bluuebunny/crossref_metadata_2025 huggingface dataset:
Aspen Soils Retain More Dissolved Organic Carbon Than Conifer Soils in a Sorption Experiment
Authors: Boča Antra , Jacobson Astrid R. , Van Miegroet Helga
Published: December 2020

The effect tree species have on soil organic carbon (SOC) has been hotly debated but, so far, few clear patterns have emerged. One example of a differing tree species effect on SOC are aspen forests in North America, which have been found to have more stable SOC than adjacent conifer forest stands. An important source for the formation of stable organo-mineral complexes in soil is dissolved organic carbon (DOC). DOC concentrations in mineral soil are often higher under the thick O-horizons of conifer forests than under aspen forests, but this does not correspond to more stable mineral SOC. This suggests that, instead of DOC concentration, DOC quality could be driving the observed differences in SOC. Therefore, we quantified the retention of contrasting forest detritus DOC in soils. Using a batch sorption experiment approach, we compared the retention of detritus leachates from four sources – aspen leaves (AL), aspen roots (AR), conifer (subalpine fir) needles (CN), and conifer (subalpine fir) roots (CR) – on soils sampled under aspen and conifer (subalpine fir and Douglas fir) overstories. The calculated sorption isotherms showed a higher retention of AL DOC than AR DOC, as indicated by all four sorption parameters – k and n (curve-fitting parameters), null point concentration (NPC; net sorption = net desorption), and endpoint (EP, retention at the highest initial DOC concentration). Leachates from CN and CR showed very similar retention behavior, and between the two species the retention of root leachates was more similar than the retention of foliage leachates. Soils sampled from aspen forests showed higher affinity for new DOC than conifer soils [higher sorption rate (n), lower NPC, and higher EP] regardless of the DOC source. The findings suggest that the higher DOC sorption on aspen soils might be a major driver for more stable SOC under aspen stands in North America.
Knowledge, Awareness, and Perception of Genetic Testing for Hereditary Disorders Among Malaysians in Klang Valley
Authors: Chin Jia-Jia , Tham Hong-Wai
Published: December 2020

Genetic testing aids patients in making important decisions in the prevention, treatment, or early detection of hereditary disorders. Low awareness of the importance of genetic testing contributes to the increase in the incidence of hereditary disorders. This study aims to explore the knowledge, awareness, and perception of genetic testing for hereditary disorders among local residents of the Klang Valley, Malaysia, and the potential variables that influence their understanding of genetic testing. A survey was conducted in different municipalities of the Klang Valley through self-administered questionnaire assessing the public's knowledge, awareness, and perception of genetic testing. Overall, the results revealed adequate knowledge and positive awareness of genetic testing, in which both were influenced by the respondent's educational level (P < 0.001), field of study (P < 0.001), and status of heard or unheard of genetic testing (P < 0.001). The perception of genetic testing was generally positive and influenced by the respondent's differences in age (P < 0.016), educational level (P < 0.001), field of study (P < 0.001), and status of heard or unheard of genetic testing (P < 0.001). Although positive responses were obtained, ~20.2% of the respondents had never heard of genetic testing. Of the respondents, 24.5% were unwilling to undergo genetic testing, with 25.1% believing that genetic testing tampers with nature and 18% believing that it opposes religion and their beliefs. Such attitude calls for the need to conduct programs to eliminate any misconception, as well as to educate the public to lessen any perceived misunderstanding of the concepts of genetic testing.
Designing Regulatory Frameworks for Access to Genetic Resources: A Multi-Stakeholder Multi-Criteria Approach
Authors: Sirakaya Aysegul , De Brucker Klaas , Vanagt Thomas
Published: December 2020

In this paper we conduct a multi-criteria analysis (MCA) from a multiple stakeholder point of view for the design of access and benefit sharing (ABS) agreements concerning genetic resources, in particular regarding the access component of such agreements. We start by analyzing the objectives defined by international law (viz. the Convention on Biodiversity and the Nagoya Protocol) that every party (i.e., all United Nations member states, except the United States) must strive to attain when developing national legislation on ABS. As countries have a certain degree of freedom concerning the way and the extent to which they need to integrate these objectives into their national frameworks and since stakeholders attach different levels of importance to these objectives, such an MCA will help identify those options that command the highest value added from the community of stakeholders. Consequently, those options are expected to hold the highest potential for successful implementation. The MCA performed in this paper is based on Saaty’s analytic hierarchy process (AHP) and starts from the objectives (i.e., criteria) enshrined in international law, and then proceeds by assessing the relative importance of these criteria from the point of view of four different stakeholder groups (industrial users, academic users, collections and provider countries). The alternatives to be evaluated in the MCA are based upon options discussed qualitatively in our previous study published inFrontiers in Plant Science(2019b). These options are now transformed into “design parameters” and are evaluated in terms of their contribution to stakeholder criteria. This evaluation is now performed in a quantitative way using MCA and is based on previous qualitative discussions with stakeholders that have been reported qualitatively in our previous paper inFrontiers in Plant Sciencereferred to above. The final result of our MCA consists of pointing out which design parameters regarding access obtain the highest priority from the community of stakeholders and hence need to be present in national regulatory frameworks on ABS that will be implemented by member states. It is our intention to undertake similar research for the Benefit Sharing component of ABS agreements in the future.
Identification and Expression Analysis of the CsMYB Gene Family in Root Knot Nematode-Resistant and Susceptible Cucumbers
Authors: Cheng Chunyan , Li Qingrong , Wang Xing , Li Ying , Qian Chuntao , Li Ji , Lou Qunfeng , Jahn Molly , Chen Jinfeng
Published: December 2020

MYB (myeloblastosis) transcription factors (TFs) play important roles in controlling various physiological processes in plants, such as responses to biotic and abiotic stress, metabolism, and defense. A previous study identified a gene, Csa6G410090, encoding a plant lipid transfer protein (LTP), as a possible regulator in cucumber (Cucumis sativus L.) of the resistance response to root-knot nematode (RKN) [Meloidogyne incognita Kofoid and White (Chitwood)]. Myb-type DNA-binding TFs were presumed to regulate downstream genes expression, including LTPs, however, the regulation mechanism remained unclear. To elucidate whether and which MYB TFs may be involved in regulation of the resistance response, this study identified 112 genes as candidate members of the CsMYB gene family by combining CDD and SMART databases, using the Hidden Markov Model (HMM) and manual calibration. Within this group, ten phylogenetic subgroups were resolved according to sequence-based classification, consistent with results from comprehensive investigation of gene structure, conserved motifs, chromosome locations, and cis-element analysis. Distribution and collinearity analysis indicated that amplification of the CsMYB gene family in cucumber has occurred mainly through tandem repeat events. Spatial gene expression analysis showed that 8 CsMYB genes were highly expressed at differing levels in ten different tissues or organs. The roots of RKN-resistant and susceptible cucumbers were inoculated with M. incognita, finding that CsMYB (Csa6G538700, Csa1G021940, and Csa5G641610) genes showed up-regulation coincident with upregulation of the “hub” gene LTP (Csa6G410090) previously implicated as a major gene in the resistance response to RKN in cucumber. Results of this study suggest hypotheses regarding the elements and regulation of the resistant response as well as possible RKN resistance-enhancing strategies in cucumber and perhaps more broadly in plants.
Transcriptome Analysis of the Cerebellum of Mice Fed a Manganese-Deficient Diet
Authors: Seo Young Ah , Choi Eun-Kyung , Aring Luisa , Paschall Molly , Iwase Shigeki
Published: December 2020

Manganese (Mn), primarily acquired through diet, is required for brain function and development. Epidemiological studies have found an association between both low and high levels of Mn and impaired neurodevelopment in children. Recent genetic studies have revealed that patients with congenital Mn deficiency display severe psychomotor disability and cerebral and cerebellar atrophy. Although the impact of Mn on gene expression is beginning to be appreciated, Mn-dependent gene expression remains to be explored in vertebrate animals. The goal of this study was to use a mouse model to define the impact of a low-Mn diet on brain metal levels and gene expression. We interrogated gene expression changes in the Mn-deficient mouse brain at the genome-wide scale by RNA-seq analysis of the cerebellum of mice fed low or normal Mn diets. A total of 137 genes were differentially expressed in Mn-deficient cerebellums compared with Mn-adequate cerebellums (Padj < 0.05). Mn-deficient mice displayed downregulation of key pathways involved with “focal adhesion,” “neuroactive ligand-receptor interaction,” and “cytokine-cytokine receptor interaction” and upregulation of “herpes simplex virus 1 infection,” “spliceosome,” and “FoxO signaling pathway.” Reactome pathway analysis identified upregulation of the splicing-related pathways and transcription-related pathways, as well as downregulation of “metabolism of carbohydrate,” and “extracellular matrix organization,” and “fatty acid metabolism” reactomes. The recurrent identifications of splicing-related pathways suggest that Mn deficiency leads to upregulation of splicing machineries and downregulation of diverse biological pathways.
Case Report: Distinctive EEG Patterns in SCARB-2 Related Progressive Myoclonus Epilepsy
Authors: Hotait Mostafa , Dirani Maya , El Halabi Tarek , Beydoun Ahmad
Published: December 2020

Action myoclonus-renal failure syndrome (AMRF) is a rare, recessively inherited form of progressive myoclonus epilepsy (PME) caused by mutations in the SCARB2 gene and associated with end-stage renal failure. In addition to severe progressive myoclonus, the neurological manifestations of this syndrome are characterized by progressive ataxia and dysarthria with preserved intellectual capacity. Since its original description, an increasing number of “AMRF-like” cases without renal failure have been reported. We describe the case of a 29-year-old woman with progressive disabling myoclonus associated with dysarthria and ataxia who was found to have a novel homozygous frameshift mutation in the SCARB2 gene. In addition, this report emphasizes the presence of two EEG patterns, fixation-off phenomenon, and bursts of parasagittal spikes exclusively seen during REM sleep that appear to be characteristic of this condition.
CRFK and Primary Macrophages Transcriptomes in Response to Feline Coronavirus Infection Differ Significantly
Authors: Drechsler Yvonne , Vasconcelos Elton J. R. , Griggs Lisa M. , Diniz Pedro P. P. V.
Published: December 2020

Coronaviruses are highly infectious and common in many species, including in humans, and agricultural and domestic animals. Host responses play an important role in viral entry, replication, assembly, and pathogenesis, although much is still to be understood, particularly host–virus interactions. Feline coronavirus is highly contagious, and ubiquitous in virtually all cat populations. Host-pathogen interactions have not been studied extensively due to the complex pathogenesis and development of clinical disease. Few studies have investigated cellular host responses to feline coronavirus infection, particularly at early time points. Transcriptome studies based on next-generation sequencing have the potential to elucidate the early responses of cells after viral infection and, consequently, give further insight into the pathogenesis of viruses. The current study aims to characterize and compare the viral- and immune-related differentially expressed genes in response to the coronavirus FIPV across different time points in a cell line which is permissive for productive replication versus primary cells implicated in pathogenesis. When comparing host responses in Crandell-Rees Feline Kidney (CRFK) cells to primary macrophages, many differences were observed with regards to expressed genes and their enrichments for both KEGG pathways and GO terms. CRFK cells which are permissive for productive replication of feline infectious peritonitis virus, showed induction of a large network of immunological and virally induced pathways. In contrast, Macrophages did not show similar host responses, with stronger pathway enrichment in downregulated transcripts. This study provides insights to better understand gene transcription in immune cells compared to epithelial cells discerning pathways relevant to pathogenesis in the early stages of infection.
Genome-Wide Identification and Expression Analysis of the Class III Peroxidase Gene Family in Potato (Solanum tuberosum L.)
Authors: Yang Xuanshong , Yuan Jiazheng , Luo Wenbin , Qin Mingyue , Yang Jiahan , Wu Weiren , Xie Xiaofang
Published: December 2020

Class III peroxidases (PRXs) are plant-specific enzymes and play important roles in plant growth, development and stress response. In this study, a total of 102 non-redundantPRXgene members (StPRXs) were identified in potato (Solanum tuberosumL.). They were divided into 9 subfamilies based on phylogenetic analysis. The members of each subfamily were found to contain similar organizations of the exon/intron structures and protein motifs. TheStPRXgenes were not equally distributed among chromosomes. There were 57 gene pairs of segmental duplication and 26 gene pairs of tandem duplication. Expression pattern analysis based on the RNA-seq data of potato from public databases indicated thatStPRXgenes were expressed differently in various tissues and responded specifically to heat, salt and drought stresses. Most of theStPRXgenes were expressed at significantly higher levels in root than in other tissues. In addition, real-time quantitative PCR (qRT-PCR) analysis for 7 selectedStPRXgenes indicated that these genes displayed various expression levels under abiotic stresses. Our results provide valuable information for better understanding the evolution ofStPRXgene family in potato and lay the vital foundation for further exploration ofPRXgene function in plants.
Applications of Support Vector Machine in Genomic Prediction in Pig and Maize Populations
Authors: Zhao Wei , Lai Xueshuang , Liu Dengying , Zhang Zhenyang , Ma Peipei , Wang Qishan , Zhang Zhe , Pan Yuchun
Published: December 2020

Genomic prediction (GP) has revolutionized animal and plant breeding. However, better statistical models that can improve the accuracy of GP are required. For this reason, in this study, we explored the genomic-based prediction performance of a popular machine learning method, the Support Vector Machine (SVM) model. We selected the most suitable kernel function and hyperparameters for the SVM model in eight published genomic data sets on pigs and maize. Next, we compared the SVM model with RBF and the linear kernel functions to the two most commonly used genome-enabled prediction models (GBLUP and BayesR) in terms of prediction accuracy, time, and the memory used. The results showed that the SVM model had the best prediction performance in two of the eight data sets, but in general, the predictions of both models were similar. In terms of time, the SVM model was better than BayesR but worse than GBLUP. In terms of memory, the SVM model was better than GBLUP and worse than BayesR in pig data but the same with BayesR in maize data. According to the results, SVM is a competitive method in animal and plant breeding, and there is no universal prediction model.
AdmixSim: A Forward-Time Simulator for Various Complex Scenarios of Population Admixture
Authors: Yang Xiong , Yuan Kai , Ni Xumin , Zhou Ying , Guo Wei , Xu Shuhua
Published: December 2020

Background: Population admixture is a common phenomenon in humans, animals, and plants, and it plays a very important role in shaping individual genetic architecture and population genetic diversity. Inference of population admixture, however, is very challenging and typically relies on in silico simulation. We are aware of the lack of a computerized tool for such a purpose. A simulator capable of generating data under various complex admixture scenarios would facilitate the study of recombination, linkage disequilibrium, ancestry tracing, and admixture dynamics in admixed populations. We described such a simulator here.

Results: We developed a forward-time simulator (AdmixSim) under the standard Wright Fisher model. It can simulate the following admixed populations: (1) multiple ancestral populations; (2) multiple waves of admixture events; (3) fluctuating population size; and (4) admixtures of fluctuating proportions. Analysis of the simulated data by AdmixSim showed that our simulator can quickly and accurately generate data resembling real-world values. We included in AdmixSim all possible parameters that would allow users to modify and simulate any kind of admixture scenario easily, so it is very flexible. AdmixSim records recombination break points and traces of each chromosomal segment from different ancestral populations, with which users can easily perform further analysis and comparative studies with empirical data.

Conclusions:AdmixSim facilitates the study of population admixture by providing a simulation framework with the flexible implementation of various admixture models and parameters.
Differential Skewing of Circulating MR1-Restricted and γδ T Cells in Human Psoriasis Vulgaris
Authors: Plužarić Vera , Štefanić Mario , Mihalj Martina , Tolušić Levak Maja , Muršić Ivanka , Glavaš-Obrovac Ljubica , Petrek Martin , Balogh Peter , Tokić Stana
Published: December 2020

Psoriasis vulgaris (PV) is a chronic, recurrent inflammatory dermatosis mediated by aberrantly activated immune cells. The role of the innate-like T cells, particularly gammadelta T (γδT) cells and MR1-restricted T lymphocytes, is incompletely explored, mainly through animal models, or by use of surrogate lineage markers, respectively. Here, we used case-control settings, multiparameter flow cytometry, 5-OP-RU-loaded MR1-tetramers, Luminex technology and targeted qRT-PCR to dissect the cellular and transcriptional landscape of γδ and MR1-restricted blood T cells in untreated PV cases (n=21, 22 matched controls). High interpersonal differences in cell composition were observed, fueling transcriptional variability at healthy baseline. A minor subset of canonical CD4+CD8+MR1-tet+TCRVα7.2+ and CD4+CD8-MR1-tet+TCRVα7.2+ T cells was the most significantly underrepresented community in male PV individuals, whereas Vδ2+ γδ T cells expressing high levels of TCR and Vδ1-δ2- γδ T cells expressing intermediate levels of TCR were selectively enriched in affected males, partly reflecting disease severity. Our findings highlight a formerly unappreciated skewing of human circulating MAIT and γδ cytomes during PV, and reveal their compositional changes in relation to sex, CMV exposure, serum cytokine content, BMI, and inflammatory burden. Complementing numerical alterations, we finally show that flow-sorted, MAIT and γδ populations exhibit divergent transcriptional changes in mild type I psoriasis, consisting of differential bulk expression for signatures of cytotoxicity/type-1 immunity (EOMES, RUNX3, IL18R), type-3 immunity (RORC, CCR6), and T cell innateness (ZBTB16).
Plasticizers as Microplastics Tracers in Tunisian Marine Environment
Authors: Gugliandolo Enrico , Licata Patrizia , Crupi Rosalia , Albergamo Ambrogina , Jebara Amel , Lo Turco Vincenzo , Potortì Angela Giorgia , Mansour Hedi Ben , Cuzzocrea Salvatore , Di Bella Giuseppa
Published: December 2020

The new knowledge on the bio-transformations to which the plastic material is subjected, raise concerns about their role as environmental contaminants. Microplastic have been reported to be responsible for the release and distribution of aquatic contaminants such organophosphorus esters, pesticides, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, and phthalate esters. The occurrence, spatiotemporal trends, and ecological risk of phthalic acid esters (PAEs) and non-phthalate plasticizers (NPPs) released from microplastic were investigated in water and fish (Sparus aurata) from five sites along the coast of Mahdia governorate (Tunisia), during April 2018-March 2019. In seawater the most abundant and frequently detected congeners were dibutyl phthalate (DBP, 0.017 mg L–1 and 0.055 mg L–1), diisobutyl phthalate (DiBP, 0.075 mg L–1 and 0.219 mg L–1), di(2-ethylhexyl)phthalate (DEHP, 0.071 mg L–1 and 4.594 mg L–1), and di(2-ethylhexyl) terephthalate (DEHT, 0.634 mg L–1 and 2.424 mg L–1). (ΣPAEs: 1.416 mg L–1 and 5.581 mg L–1; ΣNPPs: 9.191 mg L–1 and 26.296 mg L–1), confirming that such compounds bioconcentrate through the food chain. DBP (0.389 and 0.817 mg L–1), DiBP (0.101 and 0.921 mg L–1), DEHP (0.726 and 1.771 mg L–1) and DEHT (9.191 and 23.251 mg L–1) were predominant also in S. aurata affirming that such compounds bioconcentrate through the food chain. Overall, Tunisian samples i) were much more contaminated than counterparts previously investigated for the same pollutants from other world areas, and ii) revealed NPPs at higher levels than PAEs, confirming that such plasticizers are increasingly replacing conventional PAEs.
Infection of Ophiocordyceps sinensis Fungus Causes Dramatic Changes in the Microbiota of Its Thitarodes Host
Authors: Wu Hua , Rao Zhong-Chen , Cao Li , De Clercq Patrick , Han Ri-Chou
Published: December 2020

The Chinese cordyceps is a unique and valuable parasitic complex of Thitarodes/Hepialus ghost moths and the Ophiocordyceps sinensis fungus for medicine and health foods from the Tibetan Plateau. During artificial cultivation of Chinese cordyceps, the induction of blastospores into hyphae is a prerequisite for mummification of the infected Thitarodes larvae. To explore the microbial involvement in the induction of mycelia-blastospore transition, the microbiota of the hemolymph and gut from Thitarodes xiaojinensis larvae with or without injected O. sinensis blastospores were investigated by culture-dependent and -independent methods. Twenty-five culturable bacterial species and 14 fungal species, together with 537 bacterial operational taxonomic units (OTUs) and 218 fungal OTUs, were identified from the hemolymph and gut of samples from five stages including living larvae without injected fungi (A) or with high blastospore load (B), mummifying larvae without mycelia coating (C), freshly mummifying larvae coated with mycelia (D), and completely mummified larvae with mycelia (E). Two culturable bacterial species (Serratia plymuthica, Serratia proteamaculans), and 47 bacterial and 15 fungal OTUs were considered as shared species. The uninfected larval hemolymph contained 13 culturable bacterial species but no fungal species, together with 164 bacterial and 73 fungal OTUs. To our knowledge, this is the first study to detect large bacterial communities from the hemolymph of healthy insect larvae. When the living larvae contained high blastospore load, the culturable bacterial community was sharply inhibited in the hemolymph but the bacterial and fungal community greatly increased in the gut. In general, high blastospore load increased bacterial diversity but sharply decreased fungal diversity in the hemolymph and gut by OTUs. The bacterial loads of four culturable species (Chryseobacterium sp., Pseudomonas fragi, S. plymuthica, S. proteamaculans) increased significantly and O. sinensis and Pseudomonas spp. became dominant microbes, when the infected larvae became mummified, indicating their possible involvement in the larval mummification process. The discovery of many opportunistic pathogenic bacteria in the hemolymph of the healthy larvae, the larval microbial diversity influenced by O. sinensis challenge and the involvement of dominant bacteria during larval mummification process provide new insight into the infection and mummification mechanisms of O. sinensis in its Thitarodes hosts.
Chlamydia psittaci Plasmid-Encoded CPSIT_P7 Elicits Inflammatory Response in Human Monocytes via TLR4/Mal/MyD88/NF-κB Signaling Pathway
Authors: Chen Qian , Li Yumeng , Yan Xiaoliang , Sun Zhenjie , Wang Chuan , Liu Shuangquan , Xiao Jian , Lu Chunxue , Wu Yimou
Published: December 2020

The chlamydial plasmid, an essential virulence factor, encodes plasmid proteins that play important roles in chlamydial infection and the corresponding immune response. However, the virulence factors and the molecular mechanisms of Chlamydia psittaci are not well understood. In the present study, we investigated the roles and mechanisms of the plasmid-encoded protein CPSIT_P7 of C. psittaci in regulating the inflammatory response in THP-1 cells (human monocytic leukemia cell line). Based on cytokine arrays, CPSIT_P7 induces the expression of interleukin-6 (IL-6), interleukin-8 (IL-8), and monocyte chemoattractant protein-1 (MCP-1) in THP-1 cells. Moreover, the expression levels of IL-6, IL-8, and MCP-1 stimulated by CPSIT_P7 declined after silencing of the Toll-like receptor 4 (TLR4) gene using small interfering RNA and transfection of a dominant negative plasmid encoding TLR4 (pZERO-hTLR4). We further demonstrated that transfection with the dominant negative plasmid encoding MyD88 (pDeNy-hMyD88) and the dominant negative plasmid encoding Mal (pDeNy-hMal) could also abrogate the expression of the corresponding proteins. Western blot and immunofluorescence assay results showed that CPSIT_P7 could activate nuclear factor κB (NF-κB) signaling pathways in THP-1 cells. Altogether, our results indicate that the CPSIT_P7 induces the TLR4/Mal/MyD88/NF-κB signaling axis and therefore contributes to the inflammatory cytokine response.
Phosphoproteomic Analysis Reveals Rio1-Related Protein Phosphorylation Changes in Response to UV Irradiation in Sulfolobus islandicus REY15A
Authors: Huang Qihong , Lin Zijia , Wu Pengju , Ni Jinfeng , Shen Yulong
Published: December 2020

DNA damage response (DDR) in eukaryotes is largely regulated by protein phosphorylation. In archaea, many proteins are phosphorylated, however, it is unclear how the cells respond to DNA damage through global protein phosphorylation. We previously found that Δrio1, a Rio1 kinase homolog deletion strain of Sulfolobus islandicus REY15A, was sensitive to UV irradiation. In this study, we showed that Δrio1 grew faster than the wild type. Quantitative phosphoproteomic analysis of the wild type and Δrio1, untreated and irradiated with UV irradiation, revealed 562 phosphorylated sites (with a Ser/Thr/Tyr ratio of 65.3%/23.8%/10.9%) of 333 proteins in total. The phosphorylation levels of 35 sites of 30 proteins changed with >1.3-fold in the wild type strain upon UV irradiation. Interestingly, more than half of the UV-induced changes in the wild type did not occur in the Δrio1 strain, which were mainly associated with proteins synthesis and turnover. In addition, a protein kinase and several transcriptional regulators were differentially phosphorylated after UV treatment, and some of the changes were dependent on Rio1. Finally, many proteins involved in various cellular metabolisms exhibited Riol-related and UV-independent phosphorylation changes. Our results suggest that Rio1 is involved in the regulation of protein recycling and signal transduction in response to UV irradiation, and plays regulatory roles in multiple cellular processes in S. islandicus.
Chitin Attenuates Expression of Listeria monocytogenes Virulence Genes in vitro
Authors: Villoria Recio Miguel , Lee Bo-Hyung , Lillebæk Eva Maria Sternkopf , Kallipolitis Birgitte H. , Gahan Cormac G. M. , Ingmer Hanne , Larsen Marianne Halberg
Published: December 2020

External signals are crucial for bacteria to sense their immediate environment and fine-tune gene expression accordingly. The foodborne pathogen Listeria monocytogenes senses a range of environmental cues in order to activate or deactivate the virulence-inducing transcriptional factor PrfA during transition between infectious and saprophytic lifecycles. Chitin is an abundant biopolymer formed from linked β-(1–4)-N-acetyl-D-glucosamine residues associated with fungi, the exoskeleton of insects and often incorporated into foods as a thickener or stabilizer. L. monocytogenes evolved to hydrolyse chitin, presumably, to facilitate nutrient acquisition from competitive environments such as soil where the polymer is abundant. Since mammals do not produce chitin, we reasoned that the polymer could serve as an environmental signal contributing to repression of L. monocytogenes PrfA-dependent expression. This study shows a significant downregulation of the core PrfA-regulon during virulence-inducing conditions in vitro in the presence of chitin. Our data suggest this phenomenon occurs through a mechanism that differs from PTS-transport of oligosaccharides generated from either degradation or chitinase-mediated hydrolysis of the polymer. Importantly, an indication that chitin can repress virulence expression of a constitutively active PrfA∗ mutant is shown, possibly mediated via a post-translational modification inhibiting PrfA∗ activity. To our knowledge, this is the first time that chitin is reported as a molecule with anti-virulence properties against a pathogenic bacterium. Thus, our findings identify chitin as a signal which may downregulate the virulence potential of the pathogen and may provide an alternative approach toward reducing disease risk.
Antibiotic Resistance Genes and Bacterial Communities of Farmed Rainbow Trout Fillets (Oncorhynchus mykiss)
Authors: Helsens Nicolas , Calvez Ségolène , Prevost Hervé , Bouju-Albert Agnès , Maillet Aurélien , Rossero Albert , Hurtaud-Pessel Dominique , Zagorec Monique , Magras Catherine
Published: December 2020

The rise of antibiotic resistance is not only a challenge for human and animal health treatments, but is also posing the risk of spreading among bacterial populations in foodstuffs. Farmed fish-related foodstuffs, the food of animal origin most consumed worldwide, are suspected to be a reservoir of antibiotic resistance genes and resistant bacterial hazards. However, scant research has been devoted to the possible sources of diversity in fresh fillet bacterial ecosystems (farm environment including rivers and practices, and factory environment). In this study bacterial communities and the antibiotic resistance genes of fresh rainbow trout fillet were described using amplicon sequencing of the V3-V4 region of the 16S rRNA gene and high-throughput qPCR assay. The antibiotic residues were quantified using liquid chromatography/mass spectrometry methods. A total of 56 fillets (composed of muscle and skin tissue) from fish raised on two farms on the same river were collected and processed under either factory or laboratory sterile filleting conditions. We observed a core-bacterial community profile on the fresh rainbow trout fillets, but the processing conditions of the fillets has a great influence on their mean bacterial load (3.38 ± 1.01 log CFU/g vs 2.29 ± 0.72 log CFU/g) and on the inter-individual diversity of the bacterial community. The bacterial communities were dominated by Gamma- and Alpha-proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. The most prevalent genera were Pseudomonas, Escherichia-Shigella, Chryseobacterium, and Carnobacterium. Of the 73 antibiotic residues searched, only oxytetracycline residues were detected in 13/56 fillets, all below the European Union maximum residue limit (6.40–40.20 μg/kg). Of the 248 antibiotic resistance genes searched, 11 were found to be present in at least 20% of the fish population (tetracycline resistance genes tetM and tetV, β-lactam resistance genes blaDHA and blaACC, macrolide resistance gene mphA, vancomycin resistance genes vanTG and vanWG and multidrug-resistance genes mdtE, mexF, vgaB and msrA) at relatively low abundances calculated proportionally to the 16S rRNA gene.
Soil Bacterial and Archaeal Communities and Their Potential to Perform N-Cycling Processes in Soils of Boreal Forests Growing on Well-Drained Peat
Authors: Truu Marika , Nõlvak Hiie , Ostonen Ivika , Oopkaup Kristjan , Maddison Martin , Ligi Teele , Espenberg Mikk , Uri Veiko , Mander Ülo , Truu Jaak
Published: December 2020

Peatlands are unique wetland ecosystems that cover approximately 3% of the world’s land area and are mostly located in boreal and temperate regions. Around 15 Mha of these peatlands have been drained for forestry during the last century. This study investigated soil archaeal and bacterial community structure and abundance, as well as the abundance of marker genes of nitrogen transformation processes (nitrogen fixation, nitrification, denitrification, and dissimilatory nitrate reduction to ammonia) across distance gradients from drainage ditches in nine full-drained, middle-aged peatland forests dominated by Scots pine, Norway spruce, or Downy birch. The dominating tree species had a strong effect on the chemical properties (pH, N and C/N status) of initially similar Histosols and affected the bacterial and archaeal community structure and abundance of microbial groups involved in the soil nitrogen cycle. The pine forests were distinguished by having the lowest fine root biomass of trees, pH, and N content and the highest potential for N fixation. The distance from drainage ditches affected the spatial distribution of bacterial and archaeal communities (especially N-fixers, nitrifiers, and denitrifiers possessing nosZ clade II), but this effect was often dependent on the conditions created by the dominance of certain tree species. The composition of the nitrifying microbial community was dependent on the soil pH, and comammox bacteria contributed significantly to nitrate formation in the birch and spruce soils where the pH was higher than 4.6. The highest N2O emission was recorded from soils with higher bacterial and archaeal phylogenetic diversity such as birch forest soils. This study demonstrates that the long-term growth of forests dominated by birch, pine, and spruce on initially similar organic soil has resulted in tree-species-specific changes in the soil properties and the development of forest-type-specific soil prokaryotic communities with characteristic functional properties and relationships within microbial communities.
Taxonomic Diversity of Pico-/Nanoeukaryotes Is Related to Dissolved Oxygen and Productivity, but Functional Composition Is Shaped by Limiting Nutrients in Eutrophic Coastal Oceans
Authors: Wang Yaping , Li Guihao , Shi Fei , Dong Jun , Gentekaki Eleni , Zou Songbao , Zhu Ping , Zhang Xiaoli , Gong Jun
Published: December 2020

Pico-/nanoeukaryotes (P/NEs) comprise both primary producers and bacterial predators, playing important biogeochemical and ecological roles in the marine microbial loop. Besides the difference in size, these small-sized fractions can be distinguished from microplankton by certain functional and ecological traits. Nevertheless, little information is available regarding patterns of their taxonomic and functional diversity and community composition along environmental gradients in coastal marine ecosystems. In this study, we applied high-throughput sequencing of 18S rRNA gene to assess the taxonomic species richness and community composition of P/NEs in surface waters of Bohai Sea and North Yellow Sea, northern China spanning a 600-km distance during summer and winter of 2011. The richness of operational taxonomic units (OTUs) formed a U-shaped relationship with concentration of chlorophyll a (Chl-a, a proxy of primary productivity), but a stronger, negative relationship with concentration of dissolved oxygen (DO). These two factors also significantly co-varied with the OTU-based community composition of P/NEs. The effect of geographic distance on community composition of P/NEs was negligible. Among the three functional groups defined by trophic traits, heterotrophs had the highest OTU richness, which exhibited a U-shaped relationship with both DO and Chl-a. The community of P/NEs was dominated by heterotrophs and mixotrophs in terms of read numbers, which showed a trade-off along the gradient of phosphate, but no significant changes along DO and Chl-a gradients, indicating functional redundancy. Similarly, the proportion of phototrophs was significantly and positively correlated with the concentration of silicate. Our results indicate that taxonomic and functional composition of P/NEs are decoupled on a regional scale, and limiting nutrients are important factors in modulating functional composition of these microorganisms in the studied area. These findings contribute toward gaining a better understanding of how diversity of small eukaryotes and their functions are structured in coastal oceans and the effect of environmental changes on the structuring process.
Survival of the Fittest: The Relationship of (p)ppGpp With Bacterial Virulence
Authors: Kundra Shivani , Colomer-Winter Cristina , Lemos José A.
Published: December 2020

The signaling nucleotide (p)ppGpp has been the subject of intense research in the past two decades. Initially discovered as the effector molecule of the stringent response, a bacterial stress response that reprograms cell physiology during amino acid starvation, follow-up studies indicated that many effects of (p)ppGpp on cell physiology occur at levels that are lower than those needed to fully activate the stringent response, and that the repertoire of enzymes involved in (p)ppGpp metabolism is more diverse than initially thought. Of particular interest, (p)ppGpp regulation has been consistently linked to bacterial persistence and virulence, such that the scientific pursuit to discover molecules that interfere with (p)ppGpp signaling as a way to develop new antimicrobials has grown substantially in recent years. Here, we highlight contemporary studies that have further supported the intimate relationship of (p)ppGpp with bacterial virulence and studies that provided new insights into the different mechanisms by which (p)ppGpp modulates bacterial virulence.
Newly Isolated Streptomyces sp. JBS5-6 as a Potential Biocontrol Agent to Control Banana Fusarium Wilt: Genome Sequencing and Secondary Metabolite Cluster Profiles
Authors: Jing Tao , Zhou Dengbo , Zhang Miaoyi , Yun Tianyan , Qi Dengfeng , Wei Yongzan , Chen Yufeng , Zang Xiaoping , Wang Wei , Xie Jianghui
Published: December 2020

Banana is a key staple food and fruit in countries all over the world. However, the development of the global banana industry is seriously threatened by Fusarium wilt disease, which is caused by Fusarium oxysporum f. sp. cubense (Foc). In particular, Foc tropical race 4 (Foc TR4) could infect more than 80% of global banana and plantain crops. Until now, there were no commercial chemicals or resistant cultivars available to control the disease. Biological control using actinomycetes is considered a promising strategy. In this study, 88 actinomycetes were isolated from a banana orchard without symptoms of Fusarium wilt disease for more than 10 years. An actinobacterial strain labeled as JBS5-6 has exhibited strong antifungal activities against Foc TR4 and other selected 10 phytopathogenic fungi. Based on phenotypic and biochemical traits as well as complete genome analysis, strain JBS5-6 was assigned to Streptomyces violaceusniger. Extracts of the strain inhibited the mycelial growth and spore germination of Foc TR4 by destroying membrane integrity and the ultrastructure of cells. The complete genome of strain JBS5-6 was sequenced and revealed a number of key function gene clusters that contribute to the biosynthesis of active secondary metabolites. Sixteen chemical compounds were further identified by gas chromatography-mass spectrometry (GC-MS). 5-hydroxymethyl-2-furancarboxaldehyde was one of the dominant components in strain JBS5-6 extracts. Moreover, fermentation broth of strain JBS5-6 significantly reduced the disease index of banana seedlings by inhibiting the infection of Foc TR4 in a pot experiment. Hence, strain JBS5-6 is a potential biocontrol agent for the management of disease and the exploitation of biofertilizer.
Heterotrophic Foraminifera Capable of Inorganic Nitrogen Assimilation
Authors: Bird Clare , LeKieffre Charlotte , Jauffrais Thierry , Meibom Anders , Geslin Emmanuelle , Filipsson Helena L. , Maire Olivier , Russell Ann D. , Fehrenbacher Jennifer S.
Published: December 2020

Nitrogen availability often limits biological productivity in marine systems, where inorganic nitrogen, such as ammonium is assimilated into the food web by bacteria and photoautotrophic eukaryotes. Recently, ammonium assimilation was observed in kleptoplast-containing protists of the phylum foraminifera, possibly via the glutamine synthetase/glutamate synthase (GS/GOGAT) assimilation pathway imported with the kleptoplasts. However, it is not known if the ubiquitous and diverse heterotrophic protists have an innate ability for ammonium assimilation. Using stable isotope incubations (15N-ammonium and 13C-bicarbonate) and combining transmission electron microscopy (TEM) with quantitative nanoscale secondary ion mass spectrometry (NanoSIMS) imaging, we investigated the uptake and assimilation of dissolved inorganic ammonium by two heterotrophic foraminifera; a non-kleptoplastic benthic species, Ammonia sp., and a planktonic species, Globigerina bulloides. These species are heterotrophic and not capable of photosynthesis. Accordingly, they did not assimilate 13C-bicarbonate. However, both species assimilated dissolved 15N-ammonium and incorporated it into organelles of direct importance for ontogenetic growth and development of the cell. These observations demonstrate that at least some heterotrophic protists have an innate cellular mechanism for inorganic ammonium assimilation, highlighting a newly discovered pathway for dissolved inorganic nitrogen (DIN) assimilation within the marine microbial loop.
Modeling the Synchronization of Multimodal Perceptions as a Basis for the Emergence of Deterministic Behaviors
Authors: Bonzon Pierre
Published: December 2020

Living organisms have either innate or acquired mechanisms for reacting to percepts with an appropriate behavior e.g., by escaping from the source of a perception detected as threat, or conversely by approaching a target perceived as potential food. In the case of artifacts, such capabilities must be built in through either wired connections or software. The problem addressed here is to define a neural basis for such behaviors to be possibly learned by bio-inspired artifacts. Toward this end, a thought experiment involving an autonomous vehicle is first simulated as a random search. The stochastic decision tree that drives this behavior is then transformed into a plastic neuronal circuit. This leads the vehicle to adopt a deterministic behavior by learning and applying a causality rule just as a conscious human driver would do. From there, a principle of using synchronized multimodal perceptions in association with the Hebb principle of wiring together neuronal cells is induced. This overall framework is implemented as a virtual machine i.e., a concept widely used in software engineering. It is argued that such an interface situated at a meso-scale level between abstracted micro-circuits representing synaptic plasticity, on one hand, and that of the emergence of behaviors, on the other, allows for a strict delineation of successive levels of complexity. More specifically, isolating levels allows for simulating yet unknown processes of cognition independently of their underlying neurological grounding.
Accelerated Dystrophy and Decay of Oligodendrocyte Precursor Cells in the APP/PS1 Model of Alzheimer’s-Like Pathology
Authors: Chacon-De-La-Rocha Irene , Fryatt Gemma , Rivera Andrea D. , Verkhratsky Alexei , Raineteau Olivier , Gomez-Nicola Diego , Butt Arthur M.
Published: December 2020

Myelin disruption is a feature of natural aging and Alzheimer’s disease (AD). In the CNS, myelin is produced by oligodendrocytes, which are generated throughout life by oligodendrocyte progenitor cells (OPCs). Here, we examined age-related changes in OPCs in APP/PS1 mice, a model for AD-like pathology, compared with non-transgenic (Tg) age-matched controls. The analysis was performed in the CA1 area of the hippocampus following immunolabeling for NG2 with the nuclear dye Hoescht, to identify OPC and OPC sister cells, a measure of OPC replication. The results indicate a significant decrease in the number of OPCs at 9 months in APP/PS1 mice, compared to age-matched controls, without further decline at 14 months. Also, the number of OPC sister cells declined significantly at 14 months in APP/PS1 mice, which was not observed in age-matched controls. Notably, OPCs also displayed marked morphological changes at 14 months in APP/PS1 mice, characterized by an overall shrinkage of OPC process domains and increased process branching. The results indicate that OPC disruption is a pathological sign in the APP/PS1 mouse model of AD.
Surface Electromyography in Physiotherapist Educational Program in France: Enhancing Learning sEMG in Stretching Practice
Authors: Portero Pierre , Dogadov Anton A. , Servière Christine , Quaine Franck
Published: December 2020

Surface electromyography (sEMG) is a non-invasive method, which may be used in France by health practitioners without medical degree, such as physiotherapists, who are taught in Institutes of physiotherapy. However, very few hours are devoted to sEMG teaching in physiotherapist educational programs, especially in a form of practical work. In order to motivate using sEMG in physiotherapy to the students, we propose an example of sEMG practical work, applied to muscle stretching. Passive stretching exercises are often used by physiotherapists to maintain or improve range of motion. During a passive stretching session, subjects are given specific instructions to relax and not to activate their muscles during the procedure. In the proposed practical work, the sEMG is used to study the plantar flexor activation level during passive stretching. Therefore, this work may provide students with deeper understanding of physiology and biomechanics, trigger an interest in sEMG as a tool, and give knowledge about good sEMG practice, according to SENIAM and other recommendations. The integration of Institutes of physiotherapy in the University system may provide an opportunity to revisit the physiotherapist educational program and to provide students with more practical courses on sEMG application.