreatment of plant biomass for bioethanol production. Moreover, the varied response of these strains to injury in terms of sporulation, which is independent of Nox1 and NoxR suggests that additional regulators impact this phenomenon inT. reesei.
Cephalosporins Interfere With Quorum Sensing and Improve the Ability of Caenorhabditis elegans to Survive Pseudomonas aeruginosa Infection
Authors: Kumar Lokender , Brenner Nathanael , Brice John , Klein-Seetharaman Judith , Sarkar Susanta K.
Published: January 2021

Pseudomonas aeruginosa utilizes the quorum sensing (QS) system to strategically coordinate virulence and biofilm formation. Targeting QS pathways may be a potential anti-infective approach to treat P. aeruginosa infections. In the present study, we define cephalosporins’ anti-QS activity using Chromobacterium violaceum CV026 for screening and QS-regulated mutants of P. aeruginosa for validation. We quantified the effects of three cephalosporins, cefepime, ceftazidime, and ceftriaxone, on (1) pyocyanin production using spectrophotometric assay, (2) bacterial motility using agar plate assay, and (3) biofilm formation using scanning electron microscopy. We also studied isogenic QS mutant strains of PAO1 (ΔlasR,ΔrhlR,ΔpqsA, and ΔpqsR) to compare and distinguish QS-mediated effects on the motility phenotypes and bacterial growth with and without sub-MIC concentrations of antibiotics. Results showed that cephalosporins have anti-QS activity and reduce bacterial motility, pyocyanin production, and biofilm formation for CV026 and PAO1. Also, sub-MICs of cefepime increased aminoglycosides’ antimicrobial activity against P. aeruginosa PAO1, suggesting the advantage of combined anti-QS and antibacterial treatment. To correlate experimentally observed anti-QS effects with the interactions between cephalosporins and QS receptors, we performed molecular docking with ligand binding sites of quorum sensing receptors using Autodock Vina. Molecular docking predicted cephalosporins’ binding affinities to the ligand-binding pocket of QS receptors (CviR, LasR, and PqsR). To validate our results using an infection model, we quantified the survival rate of Caenorhabditis elegans following P. aeruginosa PAO1 challenge at concentrations less than the minimum inhibitory concentration (MIC) of antibiotics. C. elegans infected with PAO1 without antibiotics showed 0% survivability after 72 h. In contrast, PAO1-infected C. elegans showed 65 ± 5%, 58 ± 4%, and 49 ± 8% survivability after treatment with cefepime, ceftazidime, and ceftriaxone, respectively. We determined the survival rates of C. elegans infected by QS mutant strains ΔlasR (32 ± 11%), ΔrhlR (27 ± 8%), ΔpqsA (27 ± 10%), and ΔpqsR (37 ± 6%), which suggest essential role of QS system in virulence. In summary, cephalosporins at sub-MIC concentrations show anti-QS activity and enhance the antibacterial efficacy of aminoglycosides, a different class of antibiotics. Thus, cephalosporins at sub-MIC concentrations in combination with other antibiotics are potential candidates for developing therapies to combat infections caused by P. aeruginosa.
Thymine Sensitizes Gram-Negative Pathogens to Antibiotic Killing
Authors: Liu Yuan , Yang Kangni , Jia Yuqian , Shi Jingru , Tong Ziwen , Wang Zhiqiang
Published: January 2021

Diminished antibiotic susceptibility of bacterial pathogens is an increasingly serious threat to human and animal health. Alternative strategies are required to combat antibiotic refractory bacteria. Bacterial metabolic state has been shown to play a critical role in its susceptibility to antibiotic killing. However, the adjuvant potential of nucleotides in combination with antibiotics to kill Gram-negative pathogens remains unknown. Herein, we found that thymine potentiated ciprofloxacin killing against both sensitive and resistant-E. coli in a growth phase-independent manner. Similar promotion effects were also observed for other bactericidal antibiotics, including ampicillin and kanamycin, in the fight against four kinds of Gram-negative bacteria. The mechanisms underlying this finding were that exogenous thymine could upregulate bacterial metabolism including increased TCA cycle and respiration, which thereby promote the production of ATP and ROS. Subsequently, metabolically inactive bacteria were converted to active bacteria and restored its susceptibility to antibiotic killing. In Galleria mellonella infection model, thymine effectively improved ciprofloxacin activity against E. coli. Taken together, our results demonstrated that thymine potentiates bactericidal antibiotics activity against Gram-negative pathogens through activating bacterial metabolism, providing a universal strategy to overcome Gram-negative pathogens.
Role of Probiotics, Prebiotics, and Synbiotics in the Elderly: Insights Into Their Applications
Authors: Ale Elisa C. , Binetti Ana G.
Published: January 2021

Elderly people are an important part of the global population who suffer from the natural processes of senescence, which lead to changes in the gut microbiota composition. These modifications have a great impact on their quality of life, bringing a general putrefactive and inflammatory status as a consequence. Some of the most frequent conditions related to this status are constipation, undernutrition, neurodegenerative diseases, susceptibility to opportunistic pathogens, and metabolic disbalance, among others. For these reasons, there is an increasing interest in improving their quality of life by non-invasive treatments such as the consumption of probiotics, prebiotics, and synbiotics. The aim of the present mini-review is to describe the benefits of these functional supplements/food according to the most recent clinical and pre-clinical studies published during the last decade. In addition, insights into several aspects we consider relevant to improve the quality of future studies are provided.
Artificial Intelligence for the Future Radiology Diagnostic Service
Authors: Mun Seong K. , Wong Kenneth H. , Lo Shih-Chung B. , Li Yanni , Bayarsaikhan Shijir
Published: January 2021

Radiology historically has been a leader of digital transformation in healthcare. The introduction of digital imaging systems, picture archiving and communication systems (PACS), and teleradiology transformed radiology services over the past 30 years. Radiology is again at the crossroad for the next generation of transformation, possibly evolving as a one-stop integrated diagnostic service. Artificial intelligence and machine learning promise to offer radiology new powerful new digital tools to facilitate the next transformation. The radiology community has been developing computer-aided diagnosis (CAD) tools based on machine learning (ML) over the past 20 years. Among various AI techniques, deep-learning convolutional neural networks (CNN) and its variants have been widely used in medical image pattern recognition. Since the 1990s, many CAD tools and products have been developed. However, clinical adoption has been slow due to a lack of substantial clinical advantages, difficulties integrating into existing workflow, and uncertain business models. This paper proposes three pathways for AI's role in radiology beyond current CNN based capabilities 1) improve the performance of CAD, 2) improve the productivity of radiology service by AI-assisted workflow, and 3) develop radiomics that integrate the data from radiology, pathology, and genomics to facilitate the emergence of a new integrated diagnostic service.