bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact Analysis of Large-Scale Environmental Spot Inspection Policy on Green Innovation: Evidence From China
Authors: Chen Bo , Ren Meitong , Chen Liye
Published: May 2021

The spot inspection policy has been widely applied in environmental protection in China. This paper collects environmental enforcement announcements and green patent data published by Chinese government agencies from 2006 to 2015. First, it studies the impact of spot inspection on green innovation with the spatial Durbin model. Then, it analyzes spatial heterogeneity according to the eastern, central, and western regions including 29 provinces. The spot inspection policy significantly increases the green innovation of a current region with a negative spillover effect on neighboring regions. Even though this policy has the best performance in the eastern region, it leads to pollution transfer into the western region, while being ineffective in the central region. Further, analysis on the spatial spillover effects of the 29 provinces proves that 21 provinces have a positive spillover effect, while eight provinces have a negative spillover effect. The research study shows that although spot inspection is generally beneficial to green innovation, pollution transfer and policy failure exist because of spatial heterogeneity.
Recent and Historical Gene Flow in Cultivars, Landraces, and a Wild Taxon of Cucurbita pepo in Mexico
Authors: Martínez-González Carmina , Castellanos-Morales Gabriela , Barrera-Redondo Josué , Sánchez-de la Vega Guillermo , Hernández-Rosales Helena S. , Gasca-Pineda Jaime , Aguirre-Planter Erika , Moreno-Letelier Alejandra , Escalante Ana E. , Montes-Hernández Salvador , Lira-Saade Rafael , Eguiarte Luis E.
Published: May 2021

Gene flow among crops and their wild relatives is an active study area in evolutionary biology and horticulture, because genetic exchange between them may impact their evolutionary trajectories and increase the genetic variation of the cultivated lineages. Mexico is a center of diversity for the genus Cucurbita that includes pumpkins, squash and gourds. Gene flow between domesticated and wild species has been reported as common in Cucurbita; but gene flow among populations of C. pepo ssp. pepo from Mexico and its wild relative has not been studied. We used 2,061 SNPs, derived from tunable genotyping by sequencing (tGBS) to estimate gene flow among 14 Mexican traditional landraces of C. pepo ssp. pepo, also including individuals from five improved cultivars of C. pepo ssp. pepo and C. pepo ssp. ovifera var. ovifera, and individuals of their wild relative C. pepo ssp. fraterna. We found moderate to high levels of genetic diversity, and low to moderate genetic differentiation. In the test of introgression between lineages, we found that all possible arrangements for ancestral and derived sites between the lineages showed similar frequencies; thus, incomplete lineage sorting, but also gene flow, might be taking place in C. pepo. Overall, our results suggest that gene flow between these subspecies and cultigens, incomplete lineage sorting and the retention of ancestral characters shaped the evolutionary trajectory of C. pepo in its area of origin and diversification. In addition, we found evidence of the use of Mexican landraces as genetic material for the improvement of commercial cultivars. The landraces of Mexico are an important source of genetic diversity for C. pepo, which has been preserved both by management practices of small farmers and by the natural gene flow that exists between the different crop fields of the region.
Integrated Analyses Reveal the Multi-Omics and Prognostic Characteristics of ATP5B in Breast Cancer
Authors: Liu Min , Xu Yuxuan , Zhou Yaoyao , Lang Ronggang , Shi Zhenyu , Zhao Jing , Meng Yuanyuan , Bao Li
Published: May 2021

The beta subunit of F1Fo-ATP synthase (ATP5B) has been demonstrated to play an essential role in tumor progression and metastasis. However, there has been no comprehensive pan-cancer multi-omics analysis of ATP5B, while the clinical relevance of ATP5B and its potential mechanism in regulating breast cancer are still poorly understood. In this study, we demonstrated that ATP5B has a higher frequency of amplification than deletion in most cancer types, and the copy number variation (CNV) of ATP5B was significantly positively correlated with its mRNA expression level. DNA methylation analysis across pan-cancer also revealed a strong correlation between ATP5B expression and epigenetic changes. We identified 6 significant methylation sites involved in the regulation of ATP5B expression. Tissue microarrays (TMA) from 129 breast cancer samples, integrated with multiple additional breast cancer dataset, were used to evaluate the ATP5B expression and its correlation with prognosis. Higher levels of ATP5B expression were consistently associated with a worse OS in all datasets, and Cox regression analysis suggested that ATP5B expression was an independent prognostic factor. Gene enrichment analysis indicated that the gene signatures of DNA damage recognition, the E-cadherin nascent pathway and the PLK1 pathway were enriched in ATP5B-high patients. Moreover, somatic mutation analysis showed that a significant different mutation frequency of CDH1 and ADAMTSL3 could be observed between the ATP5B-high and ATP5B-low groups. In conclusion, this study reveals novel significance regarding the genetic characteristics and clinical value of ATP5B highlighted in predicting the outcome of breast cancer patients.
Murine Blastocysts Release Mature MicroRNAs Into Culture Media That Reflect Developmental Status
Authors: Hawke David Connor , Ahmed Danyal Baber , Watson Andrew John , Betts Dean Harvey
Published: May 2021

Extracellular microRNA (miRNA) sequences derived from the pre-implantation embryo have attracted interest for their possible contributions to the ongoing embryonic–uterine milieu, as well as their potential for use as accessible biomarkers indicative of embryonic health. Spent culture media microdroplets used to culture late-stage E4.0 murine blastocysts were screened for 641 mature miRNA sequences using a reverse transcription–quantitative polymerase chain reaction–based array. We report here 39 miRNAs exclusively detected in the conditioned media, including the implantation-relevant miR-126a-3p, miR-101a, miR-143, and miR-320, in addition to members of the highly expressed embryonic miR-125 and miR-290 families. Based on these results, an miRNA panel was assembled comprising five members of the miR-290 family (miR-291-295) and five conserved sequences with significance to the embryonic secretome (miR-20a, miR-30c, miR-142-3p, miR-191, and miR-320). Panel profiling of developing embryo cohort lysates and accompanying conditioned media microdroplets revealed extensive similarities in relative quantities of miRNAs and, as a biomarker proof of concept, enabled distinction between media conditioned with differently staged embryos (zygote, 4-cell, and blastocyst). When used to assess media conditioned with embryos of varying degrees of degeneration, the panel revealed increases in all extracellular panel sequences, suggesting cell death is an influential and identifiable factor detectable by this assessment. In situ hybridization of three panel sequences (miR-30c, miR-294, and miR-295) in late-stage blastocysts revealed primarily inner cell mass expression with a significant presence of miR-294 throughout the blastocyst cavity. Furthermore, extracellular miR-290 sequences responded significantly to high centrifugal force, suggesting a substantial fraction of these sequences may exist within a vesicle such as an exosome, microvesicle, or apoptotic bleb. Together, these results support the use of extracellular miRNA to assess embryonic health and enable development of a non-invasive viability diagnostic tool for clinical use.
Genome-Wide Association Studies Reveal Susceptibility Loci for Noninfectious Claw Lesions in Holstein Dairy Cattle
Authors: Lai Ellen , Danner Alexa L. , Famula Thomas R. , Oberbauer Anita M.
Published: May 2021

Sole ulcers (SUs) and white line disease (WLD) are two common noninfectious claw lesions (NICL) that arise due to a compromised horn production and are frequent causes of lameness in dairy cattle, imposing welfare and profitability concerns. Low to moderate heritability estimates of SU and WLD susceptibility indicate that genetic selection could reduce their prevalence. To identify the susceptibility loci for SU, WLD, SU and/or WLD, and any type of noninfectious claw lesion, genome-wide association studies (GWAS) were performed using generalized linear mixed model (GLMM) regression, chunk-based association testing (CBAT), and a random forest (RF) approach. Cows from five commercial dairies in California were classified as controls having no lameness records and ≥6 years old (n= 102) or cases having SU (n= 152), WLD (n= 117), SU and/or WLD (SU + WLD,n= 198), or any type of noninfectious claw lesion (n= 217). The top single nucleotide polymorphisms (SNPs) were defined as those passing the Bonferroni-corrected suggestive and significance thresholds in the GLMM analysis or those that a validated RF model considered important. Effects of the top SNPs were quantified using Bayesian estimation. Linkage disequilibrium (LD) blocks defined by the top SNPs were explored for candidate genes and previously identified, functionally relevant quantitative trait loci. The GLMM and CBAT approaches revealed the same regions of association on BTA8 for SU and BTA13 common to WLD, SU + WLD, and NICL. These SNPs had effects significantly different from zero, and the LD blocks they defined explained a significant amount of phenotypic variance for each dataset (6.1–8.1%,p< 0.05), indicating the small but notable contribution of these regions to susceptibility. These regions contained candidate genes involved in wound healing, skin lesions, bone growth and mineralization, adipose tissue, and keratinization. The LD block defined by the most significant SNP on BTA8 for SU included a SNP previously associated with SU. The RF models were overfitted, indicating that the SNP effects were very small, thereby preventing meaningful interpretation of SNPs and any downstream analyses. These findings suggested that variants associated with various physiological systems may contribute to susceptibility for NICL, demonstrating the complexity of genetic predisposition.
Genotypic Males Play an Important Role in the Creation of Genetic Diversity in Gynogenetic Gibel Carp
Authors: Zhao Xin , Li Zhi , Ding Miao , Wang Tao , Wang Ming-Tao , Miao Chun , Du Wen-Xuan , Zhang Xiao-Juan , Wang Yang , Wang Zhong-Wei , Zhou Li , Li Xi-Yin , Gui Jian-Fang
Published: May 2021

Unisexual lineages are commonly considered to be short-lived in the evolutionary process as accumulation of deleterious mutations stated by Muller’s ratchet. However, the gynogenetic hexaploid gibel carp (Carassius gibelio) with existence over 0.5 million years has wider ecological distribution and higher genetic diversity than its sexual progenitors, which provides an ideal model to investigate the underlying mechanisms on countering Muller’s ratchet in unisexual taxa. Unlike other unisexual lineages, the wild populations of gibel carp contain rare and variable proportions of males (1–26%), which are determined via two strategies including genotypic sex determination and temperature-dependent sex determination. Here, we used a maternal gibel carp from strain F to be mated with a genotypic male from strain A+, a temperature-dependent male from strain A+, and a male from another species common carp (Cyprinus carpio), respectively. When the maternal individual was mated with the genotypic male, a variant of gynogenesis was initiated, along with male occurrence, accumulation of microchromosomes, and creation of genetic diversity in the offspring. When the maternal individual was mated with the temperature-dependent male and common carp, typical gynogenesis was initiated that all the offspring showed the same genetic information as the maternal individual. Subsequently, we found out that the genotypic male nucleus swelled and contacted with the female nucleus after fertilization although it was extruded from the female nucleus eventually, which might be associated with the genetic variation in the offspring. These results reveal that genotypic males play an important role in the creation of genetic diversity in gynogenetic gibel carp, which provides insights into the evolution of unisexual reproduction.
Demand for Family Planning Satisfied With Modern Methods in Urban Malawi: CHAID Analysis to Identify Predictors and Women Underserved With Family Planning Services
Authors: Alhassan Nurudeen , Madise Nyovani Janet
Published: May 2021

Introduction: Family planning progress under the SDGs is measured with a novel indicator, demand for family planning satisfied with modern methods (mDFPS), which provides a better indication of modern contraceptive coverage than unmet need and contraceptive prevalence rate. Yet, few studies have examined the predictors of mDFPS and the sub-groups of women with unsatisfied mDFPS in urban Saharan Africa. The objective of this study was to examine the predictors of mDFPS in urban Malawi and to identify the sub-groups of urban women underserved with modern contraceptives.

Methods: The study analysed data from the 2015–16 Malawi Demographic and Health survey. The sample was comprised of 2,917 women in urban Malawi who had a demand for family planning services. We used a Chi-square (χ2) Automatic Interaction Detector (CHAID) model to address the study objectives.

Results: The results show that the number of living children a woman had was the most significant predictor of mDFPS. Women with one or more children, who were of Chewa, Lomwe, or Tumbuka ethnic origin and who resided in the central region had the highest mDFPS (87%). On the other hand, women with no children, and who were not exposed to FP information on television, had the lowest mDFPS (41%). Among women in union, ethnicity was the best predictor of mDFPS. Ngoni, Yao, and other ethnic minority women in union who were aged 15–19 and 40 years and above and those who were Catholic, SDA/Baptist, or Muslim had the lowest mDFPS (36%).

Conclusion: This study demonstrates significant intra-urban disparities in demand for FP satisfied with modern contraceptives in Malawi. There is a need for policymakers and reproductive health practitioners to recognise these disparities and to prioritise the underserved groups identified in this study.
Comprehensive Comparison of RNA-Seq Data of SARS-CoV-2, SARS-CoV and MERS-CoV Infections: Alternative Entry Routes and Innate Immune Responses
Authors: Cao Yingying , Xu Xintian , Kitanovski Simo , Song Lina , Wang Jun , Hao Pei , Hoffmann Daniel
Published: May 2021

Background

The pathogenesis of COVID-19 emerges as complex, with multiple factors leading to injury of different organs. Some of the studies on aspects of SARS-CoV-2 cell entry and innate immunity have produced seemingly contradictory claims. In this situation, a comprehensive comparative analysis of a large number of related datasets from several studies could bring more clarity, which is imperative for therapy development.

Methods

We therefore performed a comprehensive comparative study, analyzing RNA-Seq data of infections with SARS-CoV-2, SARS-CoV and MERS-CoV, including data from different types of cells as well as COVID-19 patients. Using these data, we investigated viral entry routes and innate immune responses.

Results and Conclusion

First, our analyses support the existence of cell entry mechanisms for SARS and SARS-CoV-2 other than the ACE2 route with evidence of inefficient infection of cells without expression of ACE2; expression of TMPRSS2/TPMRSS4 is unnecessary for efficient SARS-CoV-2 infection with evidence of efficient infection of A549 cells transduced with a vector expressing human ACE2. Second, we find that innate immune responses in terms of interferons and interferon simulated genes are strong in relevant cells, for example Calu3 cells, but vary markedly with cell type, virus dose, and virus type.
NLRP3 Inflammasome Assembly in Neutrophils Is Supported by PAD4 and Promotes NETosis Under Sterile Conditions
Authors: Münzer Patrick , Negro Roberto , Fukui Shoichi , di Meglio Lucas , Aymonnier Karen , Chu Long , Cherpokova Deya , Gutch Sarah , Sorvillo Nicoletta , Shi Lai , Magupalli Venkat Giri , Weber Alexander N. R. , Scharf Rüdiger E. , Waterman Clare M. , Wu Hao , Wagner Denisa D.
Published: May 2021

Neutrophil extracellular trap formation (NETosis) and the NLR family pyrin domain containing 3 (NLRP3) inflammasome assembly are associated with a similar spectrum of human disorders. While NETosis is known to be regulated by peptidylarginine deiminase 4 (PAD4), the role of the NLRP3 inflammasome in NETosis was not addressed. Here, we establish that under sterile conditions the cannonical NLRP3 inflammasome participates in NETosis. We show apoptosis-associated speck-like protein containing a CARD (ASC) speck assembly and caspase-1 cleavage in stimulated mouse neutrophils without LPS priming. PAD4 was needed for optimal NLRP3 inflammasome assembly by regulating NLRP3 and ASC protein levels post-transcriptionally. Genetic ablation of NLRP3 signaling resulted in impaired NET formation, because NLRP3 supported both nuclear envelope and plasma membrane rupture. Pharmacological inhibition of NLRP3 in either mouse or human neutrophils also diminished NETosis. Finally, NLRP3 deficiency resulted in a lower density of NETs in thrombi produced by a stenosis-induced mouse model of deep vein thrombosis. Altogether, our results indicate a PAD4-dependent formation of the NLRP3 inflammasome in neutrophils and implicate NLRP3 in NETosis under noninfectious conditions in vitro and in vivo.
High-End Scenarios of Sea-Level Rise for Coastal Risk-Averse Stakeholders
Authors: Dayan Hugo , Le Cozannet Goneri , Speich Sabrina , Thiéblemont Rémi
Published: May 2021

Sea-level rise (SLR) will be one of the major climate change-induced risks of the 21st century for coastal areas. The large uncertainties of ice sheet melting processes bring in a range of unlikely – but not impossible – high-end sea-level scenarios (HESs). Here, we provide global to regional HESs exploring the tails of the distribution estimates of the different components of sea level. We base our scenarios on high-end physical-based model projections for glaciers, ocean sterodynamic effects, glacial isostatic adjustment and contributions from land-water, and we rely on a recent expert elicitation assessment for Greenland and Antarctic ice-sheets. We consider two future emissions scenarios and three time horizons that are critical for risk-averse stakeholders (2050, 2100, and 2200). We present our results from global to regional scales and highlight HESs spatial divergence and their departure from global HESs through twelve coastal city and island examples. For HESs-A, the global mean-sea level (GMSL) is projected to reach 1.06(1.91) in the low(high) emission scenario by 2100. For HESs-B, GMSL may be higher than 1.69(3.22) m by 2100. As far as 2050, while in most regions SLR may be of the same order of magnitude as GMSL, at local scale where ice-sheets existed during the Last Glacial Maximum, SLR can be far lower than GMSL, as in the Gulf of Finland. Beyond 2050, as sea-level continue to rise under the HESs, in most regions increasing rates of minimum(maximum) HESs are projected at high(low-to-mid) latitudes, close to (far from) ice-sheets, resulting in regional HESs substantially lower(higher) than GMSL. In regions where HESs may be extremely high, some cities in South East Asia such as Manila are even more immediately affected by coastal subsidence, which causes relative sea-level changes that exceed our HESs by one order of magnitude in some sectors.
Diversity, Distribution and Phylogenetic Relationships of Deep-Sea Lithistids (Porifera, Heteroscleromorpha) of the Azores Archipelago
Authors: Xavier Joana R. , Rees David J. , Pereira Raquel , Colaço Ana , Pham Christopher K. , Carvalho Francisca C.
Published: May 2021

Lithistid sponges are globally distributed in temperate and sub-tropical areas, constituting an important component of deep-sea benthic communities where they form structurally complex and vulnerable marine ecosystems (VMEs). In this study, we assess the diversity and investigate the spatial and bathymetric distribution of the lithistid sponges of the Azores archipelago (North Atlantic) based on historical records and examination of samples accidentally collected during deep-sea longline fishing operations in the region. Eleven lithistid species are recognized to occur in the Azores, includingLeiodermatium tuba, recently described from material collected in several Northeast Atlantic seamounts that is hereby reported for the first time to the archipelago. We provide molecular barcodes (mtDNA COI and rRNA 28S) for seven of these species, includingDiscodermia ramifera,Macandrewia azorica, andExsuperantia archipelagus, for which the Azores constitutes the type locality. We further discuss the phylogenetic and biogeographic affinities of the Azorean lithistids in the context of the Porifera classification, and the wider Northeast Atlantic upper bathyal fauna. Our study also warrants the addition of some lithistid species to the list of VME indicators for the Northeast Atlantic in support of the sustainable management and conservation of these species and habitats, as well as the ecological functions they deliver.
Proteomic Response of the Brain to Hypoxic Stress in Marine Medaka Fish (Oryzias melastigma)
Authors: Lai Keng Po , Tam Nathan , Wang Simon Yuan , Tse William Ka Fai , Lin Xiao , Chan Ting Fung , Tong Yin , Zhang Jianwen , Au Doris Wai Ting , Wu Rudolf Shiu Sun , Kong Richard Yuen Chong
Published: May 2021

Hypoxia is a serious issue that affects the marine environment, with a growing number of hypoxic “dead zones” occurring each year. Reports have indicated that hypoxia is detrimental to the reproductive function and sexual development of fish via the disruption of endocrine signaling in organs involved in the hypothalamus–pituitary–gonad axis, including the brain. While we previously reported that hypoxia induces transcriptome-wide alterations in the brain of marine medaka (Oryzias melastigma), whether these effects were reflected at the protein level remains unclear. Therefore, the present study used high-throughput proteomic sequencing along with bioinformatics analysis to assess the short-term and multi-generational effects of hypoxia on the brain proteome of O. melastigma. We identified 36,567 peptides and 7,599 proteins (1% false discovery rate in brain samples), with functions involved in cellular and metabolic processes such as signaling and reproductive processes as well as energy production and conversion. Furthermore, we determined that hypoxia resulted in the significant differential expressions of 33 upregulated and 69 downregulated proteins in the short-term exposure group and 24 upregulated and 52 downregulated proteins in the multi-generational exposure group. Pathway enrichment analysis of the deregulated proteins indicated that hypoxia could impair brain function by altering arachidonic acid metabolism, tight junctions, and adrenergic signaling under short-term hypoxic exposure and by altering p53 and PI3K–Akt signaling under multi-generational hypoxic exposure, which may lead to the onset of neurodegenerative disorders including Alzheimer’s disease and amyotrophic lateral sclerosis. Ingenuity pathway analysis of the deregulated proteins showed that hypoxia affected common signaling pathways in the brain (e.g., integrin, paxillin, and epithelial adherens junction signaling) under both short-term and multi-generational exposures. Hypoxia also deregulated pathways specific to short-term exposure (including integrin-linked kinase, calcium, and integrin signaling) and multi-generational exposure (including sphingosine-1-phosphate signaling, endocannabinoid neuronal synapse pathway, and endoplasmic reticulum stress pathway). Overall, our results provide additional insights into the mechanisms of hypoxia disrupting neuronal function at the protein level in marine medaka.
Yellowfin Tuna Behavioural Ecology and Catchability in the South Atlantic: The Right Place at the Right Time (and Depth)
Authors: Wright Serena R. , Righton David , Naulaerts Joachim , Schallert Robert J. , Griffiths Chris A. , Chapple Taylor , Madigan Daniel , Laptikhovsky Vladimir , Bendall Victoria , Hobbs Rhys , Beare Doug , Clingham Elizabeth , Block Barbara , Collins Martin A.
Published: May 2021

The yellowfin tuna (Thunnus albacares: YFT) is a widely distributed, migratory species that supports valuable commercial fisheries. Landings of YFT are seasonally and spatially variable, reflecting changes in their availability and accessibility to different fleets and metiers which, in turn, has implications for sustainable management. Understanding the dynamics of YFT behaviour and how it is affected by biological and ecological factors is therefore of consequence to fisheries management design. Archival and pop-up satellite tags (PSAT) were used in the South Atlantic Ocean around St Helena between 2015 and 2020 to collect information on the movements, foraging and locomotory behaviour of YFT. The study aimed to (1) identify vertical behaviour of YFT within St Helena’s EEZ; (2) assess the timing and depth of potential feeding events and (3) to use the information to inform on the catchability of YFT to the local pole and line fishing fleet. Results indicate that the YFT daytime behaviour shifted between shallow with high incidence of fast starts in surface waters in summer months (December to April), to deep with high incidence of strikes at depth in colder months (May to November). Catchability of YFT was significantly reduced between May and November as YFT spent more time at depths below 100 m during the day, which coincides with a reduction in the quantity of YFT caught by the inshore fleet.
4DEMON: Integrating 40 Years of Data on PCB and Metal Contamination in Marine Sediments of the Belgian Part of the North Sea
Authors: Le Hong Minh , Bekaert Karen , Lagring Ruth , Ampe Bart , Ruttens Ann , De Cauwer Karien , Hostens Kris , De Witte Bavo
Published: May 2021

The assessment of historical data is important to understand long-term changes in the marine environment. Whereas time series analyses based on monitoring data typically span one or two decades, this work aimed to integrate 40 years of monitoring and research data on polychlorinated biphenyls (PCBs) and metals in the Belgian Part of the North Sea (BPNS). Multiple challenges were encountered: sampling locations changed over time, different analytical methods were applied, different grain size fractions were analyzed, appropriate co-factors were not always analyzed, and measurement uncertainties were not always indicated. These issues hampered the use of readily available, highly standardized trend modeling approaches like those proposed by regional sea conventions such as OSPAR, named after the Oslo and Paris conventions.Therefore, we applied alternative approaches, allowing us to include most older historical data that have been obtained during the nineteen seventies and eighties. Our approach included reproducible and quality controlled procedures from data collection up to data assessment. It included spatial clustering, data normalization and parametric linear mixed effect modeling. A Ward hierarchical clustering was applied on recently obtained contaminant data, as the basis for a spatial division of the BPNS into five distinct areas with different contamination profiles. To minimize the risk of normalization errors for the metal data analyses, four normalization approaches were applied and mutually compared: granulometric and nickel (Ni) normalization, next to two hybrid normalization methods combining aluminum (Al) and iron (Fe) normalization. The long-term models revealed decreasing trends for most metals, except zinc (Zn) for which three out of four models showed increasing concentrations in all five zones of the BPNS. Offshore sediments contained the lowest normalized mercury (Hg) and cadmium (Cd) concentrations but high arsenic (As) concentrations. Trend analysis revealed a strong decrease in PCB concentrations in the nineteen eighties and nineties, followed by a slight increase over the last decade. The extended timeframe for contaminant assessment, as applied in this study, is of added value for scientists and policy makers, as the approach allows to detect trends and effects of anthropogenic activities within the marine environment within a broad perspective.
Clinical Characteristics of Clonorchis sinensis-Associated Cholangiocarcinoma: A Large-Scale, Single-Center Study
Authors: Chang Jong-In , Lee Keol , Kim Dongwuk , Yang Ju-II , Park Jae Keun , Choi Kyu , Kang Soo Hoon , Lee Kwang Hyuck , Lee Kyu Taek , Lee Jong Kyun , Park Seon Mee , Park Joo Kyung
Published: May 2021

Background:Clonorchis sinensis (CS) infection is considered a group 1 carcinogen of cholangiocarcinoma (CCA). There were very few studies regarding clinical characteristics of CS-associated CCA (CACC). This study aimed to investigate clinical characteristics of patients with CCA with or without CS infection.

Methods: A total of 367 patients diagnosed with CCA who underwent diagnostic tests for CS infection were enrolled. CS infection was defined as follows: at least one positive serum ELISA test, skin test, stool microscopy, or bile microscopy.

Results: There were 95 (26%) patients with CS infections. The median follow-up duration was 14.9 months (range, 6.07–36.17). The following significant differences were noted among patients with CACC compared to non-CACC; diagnosis at younger age (median 62 years vs. 65 years, p = 0.018), higher male to female ratio (83.2 vs. 61.8%, p < 0.001), and residence in CS-endemic area (46.3 vs. 25.4%, p = 0.014). Univariate analysis of prognostic factors indicated that tumor location, curative resection, tumor stage, and laboratory tests including CA 19-9, CEA, and bilirubin were significantly associated with overall survival, but CS infection was not. In multivariate analysis, tumor location, CEA, curative resection and tumor stage were identified as independent prognostic factors. Among patients under age 64, CACC group had lower survival rate than non-CACC group (p = 0.022).

Conclusions: CACC had the following significant characteristics compared to non-CACC; diagnosis at younger age, higher male to female ratio, higher prevalence in CS endemic areas and poorer overall survival in patients under age 64.
Effector Avr4 in Phytophthora infestans Escapes Host Immunity Mainly Through Early Termination
Authors: Waheed Abdul , Wang Yan-Ping , Nkurikiyimfura Oswald , Li Wen-Yang , Liu Shi-Ting , Lurwanu Yahuza , Lu Guo-Dong , Wang Zong-Hua , Yang Li-Na , Zhan Jiasui
Published: May 2021

Effector genes play critical roles in the antagonistic interactions between plants and pathogens. However, knowledge of mutation mechanisms and evolutionary processes in effector genes and the contribution of climatic factors to the evolution of effector genes are fragmented but important in sustainable management of plant diseases and securing food supply under changing climates. Here, we used a population genetic approach to explore the evolution of the Avr4 gene in Phytophthora infestans, the causal agent of potato blight. We found that the Avr4 gene exhibited a high genetic diversity generated by point mutation and sequence deletion. Frameshifts caused by a single base-pair deletion at the 194th nucleotide position generate two stop codons, truncating almost the entire C-terminal, which is important for effector function and R4 recognition in all sequences. The effector is under natural selection for adaptation supported by comparative analyses of population differentiation (FST) and isolation-by-distance between Avr4 sequences and simple sequence repeat marker loci. Furthermore, we found that local air temperature was positively associated with pairwise FST in the Avr4 sequences. These results suggest that the evolution of the effector gene is influenced by local air temperature, and the C-terminal truncation is one of the main mutation mechanisms in the P. infestans effector gene to circumvent the immune response of potato plants. The implication of these results to agricultural and natural sustainability in future climate conditions is discussed.
Bacterial Biofilm Growth on 3D-Printed Materials
Authors: Hall Donald C. , Palmer Phillip , Ji Hai-Feng , Ehrlich Garth D. , Król Jarosław E.
Published: May 2021

Recent advances in 3D printing have led to a rise in the use of 3D printed materials in prosthetics and external medical devices. These devices, while inexpensive, have not been adequately studied for their ability to resist biofouling and biofilm buildup. Bacterial biofilms are a major cause of biofouling in the medical field and, therefore, hospital-acquired, and medical device infections. These surface-attached bacteria are highly recalcitrant to conventional antimicrobial agents and result in chronic infections. During the COVID-19 pandemic, the U.S. Food and Drug Administration and medical officials have considered 3D printed medical devices as alternatives to conventional devices, due to manufacturing shortages. This abundant use of 3D printed devices in the medical fields warrants studies to assess the ability of different microorganisms to attach and colonize to such surfaces. In this study, we describe methods to determine bacterial biofouling and biofilm formation on 3D printed materials. We explored the biofilm-forming ability of multiple opportunistic pathogens commonly found on the human body including Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus to colonize eight commonly used polylactic acid (PLA) polymers. Biofilm quantification, surface topography, digital optical microscopy, and 3D projections were employed to better understand the bacterial attachment to 3D printed surfaces. We found that biofilm formation depends on surface structure, hydrophobicity, and that there was a wide range of antimicrobial properties among the tested polymers. We compared our tested materials with commercially available antimicrobial PLA polymers.
Recurrent Dissemination of SARS-CoV-2 Through the Uruguayan–Brazilian Border
Authors: Mir Daiana , Rego Natalia , Resende Paola Cristina , Tort Fernando , Fernández-Calero Tamara , Noya Verónica , Brandes Mariana , Possi Tania , Arleo Mailen , Reyes Natalia , Victoria Matías , Lizasoain Andres , Castells Matías , Maya Leticia , Salvo Matías , Schäffer Gregianini Tatiana , Mar da Rosa Marilda Tereza , Garay Martins Letícia , Alonso Cecilia , Vega Yasser , Salazar Cecilia , Ferrés Ignacio , Smircich Pablo , Sotelo Silveira Jose , Fort Rafael Sebastián , Mathó Cecilia , Arantes Ighor , Appolinario Luciana , Mendonça Ana Carolina , Benítez-Galeano María José , Simoes Camila , Graña Martín , Motta Fernando , Siqueira Marilda Mendonça , Bello Gonzalo , Colina Rodney , Spangenberg Lucía
Published: May 2021

Uruguay is one of the few countries in the Americas that successfully contained the coronavirus disease 19 (COVID-19) epidemic during the first half of 2020. Nevertheless, the intensive human mobility across the dry border with Brazil is a major challenge for public health authorities. We aimed to investigate the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains detected in Uruguayan localities bordering Brazil as well as to measure the viral flux across this ∼1,100 km uninterrupted dry frontier. Using complete SARS-CoV-2 genomes from the Uruguayan–Brazilian bordering region and phylogeographic analyses, we inferred the virus dissemination frequency between Brazil and Uruguay and characterized local outbreak dynamics during the first months (May–July) of the pandemic. Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 Brazilian lineages B.1.1.28 and B.1.1.33 into Uruguayan localities at the bordering region. The most probable sources of viral strains introduced to Uruguay were the Southeast Brazilian region and the state of Rio Grande do Sul. Some of the viral strains introduced in Uruguayan border localities between early May and mid-July were able to locally spread and originated the first outbreaks detected outside the metropolitan region. The viral lineages responsible for Uruguayan urban outbreaks were defined by a set of between four and 11 mutations (synonymous and non-synonymous) with respect to the ancestral B.1.1.28 and B.1.1.33 viruses that arose in Brazil, supporting the notion of a rapid genetic differentiation between SARS-CoV-2 subpopulations spreading in South America. Although Uruguayan borders have remained essentially closed to non-Uruguayan citizens, the inevitable flow of people across the dry border with Brazil allowed the repeated entry of the virus into Uruguay and the subsequent emergence of local outbreaks in Uruguayan border localities. Implementation of coordinated bi-national surveillance systems is crucial to achieve an efficient control of the SARS-CoV-2 spread across this kind of highly permeable borderland regions around the world.
Lead Drives Complex Dynamics of a Conjugative Plasmid in a Bacterial Community
Authors: Cyriaque Valentine , Madsen Jonas Stenløkke , Fievez Laurence , Leroy Baptiste , Hansen Lars H. , Bureau Fabrice , Sørensen Søren J. , Wattiez Ruddy
Published: May 2021

Plasmids carrying metal resistance genes (MRGs) have been suggested to be key ecological players in the adaptation of metal-impacted microbial communities, making them promising drivers of bio-remediation processes. However, the impact of metals on plasmid-mediated spread of MRGs through selection, plasmid loss, and transfer is far from being fully understood. In the present study, we used two-member bacterial communities to test the impact of lead on the dispersal of the IncP plasmid pKJK5 from a Pseudomonas putida KT2440 plasmid donor and two distinct recipients, Variovorax paradoxus B4 or Delftia acidovorans SPH-1 after 4 and 10 days of mating. Two versions of the plasmid were used, carrying or not carrying the lead resistance pbrTRABCD operon, to assess the importance of fitness benefit and conjugative potential for the dispersal of the plasmid. The spread dynamics of metal resistance conveyed by the conjugative plasmid were dependent on the recipient and the lead concentration: For V. paradoxus, the pbr operon did not facilitate neither lead resistance nor variation in plasmid spread. The growth gain brought by the pbr operon to D. acidovorans SPH-1 and P. putida KT2440 at 1 mM Pb enhanced the spread of the plasmid. At 1.5 mM Pb after 4 days, the proteomics results revealed an oxidative stress response and an increased abundance of pKJK5-encoded conjugation and partitioning proteins, which most likely increased the transfer of the control plasmid to D. acidovorans SPH-1 and ensured plasmid maintenance. As a consequence, we observed an increased spread of pKJK5-gfp. Conversely, the pbr operon reduced the oxidative stress response and impeded the rise of conjugation- and partitioning-associated proteins, which slowed down the spread of the pbr carrying plasmid. Ultimately, when a fitness gain was recorded in the recipient strain, the spread of MRG-carrying plasmids was facilitated through positive selection at an intermediate metal concentration, while a high lead concentration induced oxidative stress with positive impacts on proteins encoding plasmid conjugation and partitioning.
Genome-Wide Identification and Bioinformatics Characterization of Superoxide Dismutases in the Desiccation-Tolerant Cyanobacterium Chroococcidiopsis sp. CCMEE 029
Authors: Napoli Alessandro , Iacovelli Federico , Fagliarone Claudia , Pascarella Gianmarco , Falconi Mattia , Billi Daniela
Published: May 2021

A genome-wide investigation of the anhydrobiotic cyanobacterium Chroococcidiopsis sp. CCMEE 029 identified three genes coding superoxide dismutases (SODs) annotated as MnSODs (SodA2.1 and SodA2.2) and Cu/ZnSOD (SodC) as suggested by the presence of metal-binding motifs and conserved sequences. Structural bioinformatics analysis of the retrieved sequences yielded modeled MnSODs and Cu/ZnSOD structures that were fully compatible with their functional role. A signal-peptide bioinformatics prediction identified a Tat signal peptide at the N-terminus of the SodA2.1 that highlighted its transport across the thylakoid/cytoplasmic membranes and release in the periplasm/thylakoid lumen. Homologs of the Tat transport system were identified in Chroococcidiopsis sp. CCMEE 029, and the molecular docking simulation confirmed the interaction between the signal peptide of the SodA2.1 and the modeled TatC receptor, thus supporting the SodA2.1 translocation across the thylakoid/cytoplasmic membranes. No signal peptide was predicted for the MnSOD (SodA2.2) and Cu/ZnSOD, thus suggesting their occurrence as cytoplasmic proteins. No FeSOD homologs were identified in Chroococcidiopsis sp. CCMEE 029, a feature that might contribute to its desiccation tolerance since iron produces hydroxyl radical via the Fenton reaction. The overall-overexpression in response to desiccation of the three identified SOD-coding genes highlighted the role of SODs in the antioxidant enzymatic defense of this anhydrobiotic cyanobacterium. The periplasmic MnSOD protected the cell envelope against oxidative damage, the MnSOD localized in the thylakoid lumen scavengered superoxide anion radical produced during the photosynthesis, while the cytoplasmic MnSOD and Cu/ZnSOD reinforced the defense against reactive oxygen species generated at the onset of desiccation. Results contribute to decipher the desiccation-tolerance mechanisms of this cyanobacterium and allow the investigation of its oxidative stress response during future space experiments in low Earth orbit and beyond.
Isolation and Characterization of Potential Salmonella Phages Targeting Multidrug-Resistant and Major Serovars of Salmonella Derived From Broiler Production Chain in Thailand
Authors: Pelyuntha Wattana , Ngasaman Ruttayaporn , Yingkajorn Mingkwan , Chukiatsiri Kridda , Benjakul Soottawat , Vongkamjan Kitiya
Published: May 2021

Salmonella is a major foodborne pathogen that causes foodborne disease in humans through consumption of contaminated foods, especially those of animal origin. Multiple Salmonella strains are antibiotic-resistant due to the common use of antibiotics in farm animals, including broiler farms. In this study, an alternative strategy using phage-based treatment was evaluated against Salmonella isolated from the broiler production. The prevalence of Salmonella spp. showed up to 46.2 and 44.4% in bedding samples from the broiler farms located in eastern and southern Thailand, respectively. Overall, 21 samples (36.2%) were positive for Salmonella and eight serovars were recovered from cloacal swabs, bedding materials (rice husk), and boot swabs collected from five farms. Up to 20 Salmonella phages were isolated from seven water samples from wastewater treatment ponds, a river, and a natural reservoir in Songkhla province. Isolated phages were investigated, as well as their lysis ability on eight target Salmonella serovars derived from broiler farms, five foodborne outbreak-related serovars, and 10 multidrug-resistant (MDR) serovars. All phages showed a strong lytic ability against five serovars of Salmonella derived from broiler farms including Kentucky, Saintpaul, Schwarzengrund, Corvalis, and Typhimurium; three foodborne outbreak serovars including Enteritidis, Typhimurium, and Virchow; and eight MDR serovars including Agona, Albany, Give, Kentucky, Typhimurium, Schwarzengrund, Singapore, and Weltevreden. Three phages with the highest lysis potential including vB_SenS_WP109, vB_SenS_WP110, and vB_SenP_WP128 were selected for a phage cocktail preparation. Overall, a phage cocktail could reduce Salmonella counts by 2.2–2.8 log units at 6 h of treatment. Moreover, Salmonella did not develop a resistant pattern after being treated with a phage cocktail. Findings here suggest that a phage cocktail is an effective biocontrol to combat Salmonella derived from broiler production chain, other serovars linked to foodborne outbreaks, and MDR serovars.
Heterologous Expression of Cyclodextrin Glycosyltransferase my20 in Escherichia coli and Its Application in 2-O-α-D-Glucopyranosyl-L-Ascorbic Acid Production
Authors: Song Kai , Sun Jingjing , Wang Wei , Hao Jianhua
Published: May 2021

In this study, the cgt gene my20, which encodes cyclodextrin glycosyltransferase (CGTase) and was obtained by the metagenome sequencing of marine microorganisms from the Mariana Trench, was codon optimized and connected to pET-24a for heterologous expression in Escherichia coli BL21(DE3). Through shaking flask fermentation, the optimized condition for recombinant CGTase expression was identified as 20°C for 18 h with 0.4 mM of isopropyl β-D-L-thiogalactopyranoside. The recombinant CGTase was purified by Ni2+-NTA resin, and the optimum pH and temperature were identified as pH 7 and 80°C, respectively. Activity was stable over wide temperature and pH ranges. After purification by Ni2+-NTA resin, the specific activity of the CGTase was 63.3 U/mg after 67.3-fold purification, with a final yield of 43.7%. In addition, the enzyme was used to transform L-ascorbic acid into 2-O-α-D-glucopyranosyl-L-ascorbic acid (AA-2G). The maximal AA-2G production reached 28 g/L, at 40°C, pH 4, 24 h reaction time, 50 g/L donor concentration, and 50 U/g enzyme dosage. The superior properties of recombinant CGTase strongly facilitate the industrial production of AA-2G.
A Potential High-Risk Clone of Pseudomonas aeruginosa ST463
Authors: Hu Yanyan , Peng Wenjing , Wu Yifan , Li Hui , Wang Qi , Yi Huahua , Zhang Rong , Shao Bing , Zhu Kui
Published: May 2021

Pseudomonas aeruginosa is one of the most common opportunistic pathogens, which causes severe nosocomial infections because of its well-known multidrug-resistance and hypervirulence. It is critical to curate routinely the epidemic P. aeruginosa clones encountered in the clinic. The aim of the present study was to investigate the connection between virulence factors and antimicrobial resistance profiles in epidemic clones. Herein, we found that ST463 (O4), ST1212 (O11), and ST244 (O5) were prevalent in 30 isolates derived from non-cystic fibrosis patients, based on multilocus sequence type (MLST) and serotype analysis. All isolates were multidrug-resistant (MDR) and each was resistance to at least three classes of antibiotics in antimicrobial susceptibility tests, which was consistent with the presence of the abundant resistance genes, such as blaOXA–50, blaPAO, aph(3′), catB7, fosA, crpP, and blaKPC–2. Notably, all blaKPC–2 genes were located between ISKpn6-like and ISKpn8-like mobile genetic elements. In addition, classical exotoxins encoded by exoU, exoS, and pldA were present in 43.44% (13/40), 83.33% (25/30), and 70% (21/30) of the isolates, respectively. The expression of phz operons encoding the typical toxin, pyocyanin, was observed in 60% of isolates (18/30) and was quantified using triple quadrupole liquid chromatograph mass (LC/MS) assays. Interestingly, compared with other MLST types, all ST463 isolates harbored exoU, exoS and pldA, and produced pyocyanin ranging from 0.2 to 3.2 μg/mL. Finally, we evaluated the potential toxicity of these isolates using hemolysis tests and Galleria mellonella larvae infection models. The results showed that ST463 isolates were more virulent than other isolates. In conclusion, pyocyanin-producing ST463 P. aeruginosa, carrying diverse virulence genes, is a potential high-risk clone.