bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-Wide Transcription Analysis of Electroacupuncture Precondition-Induced Ischemic Tolerance on SD Rat With Ischemia–Reperfusion Injury
Authors: Fu Shuping , Yu Meiling , Xu Houxi , Liu Qing , Li Xiaoxiao , Wang Yaling , Chen Yonglin , Meng Lingling , Qiu Yiting , Jing Xinyue , Liu Chenchen , Lu Shengfeng
Published: August 2021

Acupuncture promotes the recovery of neurological function by the overall improvement of ischemic brain injury. It is not only regarded as a rehabilitative treatment but also a pretreatment method for stroke. However, its mechanism has not been fully elucidated. In this study, rats were treated with electroacupuncture (EA) at Baihui (GV20) for 30 min/day for 6 days, ahead of conducting cerebral ischemia–reperfusion (I/R) injury. Infarction volume, Evans blue leakage, and neurological deficits were evaluated at 24 h after I/R injury. Then, the ipsilateral ischemic brain was isolated for RNA sequencing (RNA-Seq) to identify molecular consequences. The results showed that EA pretreatment decreased blood–brain barrier (BBB) permeability, reduced brain infarction volume, and improved neurological outcomes. EA pretreatment could upregulate expression of antivirus and immunity activity-associated genes (such as Ifit1, Ifit3, Irf7, and Oasla) and downregulate expression of matrix disruption-associated genes (Col24a1, Col11a1, Col27a1, etc.) in healthy rats. In addition, it could partially reverse or ameliorate genome-wide transcription changes of the ipsilateral ischemic brain. For the first time, this study provides insight into genomic network modulation of a healthy rat with EA treatment and a EA-preconditioned rat under subsequent I/R injury, which is helpful in explaining acupuncture precondition-induced ischemic tolerance of stroke. It also provides new strategies and targets for the prevention of ischemic stroke.
RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization
Authors: Wei Zhaoyuan , Sun Jiahe , Li Qinhui , Yao Ting , Zeng Haiyue , Wang Yi
Published: August 2021

Retrocopies, which are considered “junk genes,” are occasionally formed via the insertion of reverse-transcribed mRNAs at new positions in the genome. However, an increasing number of recent studies have shown that some retrocopies exhibit new biological functions and may contribute to genome evolution. Hence, the identification of retrocopies has become very meaningful for studying gene duplication and new gene generation. Current pipelines identify retrocopies through complex operations using alignment programs and filter scripts in a step-by-step manner. Therefore, there is an urgent need for a simple and convenient retrocopy annotation tool. Here, we report the development of RetroScan, a publicly available and easy-to-use tool for scanning, annotating and displaying retrocopies, consisting of two components: an analysis pipeline and a visual interface. The pipeline integrates a series of bioinformatics software programs and scripts for identifying retrocopies in just one line of command. Compared with previous methods, RetroScan increases accuracy and reduces false-positive results. We also provide a Shiny app for visualization. It displays information on retrocopies and their parental genes that can be used for the study of retrocopy structure and evolution. RetroScan is available at https://github.com/Vicky123wzy/RetroScan.
Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data
Authors: Li Jing , Singh Urminder , Arendsee Zebulun , Wurtele Eve Syrkin
Published: August 2021

The “dark transcriptome” can be considered the multitude of sequences that are transcribed but not annotated as genes. We evaluated expression of 6,692 annotated genes and 29,354 unannotated open reading frames (ORFs) in the Saccharomyces cerevisiae genome across diverse environmental, genetic and developmental conditions (3,457 RNA-Seq samples). Over 30% of the highly transcribed ORFs have translation evidence. Phylostratigraphic analysis infers most of these transcribed ORFs would encode species-specific proteins (“orphan-ORFs”); hundreds have mean expression comparable to annotated genes. These data reveal unannotated ORFs most likely to be protein-coding genes. We partitioned a co-expression matrix by Markov Chain Clustering; the resultant clusters contain 2,468 orphan-ORFs. We provide the aggregated RNA-Seq yeast data with extensive metadata as a project in MetaOmGraph (MOG), a tool designed for interactive analysis and visualization. This approach enables reuse of public RNA-Seq data for exploratory discovery, providing a rich context for experimentalists to make novel, experimentally testable hypotheses about candidate genes.
Genome-Wide Association Study of Growth Performance and Immune Response to Newcastle Disease Virus of Indigenous Chicken in Rwanda
Authors: Habimana Richard , Ngeno Kiplangat , Okeno Tobias Otieno , Hirwa Claire D’ andre , Keambou Tiambo Christian , Yao Nasser Kouadio
Published: August 2021

A chicken genome has several regions with quantitative trait loci (QTLs). However, replication and confirmation of QTL effects are required particularly in African chicken populations. This study identified single nucleotide polymorphisms (SNPs) and putative genes responsible for body weight (BW) and antibody response (AbR) to Newcastle disease (ND) in Rwanda indigenous chicken (IC) using genome-wide association studies (GWAS). Multiple testing was corrected using chromosomal false detection rates of 5 and 10% for significant and suggestive thresholds, respectively. BioMart data mining and variant effect predictor tools were used to annotate SNPs and candidate genes, respectively. A total of four significant SNPs (rs74098018, rs13792572, rs314702374, and rs14123335) significantly (p ≤ 7.6E−5) associated with BW were identified on chromosomes (CHRs) 8, 11, and 19. In the vicinity of these SNPs, four genes such as pre-B-cell leukaemia homeobox 1 (PBX1), GPATCH1, MPHOSPH6, and MRM1 were identified. Four other significant SNPs (rs314787954, rs13623466, rs13910430, and rs737507850) all located on chromosome 1 were strongly (p ≤ 7.6E−5) associated with chicken antibody response to ND. The closest genes to these four SNPs were cell division cycle 16 (CDC16), zinc finger, BED-type containing 1 (ZBED1), myxovirus (influenza virus) resistance 1 (MX1), and growth factor receptor bound protein 2 (GRB2) related adaptor protein 2 (GRAP2). Besides, other SNPs and genes suggestively (p ≤ 1.5E−5) associated with BW and antibody response to ND were reported. This work offers a useful entry point for the discovery of causative genes accountable for essential QTLs regulating BW and antibody response to ND traits. Results provide auspicious genes and SNP-based markers that can be used in the improvement of growth performance and ND resistance in IC populations based on gene-based and/or marker-assisted breeding selection.
Lower Oligomeric Form of Surfactant Protein D in Murine Acute Lung Injury Induces M1 Subtype Macrophages Through Calreticulin/p38 MAPK Signaling Pathway
Authors: Li Dandan , Pan Linyue , Zhang Xiaoju , Jiang Zhilong
Published: August 2021

Surfactant protein D (SP-D) plays an important role in innate and adaptive immune responses. In this study, we found that the expression of total and de-oligomerized SP-D was significantly elevated in mice with lipopolysaccharide (LPS)-induced acute lung injury (ALI). To investigate the role of the lower oligomeric form of SP-D in the pathogenesis of ALI, we treated bone marrow-derived macrophages (BMDMs) with ALI-derived bronchoalveolar lavage (BAL) and found that SP-D in ALI BAL predominantly bound to calreticulin (CALR) on macrophages, subsequently increasing the phosphorylation of p38 mitogen-activated protein kinase (MAPK) and expression of interleukin (IL)-6, tumor necrosis factor (TNF)-alpha, IL-10, and CD80. However, anti-SP-D (aSP-D) and anti-calreticulin (aCALR) pretreatment reversed the SP-D binding and activation of macrophages induced by ALI BAL or de-oligomerized recombinant murine SP-D (rSP-D). Lack of signal transducer and activator of transcription (STAT)6 in STAT6-/- macrophages resulted in resistance to suppression by aCALR. Further studies in an ALI mouse model showed that blockade of pulmonary SP-D by intratracheal (i.t.), but not intraperitoneal (i.p.), administration of aSP-D attenuated the severity of ALI, accompanied by lower neutrophil infiltrates and expression of IL-1beta and IL-6. Furthermore, i.t. administration of de-oligomerized rSP-D exacerbated the severity of ALI in association with more pro-inflammatory CD45+Siglec-F(-) M1 subtype macrophages and production of IL-6, TNF-alpha, IL-1beta, and IL-18. The results indicated that SP-D in the lungs of murine ALI was de-oligomerized and participated in the pathogenesis of ALI by predominantly binding to CALR on macrophages and subsequently activating the pro-inflammatory downstream signaling pathway. Targeting de-oligomerized SP-D is a promising therapeutic strategy for the treatment of ALI and acute respiratory distress syndrome (ARDS).
ICAM-1 and ICAM-2 Are Differentially Expressed and Up-Regulated on Inflamed Pulmonary Epithelium, but Neither ICAM-2 nor LFA-1: ICAM-1 Are Required for Neutrophil Migration Into the Airways In Vivo
Authors: Chong Deborah L. W. , Rebeyrol Carine , José Ricardo J. , Williams Andrew E. , Brown Jeremy S. , Scotton Chris J. , Porter Joanna C.
Published: August 2021

Neutrophil migration into the airways is an important process to fight infection and is mediated by cell adhesion molecules. The intercellular adhesion molecules, ICAM-1 (CD54) and ICAM-2 (CD102) are known ligands for the neutrophil integrins, lymphocyte function associated antigen (LFA)-1 (αLβ2; CD11a/CD18), and macrophage-1 antigen (Mac-1;αMβ2;CD11b/CD18) and are implicated in leukocyte migration into the lung. However, it is ill-defined how neutrophils exit the lung and the role for ICAMs in trans-epithelial migration (TEpM) across the bronchial or alveolar epithelium. We found that human and murine alveolar epithelium expressed ICAM-1, whilst the bronchial epithelium expressed ICAM-2, and both were up-regulated during inflammatory stimulationin vitro and in inflammatory lung diseases such as cystic fibrosis. Although β2integrins interacting with ICAM-1 and -2 mediated neutrophil migration across human bronchial epitheliumin vitro, neither ICAM-2 nor LFA-1 binding of ICAM-1 mediated murine neutrophil migration into the lung or broncho-alveolar space during LPS-induced inflammationin vivo. Furthermore, TEpM of neutrophils themselves resulted in increased epithelial junctional permeability and reduced barrier functionin vitro. This suggests that although β2integrins interacting with ICAMs may regulate low levels of neutrophil traffic in healthy lung or early in inflammation when the epithelial barrier is intact; these interactions may be redundant later in inflammation when epithelial junctions are disrupted and no longer limit TEpM.
Shrimp Plasma CREG Is a Hemocyte Activation Factor
Authors: Huang Zhiqi , Yang Peng , Wang Fan
Published: August 2021

Cytokines are a class of immunoregulatory proteins that are secreted by cells. Although vertebrate cytokine, especially mammalian cytokine has been well studied for the past decades. Much less attention has been paid to invertebrate so that only some cytokines have been identified in invertebrates. We have chosen Peaneus vannamei as a model to explore novel invertebrate cytokines. To achieve this, we previously purified shrimp plasma low abundance proteins and identified more than 400 proteins with proteomics analyses. In this study, a cellular repressor of E1A-stimulated gene (CREG)-like protein, which is highly conserved from Drosophila melanogaster to Homo sapiens, was further characterized in shrimp plasma. We found that shrimp plasma CREG was a glycoprotein which was strongly induced in hemolymph at 8 h post-LPS injection. Further function experiment unveiled that recombinant shrimp CREG protein injection significantly increased phagocytic hemocyte and lysosome-high hemocyte proportion in hemolymph. After that, hemocytes from rEGFP- and rCREG-protein injected shrimps were subjected to transcriptome analyses, which revealed that shrimp CREG protein could comprehensively promote hemocyte maturation and activation. Taken together, our data clearly indicated that shrimp plasma CREG protein is a novel hemocyte activation factor, which is probably a conserved myeloid cell lineage activation factor from invertebrate to vertebrate.
Corticosteroids for Treating Sepsis in Adult Patients: A Systematic Review and Meta-Analysis
Authors: Liang Huoyan , Song Heng , Zhai Ruiqing , Song Gaofei , Li Hongyi , Ding Xianfei , Kan Quancheng , Sun Tongwen
Published: August 2021

Objective

Corticosteroids are a common option used in sepsis treatment. However, the efficacy and potential risk of corticosteroids in septic patients have not been well assessed. This review was performed to assess the efficacy and safety of corticosteroids in patients with sepsis.

Methods

PubMed, Embase, and Cochrane library databases were searched from inception to March 2021. Randomized controlled trials (RCTs) that evaluated the effect of corticosteroids on patients with sepsis were included. The quality of outcomes in the included articles was evaluated using the Grading of Recommendations Assessment, Development, and Evaluation methodology. The data were pooled by using risk ratio (RR) and mean difference (MD). The random-effects model was used to evaluate the pooled MD or RR and 95% confidence intervals (CIs).

Results

Fifty RCTs that included 12,304 patients with sepsis were identified. Corticosteroids were not associated with the mortality in 28-day (RR, 0.94; 95% CI, 0.87–1.02; evidence rank, moderate) and long-term mortality (>60 days) (RR, 0.96; 95% CI, 0.88–1.05) in patients with sepsis (evidence rank, low). However, corticosteroids may exert a significant effect on the mortality in the intensive care unit (ICU) (RR, 0.9; 95% CI, 0.83–0.97), in-hospital (RR, 0.9; 95% CI, 0.82–0.99; evidence rank, moderate) in patients with sepsis or septic shock (evidence rank, low). Furthermore, corticosteroids probably achieved a tiny reduction in the length of hospital stay and ICU. Corticosteroids were associated with a higher risk of hypernatremia and hyperglycemia; furthermore, they appear to have no significant effect on superinfection and gastroduodenal bleeding.

Conclusions

Corticosteroids had no significant effect on the 28-day and long-term mortality; however, they decreased the ICU and hospital mortality. The findings suggest that the clinical corticosteroids may be an effective therapy for patients with sepsis during the short time.

Systematic Review Registration

https://inplasy.com/wp-content/uploads/2021/05/INPLASY-Protocol-1074-4.pdf
In Situ Overexpression of Matricellular Mechanical Proteins Demands Functional Immune Signature and Mitigates Non-Small Cell Lung Cancer Progression
Authors: Yaegashi Lygia Bertalha , Baldavira Camila Machado , Prieto Tabatha Gutierrez , Machado-Rugolo Juliana , Velosa Ana Paula Pereira , da Silveira Lizandre Keren Ramos , Assato Aline , Ab’Saber Alexandre Muxfeldt , Falzoni Roberto , Takagaki Teresa , Silva Pedro Leme , Teodoro Walcy Rosolia , Capelozzi Vera Luiza
Published: August 2021

Non-small cell lung carcinoma (NSCLC) is a complex cancer biome composed of malignant cells embedded in a sophisticated tumor microenvironment (TME) combined with different initiating cell types, including immune cells and cancer-associated fibroblasts (CAFs), and extracellular matrix (ECM) proteins. However, little is known about these tumors’ immune-matricellular relationship as functional and mechanical barriers. This study investigated 120 patients with NSCLC to describe the immune-matricellular phenotypes of their TME and their relationship with malignant cells. Immunohistochemistry (IHC) was performed to characterize immune checkpoints (PD-L1, LAG-3, CTLA-4+, VISTA 1), T cells (CD3+), cytotoxic T cells (CD8+, Granzyme B), macrophages (CD68+), regulatory T cells (FOXP3+, CD4+), natural killer cells (CD57+), and B lymphocytes (CD20+), whereas CAFs and collagen types I, III, and V were characterized by immunofluorescence (IF). We observed two distinct functional immune-cellular barriers—the first of which showed proximity between malignant cells and cytotoxic T cells, and the second of which showed distant proximity between non-cohesive nests of malignant cells and regulatory T cells. We also identified three tumor-associated matricellular barriers: the first, with a localized increase in CAFs and a low deposition of Col V, the second with increased CAFs, Col III and Col I fibers, and the third with a high amount of Col fibers and CAFs bundled and aligned perpendicularly to the tumor border. The Cox regression analysis was designed in two steps. First, we investigated the relationship between the immune-matricellular components and tumor pathological stage (I, II, and IIIA), and better survival rates were seen in patients whose tumors expressed collagen type III > 24.89 fibers/mm². Then, we included patients who had progressed to pathological stage IV and found an association between poor survival and tumor VISTA 1 expression > 52.86 cells/mm² and CD3+ ≤ 278.5 cells/mm². We thus concluded that differential patterns in the distribution of immune-matricellular phenotypes in the TME of NSCLC patients could be used in translational studies to predict new treatment strategies and improve patient outcome. These data raise the possibility that proteins with mechanical barrier function in NSCLC may be used by cancer cells to protect them from immune cell infiltration and immune-mediated destruction, which can otherwise be targeted effectively with immunotherapy or collagen therapy.
Radiation-Inactivated S. gallinarum Vaccine Provides a High Protective Immune Response by Activating Both Humoral and Cellular Immunity
Authors: Ji Hyun Jung , Byun Eui-Baek , Chen Fengjia , Ahn Ki Bum , Jung Ho Kyoung , Han Seung Hyun , Lim Jae Hyang , Won Yongkwan , Moon Ja Young , Hur Jin , Seo Ho Seong
Published: August 2021

Salmonella entericasubsp.entericaserovar Gallinarum (SG) is a common pathogen in chickens, and causes an acute systemic disease that leads to high mortality. The live attenuated vaccine 9R is able to successfully protect chickens older than six weeks by activating a robust cell-mediated immune response, but its safety and efficacy in young chickens remains controversial. An inactivated SG vaccine is being used as an alternative, but because of its low cellular immune response, it cannot be used as a replacement for live attenuated 9R vaccine. In this study, we employed gamma irradiation instead of formalin as an inactivation method to increase the efficacy of the inactivated SG vaccine. Humoral, cellular, and protective immune responses were compared in both mouse and chicken models. The radiation-inactivated SG vaccine (r-SG) induced production of significantly higher levels of IgG2b and IgG3 antibodies than the formalin-inactivated vaccine (f-SG), and provided a homogeneous functional antibody response against group D, but not group B Salmonella. Moreover, we found that r-SG vaccination could provide a higher protective immune response than f-SG by inducing higher Th17 activation. These results indicate that r-SG can provide a protective immune response similar to the live attenuated 9R vaccine by activating a higher humoral immunity and a lower, but still protective, cellular immune response. Therefore, we expect that the radiation inactivation method might substitute for the 9R vaccine with little or no side effects in chickens younger than six weeks.
Drosophila as a Model to Study Cellular Communication Between the Hematopoietic Niche and Blood Progenitors Under Homeostatic Conditions and in Response to an Immune Stress
Authors: Morin-Poulard Ismaël , Tian Yushun , Vanzo Nathalie , Crozatier Michèle
Published: August 2021

In adult mammals, blood cells are formed from hematopoietic stem progenitor cells, which are controlled by a complex cellular microenvironment called “niche”. Drosophila melanogaster is a powerful model organism to decipher the mechanisms controlling hematopoiesis, due both to its limited number of blood cell lineages and to the conservation of genes and signaling pathways throughout bilaterian evolution. Insect blood cells or hemocytes are similar to the mammalian myeloid lineage that ensures innate immunity functions. Like in vertebrates, two waves of hematopoiesis occur in Drosophila. The first wave takes place during embryogenesis. The second wave occurs at larval stages, where two distinct hematopoietic sites are identified: subcuticular hematopoietic pockets and a specialized hematopoietic organ called the lymph gland. In both sites, hematopoiesis is regulated by distinct niches. In hematopoietic pockets, sensory neurons of the peripheral nervous system provide a microenvironment that promotes embryonic hemocyte expansion and differentiation. In the lymph gland blood cells are produced from hematopoietic progenitors. A small cluster of cells called Posterior Signaling Centre (PSC) and the vascular system, along which the lymph gland develops, act collectively as a niche, under homeostatic conditions, to control the balance between maintenance and differentiation of lymph gland progenitors. In response to an immune stress such as wasp parasitism, lymph gland hematopoiesis is drastically modified and shifts towards emergency hematopoiesis, leading to increased progenitor proliferation and their differentiation into lamellocyte, a specific blood cell type which will neutralize the parasite. The PSC is essential to control this emergency response. In this review, we summarize Drosophila cellular and molecular mechanisms involved in the communication between the niche and hematopoietic progenitors, both under homeostatic and stress conditions. Finally, we discuss similarities between mechanisms by which niches regulate hematopoietic stem/progenitor cells in Drosophila and mammals.
Legal Issues for Artificial Floating Islands
Authors: Flikkema Maarten M. B. , Lin Fen-Yu (Vicky) , van der Plank Pernille P. J. , Koning Jos , Waals Olaf
Published: August 2021

Developments of multi-use floating islands are accelerated by an increase in offshore activities and pressing needs to create extra space in coastal regions for the surging population. The Horizon 2020 EU funded research project Space@Sea developed a modular floating island concept for offshore multi-use applications and examined current legal issues and barriers concerning its development. In this paper a floating island is defined to be “an artificially created floater, or set of connected floaters, moored to the seabed of which the topside can be used for activities similar to activities on land”. This paper aims to delve into governance issues like the assignment of authority on a multi-use floating island and the shift from regulating offshore living for working purposes to living purposes, as well as maritime law and property law (using the Netherlands as case study). Within the Exclusive Economic Zone (EEZ) a coastal state can establish, locate, and govern the floating island. For the high seas the International Maritime Organization (IMO) is the most probable organization to initiate a discussion on settlement of floating islands. For each activity on the floating island, limiting criteria regarding motions as well as safety rules and regulations need to be established. Industry and housing will have completely different requirements regarding safety which will not be possible to fit in a one size fits all regulation. This case study shows that current Dutch property law prohibit the division of ownership of buildings built on floating objects. They can only be owned together as one object. For urban expansion, future inhabitants will want to have the possibility to buy property, requiring an amendment of current property law. It is to be expected that other countries will have similar or additional governance challenges. The Space@Sea project has developed a technical solution for floating islands which have identified barriers for multi-use in the rules and regulations described in this paper. The paper urges the responsible institutions and stakeholders to take on their roles in overcoming these barriers.
The Reef Check Mediterranean Underwater Coastal Environment Monitoring Protocol
Authors: Turicchia Eva , Ponti Massimo , Rossi Gianfranco , Milanese Martina , Di Camillo Cristina Gioia , Cerrano Carlo
Published: August 2021

Since 2001, trained snorkelers, freedivers, and scuba diver volunteers (collectively called EcoDivers) have been recording data on the distribution, abundance, and bathymetric range of 43 selected key marine species along the Mediterranean Sea coasts using the Reef Check Mediterranean Underwater Coastal Environment Monitoring (RCMed U-CEM) protocol. The taxa, including algae, invertebrates, and fishes, were selected by a combination of criteria, including ease of identification and being a key indicator of shifts in the Mediterranean subtidal habitats due to local pressures and climate change. The dataset collected using the RCMed U-CEM protocol is openly accessible across different platforms and allows for various uses. It has proven to be useful for several purposes, such as monitoring the ecological status of Mediterranean coastal environments, assessing the effects of human impacts and management interventions, as well as complementing scientific papers on species distribution and abundance, distribution modeling, and historical series. Also, the commitment of volunteers promotes marine stewardship and environmental awareness in marine conservation. Here, we describe the RCMed U-CEM protocol from training volunteers to recording, delivering, and sharing data, including the quality assurance and control (QA/QC) procedures.
Assessing Procedural Justice in the Administration of Small-Scale Benthic Fisheries in Chile
Authors: Estévez Rodrigo A. , Jerez Gabriel , Gelcich Stefan
Published: August 2021

In order to navigate toward ocean sustainability, policies, programs, and scientific research must address issues of justice. In fisheries management, justice has generally been understood in terms of the distribution of social, cultural, and economic benefits. However, there are also important procedural justice challenges in the fisheries system, which are fundamental to the long-term sustainability and equity of the oceans. Procedural justice is related to the conditions under which the negotiation for benefit distribution takes place. That is, the procedures, structures, and processes that lead to the distribution of resources. In this study, we empirically assess fishers’ perceptions of procedural justice components within a small-scale fishery management policy in Chile which has been shifting toward a polycentric type of governance during the past 7 years. We specifically assess perceptions of management committee members. Management committees have been constituted as spaces of collective action for participatory decision-making. We decompose procedural justice in seven subcomponents and assess perceptions associated to achievement in the administration of fisheries. Our results show that management committee members perceive heterogeneity in the achievement of different procedural justice components, which is a central element in achieving equitable development in the oceans. The highest perceptions of achievement were found in the procedures for the selection of participants, the use of various types of technical and local knowledge for decision-making, and the perception by participants of ethical and impartial procedures. We also identified significant challenges related to an inflexible legal structure that hinders adaptive management and learning as a tool for institutional transformation. In addition, mechanisms for communicating decisions to users and clear accountability procedures were perceived as weak. It is critical to address these gaps as they can jeopardize the implementation and legitimacy of fisheries management. Focusing on different components of procedural justice can provide an important lens through which advances and gaps in fisheries policy can be identified and worked upon.
Instrumented Wave Gliders for Air-Sea Interaction and Upper Ocean Research
Authors: Grare Laurent , Statom Nicholas M. , Pizzo Nick , Lenain Luc
Published: August 2021

Over the last several years, the Air-Sea Interaction Laboratory at Scripps Institution of Oceanography has developed a fleet of wave-powered, uncrewed Wave Gliders (Liquid Robotics) specifically designed and instrumented for state-of-the-art air-sea interaction and upper ocean observations. In this study, measurement capabilities from these platforms are carefully described, compared, and validated against coincident measurements from well-established, independent data sources. Data collected from four major field programs from 2013 to 2020 are considered in the analysis. Case studies focusing on air-sea interaction, Langmuir circulations, and frontal processes are presented. We demonstrate here that these novel, instrumented platforms are capable of collecting observations with minimal flow-structure interaction in the air-sea boundary layer, a region of crucial current and future importance for models of weather and climate.
Evaluating the Flame Retardancy of Shaving Super Bamboo Layer by Layer Self-Assembly With Phytic Acid-Polyethyleneimine
Authors: Lin Peng , Jiang Yingqiu , Ru Xiaolin , Che Wenbo , Zhang Xiaochun , Ma Lingfei , Hou Junfeng , Yu Youming
Published: August 2021

To improve the flame retardancy of bamboo materials, layer by layer (LbL) self-assembly of phytic acid (PA)-polyethyleneimine (PEI) on the surface of shaving super bamboo specimens with different solution concentrations of PA-PEI and times of LbL self-assembly was completed in this study. Fourier transform infrared analysis results showed that PEI was well assembled to the surface of bamboo specimens by a hydrogen bond with PA as intermediation. The application of PA and PEI significantly promoted the formation of carbon residue, as characterized by simultaneous thermal measurements. Particularly, the peak heat release rate and total heat release rate of bamboo self-assembly with 10 wt% PA and 10 wt% of PEI solution were reduced by 19.36 and 22.3%, respectively. The treated bamboo specimen showed increases of 35.56 and 480.70% in fire performance index and residual mass, respectively, compared to the control sample. Besides, yields of CO and CO2 were decreased by 17.77 and 17.07% in comparison with the control group, respectively. The LbL self-assembly with PA-PEI can effectively improve the flame retardancy of bamboo materials by promoting the formation of a residual char layer.
Healthcare-Associated Infections-Related Bacteriome and Antimicrobial Resistance Profiling: Assessing Contamination Hotspots in a Developing Country Public Hospital
Authors: Sereia Aline Fernanda Rodrigues , Christoff Ana Paula , Cruz Giuliano Netto Flores , da Cunha Patrícia Amorim , da Cruz Guilherme Cezar Kniphoff , Tartari Daniela Cristina , Zamparette Caetana Paes , Klein Taise Costa Ribeiro , Masukawa Ivete Ioshiko , Silva Clarice Iomara , e Vieira Maria Luiza Vieira , Scheffer Mara Cristina , de Oliveira Luiz Felipe Valter , Sincero Thaís Cristine Marques , Grisard Edmundo Carlos
Published: August 2021

Hospital-built environment colonization by healthcare-associated infections-related bacteria (HAIrB) and the interaction with their occupants have been studied to support more effective tools for HAI control. To investigate HAIrB dynamics and antimicrobial resistance (AMR) profile we carried out a 6-month surveillance program in a developing country public hospital, targeting patients, hospital environment, and healthcare workers, using culture-dependent and culture-independent 16S rRNA gene sequencing methods. The bacterial abundance in both approaches shows that the HAIrB group has important representativeness, with the taxa Enterobacteriaceae, Pseudomonas, Staphylococcus, E. coli, and A. baumannii widely dispersed and abundant over the time at the five different hospital units included in the survey. We observed a high abundance of HAIrB in the patient rectum, hands, and nasal sites. In the healthcare workers, the HAIrB distribution was similar for the hands, protective clothing, and mobile phones. In the hospital environment, the healthcare workers resting areas, bathrooms, and bed equipment presented a wide distribution of HAIrB and AMR, being classified as contamination hotspots. AMR is highest in patients, followed by the environment and healthcare workers. The most frequently detected beta-lactamases genes were, blaSHV–like, blaOXA–23–like, blaOXA–51–like, blaKPC–like, blaCTX–M–1, blaCTX–M–8, and blaCTX–M–9 groups. Our results demonstrate that there is a wide spread of antimicrobial resistance due to HAIrB in the hospital environment, circulating among patients and healthcare workers. The contamination hotspots identified proved to be constant over time. In the fight for patient safety, these findings can reorient practices and help to set up new guidelines for HAI control.
pH Homeostasis and Sodium Ion Pumping by Multiple Resistance and pH Antiporters in Pyrococcus furiosus
Authors: Haja Dominik K. , Adams Michael W. W.
Published: August 2021

Multiple Resistance and pH (Mrp) antiporters are seven-subunit complexes that couple transport of ions across the membrane in response to a proton motive force (PMF) and have various physiological roles, including sodium ion sensing and pH homeostasis. The hyperthermophilic archaeon Pyrococcus furiosus contains three copies of Mrp encoding genes in its genome. Two are found as integral components of two respiratory complexes, membrane bound hydrogenase (MBH) and the membrane bound sulfane sulfur reductase (MBS) that couple redox activity to sodium translocation, while the third copy is a stand-alone Mrp. Sequence alignments show that this Mrp does not contain an energy-input (PMF) module but contains all other predicted functional Mrp domains. The P. furiosus Mrp deletion strain exhibits no significant changes in optimal pH or sodium ion concentration for growth but is more sensitive to medium acidification during growth. Cell suspension hydrogen gas production assays using the deletion strain show that this Mrp uses sodium as the coupling ion. Mrp likely maintains cytoplasmic pH by exchanging protons inside the cell for extracellular sodium ions. Deletion of the MBH sodium-translocating module demonstrates that hydrogen gas production is uncoupled from ion pumping and provides insights into the evolution of this Mrp-containing respiratory complex.
Dispersal Limitation Plays Stronger Role in the Community Assembly of Fungi Relative to Bacteria in Rhizosphere Across the Arable Area of Medicinal Plant
Authors: Zhang Guozhuang , Wei Guangfei , Wei Fugang , Chen Zhongjian , He Mingjun , Jiao Shuo , Wang Yong , Dong Linlin , Chen Shilin
Published: August 2021

Understanding the ecological patterns of rhizosphere microbial communities is critical for propelling sustainable agriculture and managing ecosystem functions by exploiting microorganisms. However, this knowledge is still unclear, especially under host-associated large-scale and regarding the comparison between bacteria and fungi. We examined community assembly processes and community characters including environmental thresholds and co-occurrence patterns across the cultivatable area ofPanax notoginsengfor bacteria and fungi. Both are vital members of the rhizosphere but differ considerably in their life history and dispersal potentiality. Edaphic factors drove the parallel variations of bacterial and fungal communities. Although bacterial and fungal communities exhibited similar biogeographic patterns, the assembly of fungi was more driven by dispersal limitation than selection compared with bacteria. This finding supported the ‘size-dispersal’ hypothesis. pH and total nitrogen respectively mediated the relative importance of deterministic and stochastic processes in shaping bacterial and fungal communities. In addition, fungal communities exhibited potentially broader environmental thresholds and more modular co-occurrence patterns than bacteria (bacteria: 0.67; fungi: 0.78). These results emphasized the importance of dispersal limitation in structuring rhizosphere microbiota and shaping community features of ecologically distinct microorganisms. This study provides insights into the improved prediction and management of the key functions of rhizosphere microbiota.
Bespoke Biomolecular Wires for Transmembrane Electron Transfer: Spontaneous Assembly of a Functionalized Multiheme Electron Conduit
Authors: Piper Samuel E. H. , Edwards Marcus J. , van Wonderen Jessica H. , Casadevall Carla , Martel Anne , Jeuken Lars J. C. , Reisner Erwin , Clarke Thomas A. , Butt Julea N.
Published: August 2021

Shewanella oneidensis exchanges electrons between cellular metabolism and external redox partners in a process that attracts much attention for production of green electricity (microbial fuel cells) and chemicals (microbial electrosynthesis). A critical component of this pathway is the outer membrane spanning MTR complex, a biomolecular wire formed of the MtrA, MtrB, and MtrC proteins. MtrA and MtrC are decaheme cytochromes that form a chain of close-packed hemes to define an electron transfer pathway of 185 Å. MtrA is wrapped inside MtrB for solubility across the outer membrane lipid bilayer; MtrC sits outside the cell for electron exchange with external redox partners. Here, we demonstrate tight and spontaneous in vitro association of MtrAB with separately purified MtrC. The resulting complex is comparable with the MTR complex naturally assembled by Shewanella in terms of both its structure and rates of electron transfer across a lipid bilayer. Our findings reveal the potential for building bespoke electron conduits where MtrAB combines with chemically modified MtrC, in this case, labeled with a Ru-dye that enables light-triggered electron injection into the MtrC heme chain.
Deletion of alpB Gene Influences Outer Membrane Vesicles Biogenesis of Lysobacter sp. XL1
Authors: Kudryakova Irina V. , Afoshin Alexey S. , Ivashina Tanya V. , Suzina Natalia E. , Leontyevskaya Elena A. , Leontyevskaya (Vasilyeva) Natalia V.
Published: August 2021

Outer membrane vesicles (OMVs) produced by Gram-negative bacteria constitute important factors in defining interactions with the extracellular milieu. Lysobacter sp. XL1 produces OMVs capable of lysing microbial cells due to the presence in their cargo of bacteriolytic protease L5 (AlpB). Although protein L5 has been functionally and biochemically characterized (including aspects of its packing into OMVs), its role in vesicle biogenesis through genetic deletion of alpB had not been studied previously. Here, we have successfully deleted alpB by allelic replacement and show that the alpB deletion mutant produces a significantly lower amount of OMVs that lack bacteriolytic activity and display altered ultrastructural characteristics in relation to the OMVs produced by the wild-type strain. These results confirm that, as previously proposed, protein L5 participates in OMV production through a mechanism that is not yet fully understood.
Staphylococcus aureus Cell Wall Biosynthesis Modulates Bone Invasion and Osteomyelitis Pathogenesis
Authors: Masters Elysia A. , Muthukrishnan Gowrishankar , Ho Lananh , Gill Ann Lindley , de Mesy Bentley Karen L. , Galloway Chad A. , McGrath James L. , Awad Hani A. , Gill Steven R. , Schwarz Edward M.
Published: August 2021

Staphylococcus aureus invasion of the osteocyte lacuno-canalicular network (OLCN) is a novel mechanism of bacterial persistence and immune evasion in chronic osteomyelitis. Previous work highlighted S. aureus cell wall transpeptidase, penicillin binding protein 4 (PBP4), and surface adhesin, S. aureus surface protein C (SasC), as critical factors for bacterial deformation and propagation through nanopores in vitro, representative of the confined canaliculi in vivo. Given these findings, we hypothesized that cell wall synthesis machinery and surface adhesins enable durotaxis- and haptotaxis-guided invasion of the OLCN, respectively. Here, we investigated select S. aureus cell wall synthesis mutants (Δpbp3, Δatl, and ΔmreC) and surface adhesin mutants (ΔclfA and ΔsasC) for nanopore propagation in vitro and osteomyelitis pathogenesis in vivo. In vitro evaluation in the microfluidic silicon membrane-canalicular array (μSiM-CA) showed pbp3, atl, clfA, and sasC deletion reduced nanopore propagation. Using a murine model for implant-associated osteomyelitis, S. aureus cell wall synthesis proteins were found to be key modulators of S. aureus osteomyelitis pathogenesis, while surface adhesins had minimal effects. Specifically, deletion of pbp3 and atl decreased septic implant loosening and S. aureus abscess formation in the medullary cavity, while deletion of surface adhesins showed no significant differences. Further, peri-implant osteolysis, osteoclast activity, and receptor activator of nuclear factor kappa-B ligand (RANKL) production were decreased following pbp3 deletion. Most notably, transmission electron microscopy (TEM) imaging of infected bone showed that pbp3 was the only gene herein associated with decreased submicron invasion of canaliculi in vivo. Together, these results demonstrate that S. aureus cell wall synthesis enzymes are critical for OLCN invasion and osteomyelitis pathogenesis in vivo.
Lipid Metabolism Regulates Oxidative Stress and Ferroptosis in RAS-Driven Cancers: A Perspective on Cancer Progression and Therapy
Authors: Bartolacci Caterina , Andreani Cristina , El-Gammal Yasmin , Scaglioni Pier Paolo
Published: August 2021

HRAS, NRAS and KRAS, collectively referred to as oncogenic RAS, are the most frequently mutated driver proto-oncogenes in cancer. Oncogenic RAS aberrantly rewires metabolic pathways promoting the generation of intracellular reactive oxygen species (ROS). In particular, lipids have gained increasing attention serving critical biological roles as building blocks for cellular membranes, moieties for post-translational protein modifications, signaling molecules and substrates for ß-oxidation. However, thus far, the understanding of lipid metabolism in cancer has been hampered by the lack of sensitive analytical platforms able to identify and quantify such complex molecules and to assess their metabolic flux in vitro and, even more so, in primary tumors. Similarly, the role of ROS in RAS-driven cancer cells has remained elusive. On the one hand, ROS are beneficial to the development and progression of precancerous lesions, by upregulating survival and growth factor signaling, on the other, they promote accumulation of oxidative by-products that decrease the threshold of cancer cells to undergo ferroptosis. Here, we overview the recent advances in the study of the relation between RAS and lipid metabolism, in the context of different cancer types. In particular, we will focus our attention on how lipids and oxidative stress can either promote or sensitize to ferroptosis RAS driven cancers. Finally, we will explore whether this fine balance could be modulated for therapeutic gain.
Monoacylglycerol Lipase Inhibitor MJN110 Reduces Neuronal Hyperexcitability, Restores Dendritic Arborization Complexity, and Regulates Reward-Related Behavior in Presence of HIV-1 Tat
Authors: League Alexis F. , Gorman Benjamin L. , Hermes Douglas J. , Johnson Clare T. , Jacobs Ian R. , Yadav-Samudrala Barkha J. , Poklis Justin L. , Niphakis Micah J. , Cravatt Benjamin F. , Lichtman Aron H. , Ignatowska-Jankowska Bogna M. , Fitting Sylvia
Published: August 2021

While current therapeutic strategies for people living with human immunodeficiency virus type 1 (HIV-1) suppress virus replication peripherally, viral proteins such as transactivator of transcription (Tat) enter the central nervous system early upon infection and contribute to chronic inflammatory conditions even alongside antiretroviral treatment. As demand grows for supplemental strategies to combat virus-associated pathology presenting frequently as HIV-associated neurocognitive disorders (HAND), the present study aimed to characterize the potential utility of inhibiting monoacylglycerol lipase (MAGL) activity to increase inhibitory activity at cannabinoid receptor-type 1 receptors through upregulation of 2-arachidonoylglycerol (2-AG) and downregulation of its degradation into proinflammatory metabolite arachidonic acid (AA). The MAGL inhibitor MJN110 significantly reduced intracellular calcium and increased dendritic branching complexity in Tat-treated primary frontal cortex neuron cultures. Chronic MJN110 administration in vivo increased 2-AG levels in the prefrontal cortex (PFC) and striatum across Tat(+) and Tat(–) groups and restored PFC N-arachidonoylethanolamine (AEA) levels in Tat(+) subjects. While Tat expression significantly increased rate of reward-related behavioral task acquisition in a novel discriminative stimulus learning and cognitive flexibility assay, MJN110 altered reversal acquisition specifically in Tat(+) mice to rates indistinguishable from Tat(–) controls. Collectively, our results suggest a neuroprotective role of MAGL inhibition in reducing neuronal hyperexcitability, restoring dendritic arborization complexity, and mitigating neurocognitive alterations driven by viral proteins associated with latent HIV-1 infection.
A First Clinical Trial on Botulinum Toxin-A for Chronic Muscle-Related Pain in Cerebral Palsy
Authors: Jacobson Dan , Löwing Kristina , Kullander Kjell , Rydh Britt-Marie , Tedroff Kristina
Published: August 2021

Objective: To test if botulinum toxin-A (BoNT-A) is effective in reducing chronic muscle-related pain in adults with spastic cerebral palsy (CP), as compared to placebo.

Design: A single-center, double-blind, parallel, randomized placebo-controlled trial. The design included an interim analysis to allow for confirmatory analysis, as well as pilot study outcomes.

Setting: Tertiary university hospital.

Participants: Adults with spastic CP and chronic pain associated with spastic muscle(s).

Intervention: Treatment was one session of electromyographically guided intramuscular injections of either BoNT-A or placebo normosaline.

Main Study Outcomes: The primary outcome was the proportion who achieved a reduction of pain intensity of two or more steps on the Numerical Rating Scale 6 weeks after treatment.

Results: Fifty individuals were screened for eligibility, of whom 16 were included (10 female, 6 male, mean age = 32 years, SD = 13.3 years). The randomization yielded eight participants per treatment arm, and all completed the study as randomized. The study was stopped at the interim analysis due to a low probability, under a preset threshold, of a positive primary outcome. Four individuals were treatment responders in the BoNT-A group for the primary outcome compared to five responders in the placebo group (p = 1.000). Adverse events were mild to moderate. In exploratory analysis, the BoNT-A group had a trend of continuing reduction of pain at the last follow-up, after the primary endpoint.

Conclusions: This study did not find evidence that BoNT-A was superior to placebo at the desired effect size (number needed to treat of 2.5) at 6 weeks after treatment.

Trial registration:ClinicalTrials.gov: NCT02434549