116 results on '"Xiaoyun Ren"'
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2. Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand
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Lauren Jelley, Jordan Douglas, Xiaoyun Ren, David Winter, Andrea McNeill, Sue Huang, Nigel French, David Welch, James Hadfield, Joep de Ligt, and Jemma L. Geoghegan
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Science - Abstract
Aotearoa New Zealand pursued a COVID-19 elimination strategy until October 2021 when it moved to a suppression strategy. In this genomic surveillance study, the authors describe spread of the virus during the transition between these strategies, with evidence of substantial undetected community transmission.
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- 2022
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3. Airborne Transmission of SARS-CoV-2 Delta Variant within Tightly Monitored Isolation Facility, New Zealand (Aotearoa)
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Andrew Fox-Lewis, Felicity Williamson, Jay Harrower, Xiaoyun Ren, Gerard J.B. Sonder, Andrea McNeill, Joep de Ligt, and Jemma L. Geoghegan
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COVID-19 ,airborne transmission ,coronavirus disease ,SARS-CoV-2 ,severe acute respiratory syndrome coronavirus 2 ,viruses ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
In New Zealand, international arrivals are quarantined and undergo severe acute respiratory syndrome coronavirus 2 screening; those who test positive are transferred to a managed isolation facility (MIF). Solo traveler A and person E from a 5-person travel group (BCDEF) tested positive. After transfer to the MIF, person A and group BCDEF occupied rooms >2 meters apart across a corridor. Persons B, C, and D subsequently tested positive; viral sequences matched A and were distinct from E. The MIF was the only shared location of persons A and B, C, and D, and they had no direct contact. Security camera footage revealed 4 brief episodes of simultaneous door opening during person A’s infectious period. This public health investigation demonstrates transmission from A to B, C, and D while in the MIF, with airborne transmission the most plausible explanation. These findings are of global importance for coronavirus disease public health interventions and infection control practices.
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- 2022
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4. Bamboo charcoal mediated plant secondary metabolites biosynthesis in tomato against South American tomato pinworm (Tuta absoluta)
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Limin Chen, Xiaowei Li, Jinchao Wang, Tingting Chen, Jinming Zhang, Qianggen Zhu, Jun Huang, Zhijun Zhang, Muhammad Hafeez, Shuxing Zhou, Xiaoyun Ren, Wanying Dong, Aiwu Jin, Youming Hou, and Yaobin Lu
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flavonoids ,terpenoids ,resistance to insect-pest ,South American tomato pinworm ,phytohormone signaling ,LSU hub genes ,Nutrition. Foods and food supply ,TX341-641 ,Food processing and manufacture ,TP368-456 - Abstract
IntroductionThe south American tomato pinworm (Tuta absoluta), an invasive insect pest species, has established itself in more than 33 Chinese prefectures, where it is mainly damaging tomato crops. Immediate efforts have been initiated to find strategies to control this pest. Studies have shown that biochar (BC) amendment to soil can enhance plant growth and resistance to herbivory.MethodsFirst, we quantified the morphological performance of tomato plants grown in different coconut bran and bamboo charcoal (v/v) combinations and selected the most beneficial one. Then we checked the T. absoluta survival on the tomato plants grown in the selected bamboo charcoal combination. Finally, we studied the leaf metabolite accumulation and gene expression changes in tomato plants after growing in the selected bamboo charcoal combination.ResultsWe found that the 30:1 ratio of bamboo charcoal and coconut bran is the most beneficial to tomato growth as its amendment to soil increased tomato plant height, stem thickness, and chlorophyll content, whereas, the T. absoluta survival decreased. The metabolome profiles of BC tomato leaves showed an increased accumulation of flavonoids, terpenoids, and phenolic acids compared to CK. Transcriptome sequencing resulted in the identification of 244 differentially expressed genes. Most of the upregulated genes were associated with stress-related hub proteins, flavonoid biosynthesis, MAPK and phytohormone signaling, and terpenoid biosynthesis. Additionally, the expression of many genes related to signaling and defense was changed in response to the bamboo charcoal amendment.DiscussionWe conclude that bamboo charcoal induces biosynthesis of flavonoids, terpenoids, and phenolic acids, which improve plant growth and tolerance against T. absoluta, thus reducing the survival of destructive pests.
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- 2023
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5. Linking life table and predation rate for evaluating temperature effects on Orius strigicollis for the biological control of Frankliniella occidentalis
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Xiaoyun Ren, Xiaowei Li, Jun Huang, Zhijun Zhang, Muhammad Hafeez, Jinming Zhang, Limin Chen, Shuxing Zhou, Lisheng Zhang, and Yaobin Lu
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predator ,temperature ,release ,augmentative biological control ,thrips ,Nutrition. Foods and food supply ,TX341-641 ,Food processing and manufacture ,TP368-456 - Abstract
IntroductionOrius spp. are generalist predators released in horticultural and agricultural systems to control thrips. Understanding the effects of temperature on the development, predation rate, and population dynamics of Orius is essential for identifying the optimal timing of Orius release for establishing an adequate population to facilitate synchrony with thrips population growth and to prevent thrips outbreaks. The biological control efficiency of natural enemies as well as predator–prey relationships can be precisely described by integrating life table parameters and the predation rate.MethodsIn this study, the demographic features of Orius strigicollis fed on 2nd instar nymphs of western flower thrips (WFT), Frankliniella occidentalis, were compared at 18.5, 23.5, 27, and 33°C using the TWOSEX-MSChart program. The CONSUME-MSChart program was used to examine predation rates under different temperatures (18.5, 23.5, and 27°C).ResultsThe results showed no significant difference in fecundity among those reared at 18.5, 23.5, and 27°C, but fecundity at these temperatures was significantly higher than that at 33°C. The intrinsic rate of increase (r), finite rate of increase (λ), and net reproduction rate (R0) were the highest at 27°C. The net predation rate (C0) and transformation rate (Qp) were significantly higher at 18.5°C (C0 = 168.39 prey/predator, Qp = 8.22) and 23.5°C (C0 = 140.49 prey/predator, Qp = 6.03) than at 27°C (C0 = 138.39 prey/predator, Qp= 3.81); however, the finite predation rate (ω) showed the opposite trend. In addition to temperature, the stage of O. strigicollis at release can affect population dynamics.DiscussionOur study showed that temperature influenced the demographic traits and predation rates of O. strigicollis. When planning a release, the stage of O. strigicollis and temperature should be taken into account to establish an adequate population for the control of WFT.
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- 2022
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6. Real-Time Genomics for Tracking Severe Acute Respiratory Syndrome Coronavirus 2 Border Incursions after Virus Elimination, New Zealand
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Jordan Douglas, Jemma L. Geoghegan, James Hadfield, Remco Bouckaert, Matthew Storey, Xiaoyun Ren, Joep de Ligt, Nigel French, and David Welch
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2019 novel coronavirus disease ,coronavirus disease ,COVID-19 ,severe acute respiratory syndrome coronavirus 2 ,SARS-CoV-2 ,viruses ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
Since severe acute respiratory syndrome coronavirus 2 was first eliminated in New Zealand in May 2020, a total of 13 known coronavirus disease (COVID-19) community outbreaks have occurred, 2 of which led health officials to issue stay-at-home orders. These outbreaks originated at the border via isolating returnees, airline workers, and cargo vessels. Because a public health system was informed by real-time viral genomic sequencing and complete genomes typically were available within 12 hours of community-based positive COVID-19 test results, every outbreak was well-contained. A total of 225 community cases resulted in 3 deaths. Real-time genomics were essential for establishing links between cases when epidemiologic data could not do so and for identifying when concurrent outbreaks had different origins.
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- 2021
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7. Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand
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Jemma L. Geoghegan, Jordan Douglas, Xiaoyun Ren, Matthew Storey, James Hadfield, Olin K. Silander, Nikki E. Freed, Lauren Jelley, Sarah Jefferies, Jillian Sherwood, Shevaun Paine, Sue Huang, Andrew Sporle, Michael G. Baker, David R. Murdoch, Alexei J. Drummond, David Welch, Colin R. Simpson, Nigel French, Edward C. Holmes, and Joep de Ligt
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2019 novel coronavirus disease ,coronavirus disease ,COVID-19 ,severe acute respiratory syndrome coronavirus 2 ,SARS-CoV-2 ,viruses ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
Real-time genomic sequencing has played a major role in tracking the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), contributing greatly to disease mitigation strategies. In August 2020, after having eliminated the virus, New Zealand experienced a second outbreak. During that outbreak, New Zealand used genomic sequencing in a primary role, leading to a second elimination of the virus. We generated genomes from 78% of the laboratory-confirmed samples of SARS-CoV-2 from the second outbreak and compared them with the available global genomic data. Genomic sequencing rapidly identified that virus causing the second outbreak in New Zealand belonged to a single cluster, thus resulting from a single introduction. However, successful identification of the origin of this outbreak was impeded by substantial biases and gaps in global sequencing data. Access to a broader and more heterogenous sample of global genomic data would strengthen efforts to locate the source of any new outbreaks.
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- 2021
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8. Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 during Border Quarantine and Air Travel, New Zealand (Aotearoa)
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Nick Eichler, Craig Thornley, Tara Swadi, Tom Devine, Caroline McElnay, Jillian Sherwood, Cheryl Brunton, Felicity Williamson, Josh Freeman, Sarah Berger, Xiaoyun Ren, Matt Storey, Joep de Ligt, and Jemma L. Geoghegan
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severe acute respiratory syndrome coronavirus 2 ,SARS-CoV-2 ,coronavirus ,coronavirus disease ,COVID-19 ,viruses ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
The strategy in New Zealand (Aotearoa) to eliminate coronavirus disease requires that international arrivals undergo managed isolation and quarantine and mandatory testing for severe acute respiratory syndrome coronavirus 2. Combining genomic and epidemiologic data, we investigated the origin of an acute case of coronavirus disease identified in the community after the patient had spent 14 days in managed isolation and quarantine and had 2 negative test results. By combining genomic sequence analysis and epidemiologic investigations, we identified a multibranched chain of transmission of this virus, including on international and domestic flights, as well as a probable case of aerosol transmission without direct person-to-person contact. These findings show the power of integrating genomic and epidemiologic data to inform outbreak investigations.
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- 2021
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9. Genomic Surveillance of a Globally Circulating Distinct Group W Clonal Complex 11 Meningococcal Variant, New Zealand, 2013–2018
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Zuyu Yang, Xiaoyun Ren, Heather Davies, Timothy Wood, Liza Lopez, Jill Sherwood, Audrey Tiong, and Philip E. Carter
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meningococcal disease ,whole-genome sequencing ,group W ,evolution ,Public Health Surveillance ,New Zealand ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
Genomic surveillance is an essential part of effective disease control, enabling identification of emerging and expanding strains and monitoring of subsequent interventions. Whole-genome sequencing was used to analyze the genomic diversity of all Neisseria meningitidis isolates submitted to the New Zealand Meningococcal Reference Laboratory during 2013–2018. Of the 347 isolates submitted for whole-genome sequencing, we identified 68 sequence types belonging to 18 clonal complexes (CC). The predominant CC was CC41/44; next in predominance was CC11. Comparison of the 45 New Zealand group W CC11 isolates with worldwide representatives of group W CC11 isolates revealed that the original UK strain, the 2013 UK strain, and a distinctive variant (the 2015 strain) were causing invasive group W meningococcal disease in New Zealand. The 2015 strain also demonstrated increased resistance to penicillin and has been circulating in Canada and several countries in Europe, highlighting that close monitoring is needed to prevent future outbreaks around the world.
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- 2021
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10. Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing
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Tara Swadi, Jemma L. Geoghegan, Tom Devine, Caroline McElnay, Jillian Sherwood, Phil Shoemack, Xiaoyun Ren, Matt Storey, Sarah Jefferies, Erasmus Smit, James Hadfield, Aoife Kenny, Lauren Jelley, Andrew Sporle, Andrea McNeill, G. Edwin Reynolds, Kip Mouldey, Lindsay Lowe, Gerard Sonder, Alexei J. Drummond, Sue Huang, David Welch, Edward C. Holmes, Nigel French, Colin R. Simpson, and Joep de Ligt
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2019 novel coronavirus disease ,coronavirus disease ,COVID-19 ,severe acute respiratory syndrome coronavirus 2 ,SARS-CoV-2 ,viruses ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
Since the first wave of coronavirus disease in March 2020, citizens and permanent residents returning to New Zealand have been required to undergo managed isolation and quarantine (MIQ) for 14 days and mandatory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of October 20, 2020, of 62,698 arrivals, testing of persons in MIQ had identified 215 cases of SARS-CoV-2 infection. Among 86 passengers on a flight from Dubai, United Arab Emirates, that arrived in New Zealand on September 29, test results were positive for 7 persons in MIQ. These passengers originated from 5 different countries before a layover in Dubai; 5 had negative predeparture SARS-CoV-2 test results. To assess possible points of infection, we analyzed information about their journeys, disease progression, and virus genomic data. All 7 SARS-CoV-2 genomes were genetically identical, except for a single mutation in 1 sample. Despite predeparture testing, multiple instances of in-flight SARS-CoV-2 transmission are likely.
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- 2021
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11. Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand
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Jemma L. Geoghegan, Xiaoyun Ren, Matthew Storey, James Hadfield, Lauren Jelley, Sarah Jefferies, Jill Sherwood, Shevaun Paine, Sue Huang, Jordan Douglas, Fábio K. Mendes, Andrew Sporle, Michael G. Baker, David R. Murdoch, Nigel French, Colin R. Simpson, David Welch, Alexei J. Drummond, Edward C. Holmes, Sebastián Duchêne, and Joep de Ligt
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Science - Abstract
New Zealand implemented stringent COVID-19 control measures early after identification of its first case. Here, the authors perform whole genome sequencing of samples taken until 22 May 2020 and find high viral diversity indicative of multiple separate introductions and limited community transmission.
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- 2020
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12. Spodoptera exigua Multiple Nucleopolyhedrovirus Increases the Susceptibility to Insecticides: A Promising Efficient Way for Pest Resistance Management
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Shuxing Zhou, Jinming Zhang, Ya Lin, Xiaowei Li, Min Liu, Muhammad Hafeez, Jun Huang, Zhijun Zhang, Limin Chen, Xiaoyun Ren, Wanying Dong, and Yaobin Lu
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Spodoptera exigua ,S. exigua multiple nucleopolyhedrovirus ,insecticides ,combined application ,pest resistance management ,Biology (General) ,QH301-705.5 - Abstract
Spodoptera exigua is a polyphagous pest of diverse crops and causes considerable economic losses. The overuse of chemical insecticides for controlling this pest results in insecticide resistance, environmental pollution and toxicity to other non-target organisms. Therefore, a sustainable and efficient way for pest management is urgently required. In this study, laboratory bioassays of eleven commonly used insecticides, the specific entomopathogen of S. exigua (Spodoptera exigua multiple nucleopolyhedrovirus, SeMNPV), and SeMNPV-insecticide combinations against the S. exigua laboratory population and two field populations were tested. Our results indicated that the two field populations had developed resistance to almost half of the tested insecticides, while SeMNPV had good virulence in all populations. Interestingly, the combined use of SeMNPV enhanced the toxicity of the tested insecticides against all populations to a different extent and considerably reduced the insecticide resistance of S. exigua field populations or even recovered the susceptibility to above insecticides. Furthermore, the field trial showed that the combined application of SeMNPV contributed to promoting the control efficacy of emamectin benzonate and chlorfenapyr. These results provide a promising efficient way for pest resistance management and an environmentally friendly approach for controlling S. exigua with the combined application of nucleopolyhedroviruses and insecticides.
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- 2023
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13. Comprehensive Metabolome and Volatilome Analyses in Eggplant and Tomato Reveal Their Differential Responses to Tuta absoluta Infestation
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Limin Chen, Xiaowei Li, Jinming Zhang, Tianjun He, Jun Huang, Zhijun Zhang, Yeyang Wang, Muhammad Hafeez, Shuxing Zhou, Xiaoyun Ren, Youming Hou, and Yaobin Lu
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electroantennography ,biocontrol approach ,host preference ,plant defense metabolites ,volatiles ,Plant culture ,SB1-1110 - Abstract
The South American tomato pinworm, Tuta absoluta, is one of the most destructive insect pests in Solanaceae crops, particularly in tomatoes. Current methods of management have proven somewhat effective but still require a more efficacious management strategy to limit its havoc on crop yield. Tomato is much more predisposed to T. absoluta as compared with other plants such as eggplants, but the underlying causes have not been fully determined. We conducted this study to unravel the volatile organic compounds (VOCs) and primary/secondary metabolites that account for the differential response of tomatoes and eggplants to T. absoluta infestation. We performed widely targeted comparative metabolome and volatilome profiling by ultraperformance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) and headspace solid-phase microextraction coupled to gas chromatography–mass spectrometry (HS-SPME/GC-MS), respectively, on eggplants and tomatoes under control and T. absoluta infestation conditions. Overall, 141 VOCs and 797 primary/secondary metabolites were identified, largely dominated by aldehyde, alcohols, alkanes, amine, aromatics, a heterocyclic compound, ketone, olefin, phenol, and terpenes. Most of the VOCs and primary/secondary metabolites from the terpene class were largely differentially regulated in eggplants compared with tomatoes. Eggplants emitted several compounds that were lower or completely absent in tomatoes either under control conditions or after T. absoluta infestation. The results from an electroantennogram showed that 35 differentially accumulated VOCs could elicit female T. absoluta response, implying that these volatile compounds significantly alter the behavior of this pest. These findings demonstrated that differentially accumulated metabolites and volatile compounds play major roles in eggplant resistance to T. absoluta infestation as these compounds were regulated upon attack by T. absoluta. Our findings can assist in integrated pest management efforts by developing appropriate control measures against T. absoluta in Solanaceae production.
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- 2021
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14. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch [version 2; peer review: 3 approved]
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Áine O'Toole, Verity Hill, Oliver G. Pybus, Alexander Watts, Issac I. Bogoch, Kamran Khan, Jane P. Messina, The COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, Houriiyah Tegally, Richard R. Lessells, Jennifer Giandhari, Sureshnee Pillay, Kefentse Arnold Tumedi, Gape Nyepetsi, Malebogo Kebabonye, Maitshwarelo Matsheka, Madisa Mine, Sima Tokajian, Hamad Hassan, Tamara Salloum, Georgi Merhi, Jad Koweyes, Jemma L. Geoghegan, Joep de Ligt, Xiaoyun Ren, Matthew Storey, Nikki E. Freed, Chitra Pattabiraman, Pramada Prasad, Anita S. Desai, Ravi Vasanthapuram, Thomas F. Schulz, Lars Steinbrück, Tanja Stadler, Swiss Viollier Sequencing Consortium, Antonio Parisi, Angelica Bianco, Darío García de Viedma, Sergio Buenestado-Serrano, Vítor Borges, Joana Isidro, Sílvia Duarte, João Paulo Gomes, Neta S. Zuckerman, Michal Mandelboim, Orna Mor, Torsten Seemann, Alicia Arnott, Jenny Draper, Mailie Gall, William Rawlinson, Ira Deveson, Sanmarié Schlebusch, Jamie McMahon, Lex Leong, Chuan Kok Lim, Maria Chironna, Daniela Loconsole, Antonin Bal, Laurence Josset, Edward Holmes, Kirsten St. George, Erica Lasek-Nesselquist, Reina S. Sikkema, Bas Oude Munnink, Marion Koopmans, Mia Brytting, V. Sudha rani, S. Pavani, Teemu Smura, Albert Heim, Satu Kurkela, Massab Umair, Muhammad Salman, Barbara Bartolini, Martina Rueca, Christian Drosten, Thorsten Wolff, Olin Silander, Dirk Eggink, Chantal Reusken, Harry Vennema, Aekyung Park, Christine Carrington, Nikita Sahadeo, Michael Carr, Gabo Gonzalez, SEARCH Alliance San Diego, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC), Communicable Diseases Genomic Network (CDGN), Dutch National SARS-CoV-2 surveillance program, Division of Emerging Infectious Diseases (KDCA), Tulio de Oliveira, Nuno Faria, Andrew Rambaut, and Moritz U. G. Kraemer
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Medicine ,Science - Abstract
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
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- 2021
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15. Characterization of Indoxacarb Resistance in the Fall Armyworm: Selection, Inheritance, Cross-Resistance, Possible Biochemical Mechanisms, and Fitness Costs
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Muhammad Hafeez, Xiaowei Li, Farman Ullah, Zhijun Zhang, Jinming Zhang, Jun Huang, Limin Chen, Junaid Ali Siddiqui, Xiaoyun Ren, Shuxing Zhou, Muhammad Imran, Mohammed A. Assiri, Myron P. Zalucki, Yonggen Lou, and Yaobin Lu
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Spodoptera frugiperda ,indoxacarb selection ,cross-resistance ,inheritance of resistance ,fitness cost ,Biology (General) ,QH301-705.5 - Abstract
The fall armyworm, Spodoptera frugiperda (J.E. Smith), is a voracious insect pest that is difficult to control due to resistance to insecticides and Bt proteins. We assessed cross-resistance, resistance mechanism, and fitness costs based on the life history traits of S. frugiperda. We established an S. frugiperda strain selected for resistance to indoxacarb (Ind-SEL) from a field-collected population and an unselected strain, Ind-UNSEL. Results indicated that after 24 generations of selection, the resistance to indoxacarb was increased by 472.67-fold as compared to the Ind-UNSEL. There was high cross-resistance to deltamethrin (31.23-fold) with very low or negligible cross-resistance to chlorantraniliprole, emamectin benzoate, and/or methoxyfenozide in the Ind-SEL population. Butoxide synergist increased susceptibility to indoxacarb, indicating that P450 enzymes may be involved in indoxacarb resistance. Significantly longer developmental time of larvae extended pupal duration, shorter adult longevity, and lower fecundity were observed in Ind-SEL as compared with the Ind-UNSEL population. The Net reproductive rate (R0) was the only growth parameter that differs between crosses of Ind-SEL♂ × Ind-UNSEL♀ (176 ± 46) and Ind-SEL♀ × Ind-UNSEL♂ (328 ± 57). On the other hand, all population growth parameters differ between Ind-SEL and Ind-UNSEL strains. Our work contributes to the growing body of research that demonstrates the importance of strain genetics in fitness cost experiments and helps resistance management programs make decisions.
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- 2022
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16. Comparison and Functional Analysis of Odorant-Binding Proteins and Chemosensory Proteins in Two Closely Related Thrips Species, Frankliniella occidentalis and Frankliniella intonsa (Thysanoptera: Thripidae) Based on Antennal Transcriptome Analysis
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Xiaowei Li, Jianghui Cheng, Limin Chen, Jun Huang, Zhijun Zhang, Jinming Zhang, Xiaoyun Ren, Muhammad Hafeez, Shuxing Zhou, Wanying Dong, and Yaobin Lu
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Frankliniella occidentalis ,Frankliniella intonsa ,odorant-binding proteins ,chemosensory proteins ,aggregation pheromone ,molecular docking ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Two closely related thrips species, Frankliniella occidentalis and Frankliniella intonsa, are important pests on agricultural and horticultural crops. They have several similarities, including occurrence patterns, host range, and aggregation pheromone compounds. However, there are very few reports about the chemosensory genes and olfactory mechanisms in these two species. To expand our knowledge of the thrips chemosensory system, we conducted antennal transcriptome analysis of two thrips species, and identified seven odorant-binding proteins (OBPs) and eight chemosensory proteins (CSPs) in F. occidentalis, as well as six OBPs and six CSPs in F. intonsa. OBPs and CSPs showed high sequence identity between the two thrips species. The RT-qPCR results showed that the orthologous genes FoccOBP1/3/4/5/6, FintOBP1/3/4/6, FoccCSP1/2/3, and FintCSP1/2 were highly expressed in male adults. Molecular docking results suggested that orthologous pairs FoccOBP4/FintOBP4, FoccOBP6/FintOBP6, and FoccCSP2/FintCSP2 might be involved in transporting the major aggregation pheromone compound neryl (S)-2-methylbutanoate, while orthologous pairs FoccOBP6/FintOBP6, FoccCSP2/FintCSP2, and FoccCSP3/FintCSP3 might be involved in transporting the minor aggregation pheromone compound (R)-lavandulyl acetate. These results will provide a fundamental basis for understanding the molecular mechanisms of pheromone reception in the two thrips species.
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- 2022
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17. The predatory bug Orius strigicollis shows a preference for egg-laying sites based on plant topography
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Chendi Yu, Jun Huang, Xiaoyun Ren, G Mandela Fernández-Grandon, Xiaowei Li, Muhammad Hafeez, and Yaobin Lu
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Oviposition behavior ,Site selection preference ,Egg hatching ,Plant topography ,Orius strigicollis ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Background Oviposition site selection is an important factor in determining the success of insect populations. Orius spp. are widely used in the biological control of a wide range of soft-bodied insect pests such as thrips, aphids, and mites. Orius strigicollis (Heteroptera: Anthocoridae) is the dominant Orius species in southern China; however, what factor drives its selection of an oviposition site after mating currently remains unknown. Methods Here, kidney bean pods (KBPs) were chosen as the oviposition substrate, and choice and nonchoice experiments were conducted to determine the preferences concerning oviposition sites on the KBPs of O. strigicollis. The mechanism of oviposition behavior was revealed through observation and measurement of oviposition action, the egg hatching rate, and the oviposition time. Results We found that O. strigicollis preferred the seams of the pods for oviposition, especially the seams at the tips of the KBPs. Choice and nonchoice experiments showed that females did not lay eggs when the KBP tail parts were unavailable. The rates of egg hatching on different KBP parts were not significantly different, but the time required for females to lay eggs on the tip seam was significantly lower. Decreased oviposition time is achieved on the tip seam because the insect can exploit support points found there and gain leverage for insertion of the ovipositor. Discussion The preferences for oviposition sites of O. strigicollis are significantly influenced by the topography of the KBP surface. Revealing such behavior and mechanisms will provide an important scientific basis for the mass rearing of predatory bugs.
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- 2021
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18. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 [version 1; peer review: 2 approved]
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Áine O'Toole, Verity Hill, Oliver G. Pybus, Alexander Watts, Issac I. Bogoch, Kamran Khan, Jane P. Messina, The COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, Houriiyah Tegally, Richard R. Lessells, Jennifer Giandhari, Sureshnee Pillay, Kefentse Arnold Tumedi, Gape Nyepetsi, Malebogo Kebabonye, Maitshwarelo Matsheka, Madisa Mine, Sima Tokajian, Hamad Hassan, Tamara Salloum, Georgi Merhi, Jad Koweyes, Jemma L. Geoghegan, Joep de Ligt, Xiaoyun Ren, Matthew Storey, Nikki E. Freed, Chitra Pattabiraman, Pramada Prasad, Anita S. Desai, Ravi Vasanthapuram, Thomas F. Schulz, Lars Steinbrück, Tanja Stadler, Swiss Viollier Sequencing Consortium, Antonio Parisi, Angelica Bianco, Darío García de Viedma, Sergio Buenestado-Serrano, Vítor Borges, Joana Isidro, Sílvia Duarte, João Paulo Gomes, Neta S. Zuckerman, Michal Mandelboim, Orna Mor, Torsten Seemann, Alicia Arnott, Jenny Draper, Mailie Gall, William Rawlinson, Ira Deveson, Sanmarié Schlebusch, Jamie McMahon, Lex Leong, Chuan Kok Lim, Maria Chironna, Daniela Loconsole, Antonin Bal, Laurence Josset, Edward Holmes, Kirsten St. George, Erica Lasek-Nesselquist, Reina S. Sikkema, Bas Oude Munnink, Marion Koopmans, Mia Brytting, V. Sudha rani, S. Pavani, Teemu Smura, Albert Heim, Satu Kurkela, Massab Umair, Muhammad Salman, Barbara Bartolini, Martina Rueca, Christian Drosten, Thorsten Wolff, Olin Silander, Dirk Eggink, Chantal Reusken, Harry Vennema, Aekyung Park, Christine Carrington, Nikita Sahadeo, Michael Carr, Gabo Gonzalez, SEARCH Alliance San Diego, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC), Communicable Diseases Genomic Network (CDGN), Dutch National SARS-CoV-2 surveillance program, Division of Emerging Infectious Diseases (KDCA), Tulio de Oliveira, Nuno Faria, Andrew Rambaut, and Moritz U. G. Kraemer
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Medicine ,Science - Abstract
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
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- 2021
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19. Behavioral and Physiological Plasticity Provides Insights into Molecular Based Adaptation Mechanism to Strain Shift in Spodoptera frugiperda
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Muhammad Hafeez, Xiaowei Li, Farman Ullah, Zhijun Zhang, Jinming Zhang, Jun Huang, Muhammad Musa Khan, Limin Chen, Xiaoyun Ren, Shuxing Zhou, G. Mandela Fernández-Grandon, Myron P. Zalucki, and Yaobin Lu
- Subjects
midgut ,antennal response ,host plants adaptation ,molecular mechanism ,Spodoptera frugiperda ,behavioral response ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
How herbivorous insects adapt to host plants is a key question in ecological and evolutionary biology. The fall armyworm, (FAW) Spodoptera frugiperda (J.E. Smith), although polyphagous and a major pest on various crops, has been reported to have a rice and corn (maize) feeding strain in its native range in the Americas. The species is highly invasive and has recently established in China. We compared behavioral changes in larvae and adults of a corn population (Corn) when selected on rice (Rice) and the molecular basis of these adaptational changes in midgut and antennae based on a comparative transcriptome analysis. Larvae of S. frugiperda reared on rice plants continuously for 20 generations exhibited strong feeding preference for with higher larval performance and pupal weight on rice than on maize plants. Similarly, females from the rice selected population laid significantly more eggs on rice as compared to females from maize population. The most highly expressed DEGs were shown in the midgut of Rice vs. Corn. A total of 6430 DEGs were identified between the populations mostly in genes related to digestion and detoxification. These results suggest that potential adaptations for feeding on rice crops, may contribute to the current rapid spread of fall armyworm on rice crops in China and potentially elsewhere. Consistently, highly expressed DEGs were also shown in antennae; a total of 5125 differentially expressed genes (DEGs) s were identified related to the expansions of major chemosensory genes family in Rice compared to the Corn feeding population. These results not only provide valuable insight into the molecular mechanisms in host plants adaptation of S. frugiperda but may provide new gene targets for the management of this pest.
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- 2021
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20. Behavioral Responses of Western Flower Thrips (Frankliniella occidentalis) to Visual and Olfactory Cues at Short Distances
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Xiaoyun Ren, Shengyong Wu, Zhenlong Xing, Ruirui Xu, Wanzhi Cai, and Zhongren Lei
- Subjects
frankliniella occidentalis ,visual cue ,olfactory cue ,short distance ,trapping efficacy ,Science - Abstract
Western flower thrips (WFT), Frankliniella occidentalis (Pergande), is a highly invasive pest, infesting many species of plants worldwide, but few studies have investigated the visual and olfactory cues associated with their foraging behaviors. In this study, the distance traveled by WFT to locate yellow cards using only visual cues and visual cues plus olfactory cues was studied first. Subsequently, preferences for colors (white, red, green, purple, yellow and blue) and patterns (triangle, rectangle, circle and flower-shape) over short distances were assessed with free-choice tests. Finally, as yellow was the most efficient color to catch WFT under laboratory conditions, the yellow flower-shape was used as the visual cue, and preferences between visual and olfactory cues were evaluated with dual choice tests. The results showed that the capture rate of WFT by visual cues decreased as selection distance increased, however capture rate remained higher with the addition of olfactory cues. The flower shape attracted the greatest number of WFT among all shapes tested. The combination of visual cues and extracted volatiles from flowering Medicago sativa L. attracted higher numbers of WFT than to the olfactory cues alone, however these were similar to visual cues alone. The presence of olfactory cues resulted in higher residence times by WFT than did the absence of olfactory cues. These results show the relative effects of visual and olfactory cues on the orientation of WFT to hosts and highlight that visual cues dominate selection behavior at short distances. These findings can be used in the development of efficient trapping products and management strategies for thrips.
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- 2020
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21. Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts
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Xiaoyun Ren, David A. Eccles, Gabrielle A. Greig, Jane Clapham, Nicole E. Wheeler, Stinus Lindgreen, Paul P. Gardner, and Joanna K. MacKichan
- Subjects
Neisseria meningitidis ,type IV pili ,carriage ,household contact ,Microbiology ,QR1-502 - Abstract
ABSTRACT Neisseria meningitidis (meningococcus) can cause meningococcal disease, a rapidly progressing and often fatal disease that can occur in previously healthy children. Meningococci are found in healthy carriers, where they reside in the nasopharynx as commensals. While carriage is relatively common, invasive disease, associated with hypervirulent strains, is a comparatively rare event. The basis of increased virulence in some strains is not well understood. New Zealand suffered a protracted meningococcal disease epidemic, from 1991 to 2008. During this time, a household carriage study was carried out in Auckland: household contacts of index meningococcal disease patients were swabbed for isolation of carriage strains. In many households, healthy carriers harbored strains identical, as determined by laboratory typing, to the ones infecting the associated patient. We carried out more-detailed analyses of carriage and disease isolates from a select number of households. We found that isolates, although indistinguishable by laboratory typing methods and likely closely related, had many differences. We identified multiple genome variants and transcriptional differences between isolates. These studies enabled the identification of two new phase-variable genes. We also found that several carriage strains had lost their type IV pili and that this loss correlated with reduced tumor necrosis factor alpha (TNF-α) expression when cultured with epithelial cells. While nonpiliated meningococcal isolates have been previously found in carriage strains, this is the first evidence of an association between type IV pili from meningococci and a proinflammatory epithelial response. We also identified potentially important metabolic differences between carriage and disease isolates, including the sulfate assimilation pathway. IMPORTANCE Neisseria meningitidis causes meningococcal disease but is frequently carried in the throats of healthy individuals; the factors that determine whether invasive disease develops are not completely understood. We carried out detailed studies of isolates, collected from patients and their household contacts, to identify differences between commensal throat isolates and those that caused invasive disease. Though isolates were identical by laboratory typing methods, we uncovered many differences in their genomes, in gene expression, and in their interactions with host cells. In particular, we found that several carriage isolates had lost their type IV pili, a surprising finding since pili are often described as essential for colonization. However, loss of type IV pili correlated with reduced secretion of a proinflammatory cytokine, TNF-α, when meningococci were cocultured with human bronchial epithelial cells; hence, the loss of pili could provide an advantage to meningococci, by resulting in a dampened localized host immune response.
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- 2017
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22. Ability to Remove Na+ and Retain K+ Correlates with Salt Tolerance in Two Maize Inbred Lines Seedlings
- Author
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Yong Gao, Yi Lu, Meiqin Wu, Enxing Liang, Yan Li, Dongping Zhang, Zhitong Yin, Xiaoyun Ren, Yi Dai, Dexiang Deng, and Jianmin Chen
- Subjects
Physiology ,Maize ,transcription ,salt stress ,osmotic stress ,ion toxicity ,Plant culture ,SB1-1110 - Abstract
Maize is moderately sensitive to salt stress; therefore, soil salinity is a serious threat to its production worldwide. Here, excellent salt-tolerant maize inbred line TL1317 and extremely salt-sensitive maize inbred line SL1303 were screened to understand the maize response to salt stress and its tolerance mechanisms. Relative water content, membrane stability index, stomatal conductance, chlorophyll content, maximum photochemical efficiency, photochemical efficiency, shoot and root fresh/dry weight, and proline and water soluble sugar content analyses were used to identify that the physiological effects of osmotic stress of salt stress were obvious and manifested at about 3 days after salt stress in maize. Moreover, the ion concentration of two maize inbred lines revealed that the salt-tolerant maize inbred line could maintain low Na+ concentration by accumulating Na+ in old leaves and gradually shedding them to exclude excessive Na+. Furthermore, the K+ uptake and retention abilities of roots were important in maintaining K+ homeostasis for salt tolerance in maize. RNA-seq and qPCR results revealed some Na+/H+ antiporter genes and Ca2+ transport genes were up-regulated faster and higher in TL1317 than those in SL1303. Some K+ transport genes were down-regulated in SL1303 but up-regulated in TL1317. RNA-seq results, along with the phenotype and physiological results, suggested that the salt-tolerant maize inbred line TL1317 possesses more rapidly and effectively responses to remove toxic Na+ ions and maintain K+ under salt stress than the salt-sensitive maize inbred line SL1303. This response should facilitate cell homoeostasis under salt stress and result in salt tolerance in TL1317.
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- 2016
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23. Metagenomic detection of viruses in aerosol samples from workers in animal slaughterhouses.
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Richard J Hall, Mily Leblanc-Maridor, Jing Wang, Xiaoyun Ren, Nicole E Moore, Collin R Brooks, Matthew Peacey, Jeroen Douwes, and David J McLean
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Medicine ,Science - Abstract
Published studies have shown that workers in animal slaughterhouses are at a higher risk of lung cancers as compared to the general population. No specific causal agents have been identified, and exposures to several chemicals have been examined and found to be unrelated. Evidence suggests a biological aetiology as the risk is highest for workers who are exposed to live animals or to biological material containing animal faeces, urine or blood. To investigate possible biological exposures in animal slaughterhouses, we used a metagenomic approach to characterise the profile of organisms present within an aerosol sample. An assessment of aerosol exposures for individual workers was achieved by the collection of personal samples that represent the inhalable fraction of dust/bioaerosol in workplace air in both cattle and sheep slaughterhouses. Two sets of nine personal aerosol samples were pooled for the cattle processing and sheep processing areas respectively, with a total of 332,677,346 sequence reads and 250,144,492 sequence reads of 85 bp in length produced for each. Eukaryotic genome sequence was found in both sampling locations, and bovine, ovine and human sequences were common. Sequences from WU polyomavirus and human papillomavirus 120 were detected in the metagenomic dataset from the cattle processing area, and these sequences were confirmed as being present in the original personal aerosol samples. This study presents the first metagenomic description of personal aerosol exposure and this methodology could be applied to a variety of environments. Also, the detection of two candidate viruses warrants further investigation in the setting of occupational exposures in animal slaughterhouses.
- Published
- 2013
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24. A polarised population of dynamic microtubules mediates homeostatic length control in animal cells.
- Author
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Remigio Picone, Xiaoyun Ren, Kenzo D Ivanovitch, Jon D W Clarke, Rachel A McKendry, and Buzz Baum
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Because physical form and function are intimately linked, mechanisms that maintain cell shape and size within strict limits are likely to be important for a wide variety of biological processes. However, while intrinsic controls have been found to contribute to the relatively well-defined shape of bacteria and yeast cells, the extent to which individual cells from a multicellular animal control their plastic form remains unclear. Here, using micropatterned lines to limit cell extension to one dimension, we show that cells spread to a characteristic steady-state length that is independent of cell size, pattern width, and cortical actin. Instead, homeostatic length control on lines depends on a population of dynamic microtubules that lead during cell extension, and that are aligned along the long cell axis as the result of interactions of microtubule plus ends with the lateral cell cortex. Similarly, during the development of the zebrafish neural tube, elongated neuroepithelial cells maintain a relatively well-defined length that is independent of cell size but dependent upon oriented microtubules. A simple, quantitative model of cellular extension driven by microtubules recapitulates cell elongation on lines, the steady-state distribution of microtubules, and cell length homeostasis, and predicts the effects of microtubule inhibitors on cell length. Together this experimental and theoretical analysis suggests that microtubule dynamics impose unexpected limits on cell geometry that enable cells to regulate their length. Since cells are the building blocks and architects of tissue morphogenesis, such intrinsically defined limits may be important for development and homeostasis in multicellular organisms.
- Published
- 2010
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25. Screening the optimal dose of gamma radiation for Tuta absoluta sterility: paving the way for sterile insect technique programs.
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Shuxing Zhou, Xiaowei Li, Jinming Zhang, Chaogang Liu, Jun Huang, Zhijun Zhang, Xiaoyun Ren, Limin Chen, Hafeez, Muhammad, Peng Han, Bingkui Wang, and Yaobin Lu
- Subjects
RADIATION doses ,GAMMA rays ,INSECTS ,FERTILITY ,SEX ratio ,AGRICULTURAL pests - Abstract
Tuta absoluta (Meyrick) is a destructive pest of tomato crops. The cryptic nature of larvae often leads to low control efficacy. Sterile insect technique (SIT) has the potential to be an alternative management option for T. absoluta. In this study, the optimal dose for T. absoluta sterility was determined by estimating the effect of gamma radiation on parental generation (F0) and their descendants (first and second generation, F1 and F2). Adult emergence was not affected when T. absoluta pupae were exposed to gamma radiation at doses of 100~400 Gy. However, increasing doses of radiation increased deformed individuals and shortened their longevity. Furthermore, as the dose increased, F0 females showed decreased fecundity and fertility, and they were completely sterile when exposed to 300 Gy. The survival and sex ratio of females declined significantly in F1 of irradiated males with increasing doses. Moreover, we found that 300 Gy of gamma radiation did not affect the mating competitiveness of F0 males. Interestingly, this treatment caused a considerable reduction in the number of descendants and caused inherited sterility in F1 by lowering their fecundity and fertility. Therefore, the optimal radiation dose was 300 Gy, and the release of sterile adults may suppress T. absoluta population growth in the field. Our findings provide basis for controlling T. absoluta through SIT programs. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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26. Frozen lepidopteran larvae as promising alternative factitious prey for rearing of Orius species
- Author
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Xiaoyun Ren, Jun Huang, Xiaowei Li, Jinming Zhang, Zhijun Zhang, Limin Chen, Muhammad Hafeez, Shuxing Zhou, and Yaobin Lu
- Subjects
Insect Science - Published
- 2022
27. Connecting the dots: How parental and current socioeconomic status shape individuals’ transformational leadership
- Author
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Jinyun Duan, Xiaoyun Ren, Zhengguang Liu, and Ronald E. Riggio
- Subjects
Marketing - Published
- 2022
28. Water and nitrogen supply on photosynthetic physiological response of sugar beet (Beta vulgaris) under mulched drip irrigation
- Author
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Zhi Li, Guolong Li, Yaqing Sun, Wenbin Su, Fuyi Fan, Chunyan Huang, Xiaoxia Guo, Caiyuan Jian, Lu Tian, Kang Han, Xiaoyun Ren, Qianheng Gong, and Shaoying Zhang
- Subjects
Physiology ,Agronomy and Crop Science - Published
- 2022
29. Through the Looking-Glass: A curious outbreak of extended-spectrum beta-lactamase-producing Escherichia coli in Aotearoa New Zealand
- Author
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White, Rhys Thomas, Ashcroft, Melinda M., Kok-Gan Chan, Teik-Min Chong, Forde, Brian M, Peters, Kate M., Minh-Duy Phan, Xiaoyun Ren, Schembri, Mark A, Yin, Wai-Fong, Williamson, Deborah A., Dyet, Kristin H., Beatson, Scott A., and De Ligt, Joep
- Published
- 2023
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30. Using whole-genome sequencing in the rapid response to SARS-CoV-2 in Aotearoa New Zealand
- Author
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White, Rhys T, Jelley, Lauren, Douglas, Jordan, Xiaoyun Ren, Winter, David, Genomics Team, Covid-19 Wgs, Bunce, Michael, Carr, Sam, Mcneill, Andrea, Q Sue Huang, Swadi, Tara, Devine, Tom, Mcelnay, Caroline, Sherwood, Jillian, Shoemack, Phil, Fox-Lewis, Andrew, Williamson, Felicity, Harrower, Jay, Storey, Matt, Jefferies, Sarah, Smit, Erasmus, Hadfield, James, Kenny, Aoife, Sporle, Andrew, G Edwin Reynolds, Mouldey, Kip, Lowe, Lindsay, Sonder, Gerard, Drummond, Alexei J, Welch, David, Holmes, Edward C, French, Nigel, Simpson, Colin R, De Ligt, Joep, and Geoghegan, Jemma
- Published
- 2023
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31. Paradoxical Effect of Exploitative Leadership on Employee Performance (WITHDRAWN)
- Author
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Jinyun Duan, Xiaoyun Ren, Yue Xu, and Jie Li
- Subjects
General Medicine - Published
- 2022
32. The Influence of Family Social Class on Career Choice: From the Perspective of Social Cognition
- Author
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Jinyun Duan, Xiaoyun Ren, Wenjie Luo, and Xiaoming Tian
- Abstract
Based on the cognitive theory of social stratum, this paper discusses the influence of family social stratum on self-concern and others’ concern career choice, as well as its mechanism and boundary conditions. Through questionnaire method (Study 1)and experimental method (Study 2), the results show that family social class is positively correlated with ego-focused occupations and negatively correlated with others concerned occupations; independent self-construal plays a mediating role between family social stratum and ego-focused occupation, while interdependent self-construal plays a mediating role between family social stratum and other concerned occupation; individual and collectivist values regulate the family social class by predicting the indirect effect of career choice through self-construal.
- Published
- 2022
33. Genomic Surveillance of a Globally Circulating Distinct Group W Clonal Complex 11 Meningococcal Variant, New Zealand, 2013–2018
- Author
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Tim Wood, Heather Davies, Audrey Tiong, Jill Sherwood, Philip E. Carter, Liza Lopez, Xiaoyun Ren, and Zuyu Yang
- Subjects
Microbiology (medical) ,Canada ,group W ,Epidemiology ,030231 tropical medicine ,lcsh:Medicine ,Neisseria meningitidis ,Biology ,Reference laboratory ,Serogroup ,medicine.disease_cause ,Meningococcal disease ,lcsh:Infectious and parasitic diseases ,03 medical and health sciences ,0302 clinical medicine ,evolution ,medicine ,Humans ,Public Health Surveillance ,lcsh:RC109-216 ,030212 general & internal medicine ,bacteria ,Genomic Surveillance of a Globally Circulating Distinct Group W Clonal Complex 11 Meningococcal Variant, New Zealand, 2013–2018 ,Whole genome sequencing ,Genetics ,meningococcal disease ,Research ,Strain (biology) ,invasive meningococcal disease ,lcsh:R ,Outbreak ,Genomics ,Sequence types ,medicine.disease ,Europe ,Meningococcal Infections ,Penicillin ,Infectious Diseases ,whole-genome sequencing ,meningitis/encephalitis ,medicine.drug ,New Zealand - Abstract
Genomic surveillance is an essential part of effective disease control, enabling identification of emerging and expanding strains and monitoring of subsequent interventions. Whole-genome sequencing was used to analyze the genomic diversity of all Neisseria meningitidis isolates submitted to the New Zealand Meningococcal Reference Laboratory during 2013-2018. Of the 347 isolates submitted for whole-genome sequencing, we identified 68 sequence types belonging to 18 clonal complexes (CC). The predominant CC was CC41/44; next in predominance was CC11. Comparison of the 45 New Zealand group W CC11 isolates with worldwide representatives of group W CC11 isolates revealed that the original UK strain, the 2013 UK strain, and a distinctive variant (the 2015 strain) were causing invasive group W meningococcal disease in New Zealand. The 2015 strain also demonstrated increased resistance to penicillin and has been circulating in Canada and several countries in Europe, highlighting that close monitoring is needed to prevent future outbreaks around the world.
- Published
- 2021
34. Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing
- Author
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Aoife Kenny, Nigel P. French, Alexei J. Drummond, Tom Devine, Joep de Ligt, Sue Huang, Lindsay Lowe, Phil Shoemack, Lauren Jelley, Jemma L. Geoghegan, James Hadfield, Matt Storey, Andrew Sporle, Kip Mouldey, David Welch, Jillian Sherwood, Gerard J.B. Sonder, Colin R Simpson, Edward C. Holmes, G. Edwin Reynolds, Caroline McElnay, Tara Swadi, Xiaoyun Ren, Andrea McNeill, Sarah Jefferies, and Erasmus Smit
- Subjects
Microbiology (medical) ,Aircraft ,Isolation (health care) ,Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing ,Epidemiology ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,viruses ,Physical Distancing ,030231 tropical medicine ,United Arab Emirates ,lcsh:Medicine ,Disease ,medicine.disease_cause ,law.invention ,2019 novel coronavirus disease ,lcsh:Infectious and parasitic diseases ,respiratory infections ,03 medical and health sciences ,0302 clinical medicine ,in-flight transmission ,law ,Quarantine ,Humans ,Medicine ,lcsh:RC109-216 ,030212 general & internal medicine ,Coronavirus ,business.industry ,Transmission (medicine) ,SARS-CoV-2 ,Disease progression ,lcsh:R ,Masks ,COVID-19 ,zoonoses ,Infectious Diseases ,coronavirus disease ,Synopsis ,business ,Single mutation ,New Zealand ,Demography ,severe acute respiratory syndrome coronavirus 2 - Abstract
Since the first wave of coronavirus disease in March 2020, citizens and permanent residents returning to New Zealand have been required to undergo managed isolation and quarantine (MIQ) for 14 days and mandatory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of October 20, 2020, of 62,698 arrivals, testing of persons in MIQ had identified 215 cases of SARS-CoV-2 infection. Among 86 passengers on a flight from Dubai, United Arab Emirates, that arrived in New Zealand on September 29, test results were positive for 7 persons in MIQ. These passengers originated from 5 different countries before a layover in Dubai; 5 had negative predeparture SARS-CoV-2 test results. To assess possible points of infection, we analyzed information about their journeys, disease progression, and virus genomic data. All 7 SARS-CoV-2 genomes were genetically identical, except for a single mutation in 1 sample. Despite predeparture testing, multiple instances of in-flight SARS-CoV-2 transmission are likely.
- Published
- 2021
35. Individuals vs groups: Advice-taking in decision making
- Author
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Jinyun Duan, Xiaoyun Ren, and Chengzhi Feng
- Subjects
Applied psychology ,Group dynamic ,Psychology ,General Economics, Econometrics and Finance ,Advice (complexity) - Published
- 2021
36. From elimination to suppression: genomic epidemiology of a large Delta SARS-CoV-2 outbreak in Aotearoa New Zealand
- Author
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Lauren Jelley, Jordan Douglas, Xiaoyun Ren, David Winter, Andrea McNeill, Sue Huang, Nigel French, David Welch, James Hadfield, Joep de Ligt, and Jemma L Geoghegan
- Abstract
New Zealand’s COVID-19 elimination strategy heavily relied on the use of genomics to inform contact tracing, linking cases to the border and to clusters during community outbreaks. In August 2021, New Zealand entered its second nationwide lockdown after the detection of a single community case with no immediately apparent epidemiological link to the border. This incursion resulted in the largest outbreak seen in New Zealand caused by the Delta Variant of Concern. Here we generated 3806 high quality SARS-CoV-2 genomes from cases reported in New Zealand between 17 August and 1 December 2021, representing 43% of reported cases. We detected wide geographical spread coupled with undetected community transmission, characterised by the apparent extinction and reappearance of genomically linked clusters. We also identified the emergence, and near replacement, of genomes possessing a 10-nucleotide frameshift deletion that caused the likely truncation of accessory protein ORF7a. By early October, New Zealand moved from elimination to suppression and the role of genomics changed markedly from being used to track and trace, towards population-level surveillance.
- Published
- 2022
37. Abundances of thrips on plants in vegetative and flowering stages are related to plant volatiles
- Author
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Shengyong Wu, Zhongren Lei, Wanzhi Cai, Xiaoyun Ren, Yulin Gao, and Zhenlong Xing
- Subjects
food.ingredient ,biology ,Thrips ,media_common.quotation_subject ,Basilicum ,Insect ,biology.organism_classification ,Ocimum ,Western flower thrips ,food.food ,Horticulture ,food ,Allium fistulosum ,Abundance (ecology) ,Insect Science ,Medicago sativa ,Agronomy and Crop Science ,media_common - Abstract
Western flower thrips (WFTs), Frankliniella occidentalis Pergrande, and onion thrips (OTs), Thrips tabaci Lindeman, are two cosmopolitan insect pests of agricultural and horticultural plants. Understanding the occurrence and development of thrips on plants is crucial for identifying suitable plants that can be used for developing a “push‐pull” strategy against thrips. In this study, the dynamics of WFTs and OTs on plants (Allium fistulosum L., Medicago sativa L., Luffa cylindrica (L.) Roem., Ocimum basilicum L., and Schizonepeta tenuifolia (Benth.) Briq.) were investigated for two consecutive years (2018–2019). Throughout the survey, the abundances of both thrips species were strongly associated with plant species and plant phenology; both thrips species were present at relatively high densities on M. sativa but very low densities on O. basilicum and S. tenuifolia. Populations of both thrips species greatly increased during plant flowering. A Y‐tube olfactory test was used to study the effects of plant volatiles in mediating thrips behaviour and showed that volatiles of M. sativa were attractive to both thrips species whether emitted by the plant in the vegetative or flowering stage, while volatiles of O. basilicum and S. tenuifolia were repellent to thrips. Additionally, because of the presence of a high number of floral chemicals, both thrips species exhibited a greater preference for volatiles emitted by plants in the flowering period over those emitted by plants in the vegetative period. Our observations indicate that plant species and flowering status play an important role in the abundance dynamics of thrips and that the volatiles of flowering plants attract thrips more strongly than volatiles emitted by vegetative plants. These findings can facilitate the screening of attractive/unattractive plants for developing push‐pull strategies to control thrips.
- Published
- 2020
38. The Neisseria meningitidis iron acquisition protein HpuA moonlights as an adhesin and inhibits host cell migration
- Author
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Gabrielle A. Shortt, Xiaoyun Ren, Brianna M. Otto, and Joanna K. MacKichan
- Abstract
Neisseria meningitidis can cause meningococcal disease, a rapidly developing and potentially fatal infection. Despite this, it normally resides as a commensal in the nasopharynx of healthy individuals. The mechanisms by which meningococci access deeper tissues remain unknown. Epidemiological data suggest that mucosal disruptions increase the risk of meningococcal disease. We previously investigated whether meningococci inhibit host cell wound repair, enhancing invasive disease risk. Here, using genome sequencing and a collection of closely related household isolates that differ in their ability to inhibit host wound repair, we identify the responsible meningococcal factor. This protein, HpuA, has previously been characterized as part of a bipartite heme acquisition transporter. We constructed mutants to demonstrate that HpuA, but not HpuB, inhibits wound repair, acts as an adhesin for epithelial cells, and promotes cellular invasion. We showed this was not due to iron starvation resulting from the bacteria, differences in growth rate, or manipulation of host haptoglobin. Heterologous expression of HpuA in E. coli mediated adherence to 16HBE cells in an HpuA-dependent manner and conferred an aggregative phenotype onto E. coli, suggesting that HpuA may play a role in the formation of microcolonies on host cells. We also demonstrated that iron supplementation of meningococci restored the inhibition of wound repair in strains lacking HpuA (NZCM112, ΔhpuA mutant) to levels seen with the wild type. This was also seen with unrelated carriage strains previously shown not to inhibit wound repair. Iron supplementation also increased adherence and invasion of meningococci for strains lacking HpuA, while not affecting those that expressed HpuA. These findings suggest there may be a second meningococcal protein that inhibits wound repair. Together, these results suggest that HpuA is an important meningococcal virulence factor with multiple moonlighting functions, mediating adherence, invasion, inhibition of wound repair, and bacterial aggregation.Author SummaryNeisseria meningitidis causes meningococcal disease, a potentially fatal and rapidly developing illness that most often occurs in children. Despite this, the bacteria are frequently carried harmlessly as part of the normal airway microflora in healthy people, only rarely causing invasive disease, which involves replication in the bloodstream or central nervous system. It remains unknown precisely how the bacteria reach the deeper tissues from the airways, though some epidemiological evidence suggests that wounds or disruptions to the airways may increase risk. Here, we show that a N. meningitidis protein, HpuA, moonlights from its usual job of acquiring nutrients from the host, to enable the bacteria to adhere to and invade host cells, as well as inhibiting wound closure. Furthermore, we also show that meningococci that lack HpuA acquire the ability to inhibit wound repair when they are supplemented with iron, suggesting that there are additional meningococcal proteins to be discovered that may inhibit wound repair.
- Published
- 2022
39. Optimization of berth and quay crane joint scheduling considering efficiency and energy consumption
- Author
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Mingjun Ji, Xiaoyun Ren, Xumao Li, Dusu Wen, and Qiuxi Long
- Subjects
Management of Technology and Innovation ,Transportation ,Management Science and Operations Research ,Business and International Management - Published
- 2023
40. Behavioral and physiological plasticity provides insights into molecular based adaptation mechanism to strain shift in Spodoptera frugiperda
- Author
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Myron P. Zalucki, Zhijun Zhang, Farman Ullah, G. Mandela Fernández-Grandon, Xiaoyun Ren, Huang Jun, Muhammad Hafeez, Li Xiaowei, Muhammad Musa Khan, Limin Chen, Shuxing Zhou, Jinming Zhang, and Yaobin Lu
- Subjects
S1 ,QH301-705.5 ,Population ,behavioral response ,Zoology ,midgut ,Spodoptera ,Catalysis ,Inorganic Chemistry ,Physical and Theoretical Chemistry ,host plants adaptation ,Biology (General) ,education ,Molecular Biology ,QD1-999 ,Spectroscopy ,Larva ,education.field_of_study ,QL ,biology ,Strain (biology) ,Organic Chemistry ,fungi ,food and beverages ,Midgut ,General Medicine ,biology.organism_classification ,Computer Science Applications ,Chemistry ,Spodoptera frugiperda ,Fall armyworm ,sense organs ,PEST analysis ,Adaptation ,molecular mechanism ,antennal response - Abstract
How herbivorous insects adapt to host plants is a key question in ecological and evolutionary biology. The fall armyworm, (FAW) Spodoptera frugiperda (J.E. Smith), although polyphagous and a major pest on various crops, has been reported to have a rice and corn (maize) feeding strain in its native range in the Americas. The species is highly invasive and has recently established in China. We compared behavioral changes in larvae and adults of a corn population (Corn) when selected on rice (Rice) and the molecular basis of these adaptational changes in midgut and antennae based on a comparative transcriptome analysis. Larvae of S. frugiperda reared on rice plants continuously for 20 generations exhibited strong feeding preference for with higher larval performance and pupal weight on rice than on maize plants. Similarly, females from the rice selected population laid significantly more eggs on rice as compared to females from maize population. The most highly expressed DEGs were shown in the midgut of Rice vs. Corn. A total of 6430 DEGs were identified between the populations mostly in genes related to digestion and detoxification. These results suggest that potential adaptations for feeding on rice crops, may contribute to the current rapid spread of fall armyworm on rice crops in China and potentially elsewhere. Consistently, highly expressed DEGs were also shown in antennae, a total of 5125 differentially expressed genes (DEGs) s were identified related to the expansions of major chemosensory genes family in Rice compared to the Corn feeding population. These results not only provide valuable insight into the molecular mechanisms in host plants adaptation of S. frugiperda but may provide new gene targets for the management of this pest.
- Published
- 2021
41. Analyzing Spatio-Temporal Change in Ecosystem Quality and Its Driving Mechanism in Henan Province, China, from 2010 to 2020
- Author
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Xiaoyun Ren, Mingkong Zhang, Juncheng Qian, Shuangquan Li, Jingxu Wang, and Jun Du
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Renewable Energy, Sustainability and the Environment ,Geography, Planning and Development ,Building and Construction ,ecosystem ,Geo-detector ,Henan province ,formation mechanism ,Management, Monitoring, Policy and Law - Abstract
Henan Province is an important ecological barrier in the middle and lower reaches of the Yellow River. It is of great significance to study its ecosystem quality and the driving mechanisms behind this in order to realize ecological conservation and high-quality development in the Yellow River Basin. In this study, from the perspective of physical elements, socioeconomic elements, and policy adjustments, multi-source data on land use, population density, forestry engineering, and other indicators were selected to construct an index system of the driving factors of ecosystem quality in Henan Province. The characteristics of spatio-temporal change and the formation mechanism of ecosystem quality in Henan Province from 2010 to 2020 were analyzed by comprehensively using the gravity center analysis method and a geo-detector tool. The results showed the following: (1) The ecosystem quality of Henan Province in 2020 has increased by 27.7% compared with that in 2010, and the center of gravity of ecosystem quality continued to move to the northwest of Henan Province. The quality of ecosystems in the hilly region of Western Henan, Tongbai, and Nanyang was better than that in the northern Loess Platform Hilly Area and the Yellow River Plain, and it presented a spatial pattern in which the quality of the south was higher than that of the north, while the east and west were equal; (2) From 2010 to 2020, the average GDP and population density in Henan Province were the most important factors affecting the quality of its ecosystem. The effect of land-use diversity on ecosystem quality in the hilly region of Henan Province was stronger than that in the central and eastern plains; and (3) The interactions among the driving factors were mainly nonlinear enhancement and double factor enhancement, in which the interaction between socio-economic elements and natural environmental elements was the dominant interaction mode and could enhance the impact on the quality of the regional ecological environment. The results of this study indicate that attention should be paid to generating targeted industrial economy layout and land use policies in different natural domains. Moreover, forestry protection engineering policies should be further strengthened to improve the resilience of ecosystem quality to human activities.
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- 2022
42. Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations
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Jemma L. Geoghegan, Matt Storey, Xiaoyun Ren, Christiaan Swanepoel, Cinthy L. Jiménez-Silva, Alexei J. Drummond, James Hadfield, Colin R Simpson, Joep de Ligt, Dong Xie, Fábio K. Mendes, David Welch, Jordan Douglas, and Remco R. Bouckaert
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0301 basic medicine ,Official statistics ,medicine.medical_specialty ,Coronavirus disease 2019 (COVID-19) ,Range (biology) ,coronavirus ,Taiwan ,Iceland ,Context (language use) ,human movement ,medicine.disease_cause ,Microbiology ,contact tracing ,law.invention ,03 medical and health sciences ,0302 clinical medicine ,law ,Virology ,Pandemic ,Epidemiology ,Added value ,Regional science ,medicine ,AcademicSubjects/MED00860 ,030212 general & internal medicine ,Coronavirus ,AcademicSubjects/SCI01130 ,AcademicSubjects/SCI02285 ,Australia ,COVID-19 ,phylogenomics ,030104 developmental biology ,Geography ,Transmission (mechanics) ,Viral phylodynamics ,Mobile phone ,Contact tracing ,Research Article ,New Zealand ,Demography - Abstract
BackgroundNew Zealand, Australia, Iceland, and Taiwan all saw success at controlling the first wave of the COVID-19 pandemic. As islands, they make excellent case studies for exploring the effects of international travel and human movement on the spread of COVID-19.MethodsWe employed a range of robust phylodynamic methods and genome subsampling strategies to infer the epidemiological history of SARS-CoV-2 in these four countries. We compared these results to transmission clusters identified by the New Zealand Ministry of Health by contract tracing strategies.FindingsWe estimated the effective reproduction number of COVID-19 as 1–1.4 during early stages of the pandemic, and show that it declined below 1 as human movement was restricted. We also showed that this disease was introduced many times into each country, and that introductions slowed down markedly following the reduction of international travel in mid March 2020. Finally, we confirmed that New Zealand transmission clusters identified via standard health surveillance strategies largely agree with those defined by genomic data.InterpretationWe have demonstrated how the use of genomic data and computational biology methods can assist health officials in characterising the epidemiology of viral epidemics, and for contact tracing.FundingThis research was funded by the Health Research Council of New Zealand, the Ministry of Business, Innovation, and Employment, the Royal Society of New Zealand, and the New Zealand Ministry of Health.Research in ContextEvidence before this studyOur study looks at the early months of the COVID-19 pandemic, a period in which the first wave was controlled in four “island” nations – New Zealand, Australia, Taiwan, and Iceland. All prior data used in this study was collected from late 2019 until the end of April 2020. This includes over 3000 SARS-CoV-2 genomic sequences which were collected in this period (and subsequently deposited into GISAID), as well as arrival and departure information (provided by official statistics from each country), human mobility data collected from mobile phones (by Apple), and COVID-19 case data (released by the World Health Organisation). Even early on during the COVID-19 pandemic, the properties of SARS-CoV-2 – including the reproduction number and mutation rate – were well characterised, and a range of these estimates have been covered in our article. Our Bayesian phylodynamic models, including their prior distributions, are informed by all of the above sources of information. Finally, we have incorporated all of the available information on COVID-19 transmission clusters identified by the New Zealand Ministry of Health during this period.Added value of this studyWe quantified the decline in the reproduction number of SARS-CoV-2, following the decline in human mobility, in four “island” countries. We also demonstrated how importation events of SARS-CoV-2 into each considered country declined markedly following the reduction of international travel. Our results shed a different light on these patterns because of (i) our locations of choice – the four countries had success in dealing with the first pandemic wave, with their geographic isolation contributing to cleaner signals of human mobility, and (ii) our novel and empirically driven phylodynamic model, which we built from explicitly modelling mobile phone data in the four islands. Furthermore, by crossing epidemiological against ge3nomic data, our paper quantitatively assesses the ability of contact tracing, as implemented by the New Zealand Ministry of Health (NZMH), in identifying COVID-19 transmission clusters. We find evidence for a high efficacy of the specific measures taken – and when they were taken – by the NZMH in identifying transmission clusters, considered worldwide to have been successful in its response to the pandemic. Our analyses also illustrate the power of viral genomic data in assisting contact tracing.Implications of all the available evidenceThe conclusions drawn from this research inform effective policy for locations pursuing an elimination strategy. We confirm the accuracy of standard contact tracing methods at identifying clusters and show how these methods are improved using genomic data. We demonstrate how the overseas introduction rates and domestic transmission rates of an infectious viral agent can be surveilled using genomic data, and the important role each plays in overall transmission. Specifically, we have quantified these processes for four countries and have shown that they did decline significantly following declines in human travel and mobility. The phylodynamic methods used in this work is shown to be robust and applicable to a range of scenarios where appropriate subsampling is used.
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- 2021
43. Co-occurrence of mcr-1 and mcr-3 genes in a single Escherichia coli in New Zealand
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Xiaoyun Ren, Kristin Dyet, Julie Creighton, Julia Howard, Trevor P. Anderson, and Joshua T. Freeman
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Microbiology (medical) ,Transferases (Other Substituted Phosphate Groups) ,Microbial Sensitivity Tests ,Drug resistance ,Biology ,medicine.disease_cause ,Microbiology ,Bacterial genetics ,Drug Resistance, Bacterial ,Escherichia coli ,medicine ,Animals ,Humans ,Pharmacology (medical) ,Gene ,Escherichia coli Infections ,Aged ,Pharmacology ,Colistin ,Escherichia coli Proteins ,Anti-Bacterial Agents ,Infectious Diseases ,Female ,MCR-1 ,New Zealand ,Plasmids - Published
- 2019
44. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch
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Darío García de Viedma, Angelica Bianco, Torsten Seemann, Nikita Sahadeo, Orna Mor, Richard R. Lessells, Christian Drosten, Nikki E. Freed, Aekyung Park, Chuan Kok Lim, Michal Mandelboim, Sanmarié Schlebusch, Georgi Merhi, Tanja Stadler, Kamran Khan, Ira Deveson, Joep de Ligt, Kirsten St. George, Nuno R. Faria, Mailie Gall, Matthew Storey, Chitra Pattabiraman, Teemu Smura, Andrew Rambaut, Tamara Salloum, Antonio Parisi, Sureshnee Pillay, Erica Lasek-Nesselquist, Ravi Vasanthapuram, Issac I. Bogoch, Xiaoyun Ren, Dirk Eggink, Jamie McMahon, Reina S. Sikkema, Satu Kurkela, William D. Rawlinson, Jennifer Giandhari, Maitshwarelo Matsheka, Tulio de Oliveira, Daniela Loconsole, Laurence Josset, Malebogo Kebabonye, Gape Nyepetsi, V. Sudha rani, Joana Isidro, Madisa Mine, Lars Steinbrück, Albert Heim, Áine O'Toole, Pramada Prasad, Martina Rueca, Alexander Watts, Chantal Reusken, Lex E. X. Leong, SeqCOVID-Spain, Marion Koopmans, Hamad Hassan, Antonin Bal, Alicia Arnott, Search Alliance San Diego, Jenny Draper, Vítor Borges, Houriiyah Tegally, Jemma L. Geoghegan, Jane P. Messina, Massab Umair, Neta S. Zuckerman, Sílvia Duarte, Olin K. Silander, Jad Koweyes, Mia Brytting, Maria Chironna, Anita Desai, S. Pavani, Harry Vennema, Verity Hill, Michael J. Carr, Kefentse Arnold Tumedi, Sergio Buenestado-Serrano, Thomas F. Schulz, Barbara Bartolini, Gabo Gonzalez, Bas B. Oude Munnink, Thorsten Wolff, Oliver G. Pybus, Edward C. Holmes, Christine V.F. Carrington, João Paulo Gomes, Moritz U. G. Kraemer, Muhammad Salman, Sima Tokajian, and Virology
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Infecções Respiratórias ,genomic surveillance ,air travel ,SARS-CoV-2 ,Genomics ,genome sequencing ,Virus ,Surveillance ,Pandemic ,B.1.1.7 ,B.1.351 ,N501Y ,Coronavirus ,Sequencing ,genomic epidemiology ,viruses ,Lineage (evolution) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Medicine (miscellaneous) ,medicine.disease_cause ,General Biochemistry, Genetics and Molecular Biology ,DNA sequencing ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Genome Sequencing ,Genomic Epidemiology ,030304 developmental biology ,0303 health sciences ,Genomic Surveillance ,Haplotype ,virus diseases ,COVID-19 ,3. Good health ,Geography ,Air Travel ,Evolutionary biology ,Biological dispersal ,030217 neurology & neurosurgery - Abstract
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501YV2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected., Wellcome Open Research, 6
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- 2021
45. Real-time genomics to track COVID-19 post-elimination border incursions in Aotearoa New Zealand
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Jordan Douglas, Matthew Storey, Jemma L. Geoghegan, David Welch, Nigel P. French, Joep de Ligt, Xiaoyun Ren, James Hadfield, and Remco R. Bouckaert
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medicine.medical_specialty ,2019-20 coronavirus outbreak ,Geography ,Coronavirus disease 2019 (COVID-19) ,Public health ,Genomic sequencing ,Viral transmission ,medicine ,Outbreak ,Genomics ,Aotearoa ,Genealogy - Abstract
There have been thirteen known COVID-19 community outbreaks in Aotearoa New Zealand since the virus was first eliminated in May 2020, two of which led to stay-at-home orders being issued by health officials. These outbreaks originated at the border; via isolating returnees, airline workers, and cargo vessels. With a public health system informed by real-time viral genomic sequencing which typically had complete genomes within 12 hours after a community-based positive COVID-19 test, every outbreak was well-contained with a total of 225 community cases, resulting in three deaths. Real-time genomics were essential for establishing links between cases when epidemiological data could not, and for identifying when concurrent outbreaks had different origins. By reconstructing the viral transmission history from genomic sequences, here we recount all thirteen community outbreaks and demonstrate how genomics played a vital role in containing them.SummaryThe authors recount the role of real-time viral genomics in containing the COVID-19 community outbreaks of Aotearoa New Zealand.
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- 2021
46. Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 during Border Quarantine and Air Travel, New Zealand (Aotearoa)
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Tara Swadi, Cheryl Brunton, Joep de Ligt, Craig Thornley, Jemma L. Geoghegan, Matt Storey, Sarah Berger, Nick Eichler, Felicity Williamson, Caroline McElnay, Xiaoyun Ren, Jillian Sherwood, Tom Devine, and Josh Freeman
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Microbiology (medical) ,medicine.medical_specialty ,case-patients ,Isolation (health care) ,Epidemiology ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Expedited ,030231 tropical medicine ,coronavirus ,Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 during Border Quarantine and Air Travel, New Zealand (Aotearoa) ,Disease ,Infectious and parasitic diseases ,RC109-216 ,medicine.disease_cause ,law.invention ,03 medical and health sciences ,respiratory infections ,0302 clinical medicine ,law ,Quarantine ,Medicine ,Humans ,viruses ,030212 general & internal medicine ,Coronavirus ,Travel ,business.industry ,Transmission (medicine) ,SARS-CoV-2 ,Outbreak ,COVID-19 ,Aotearoa ,air travel ,zoonoses ,Infectious Diseases ,coronavirus disease ,Emergency medicine ,Synopsis ,business ,border quarantine ,New Zealand ,severe acute respiratory syndrome coronavirus 2 - Abstract
The strategy in New Zealand (Aotearoa) to eliminate coronavirus disease requires that international arrivals undergo managed isolation and quarantine and mandatory testing for severe acute respiratory syndrome coronavirus 2. Combining genomic and epidemiologic data, we investigated the origin of an acute case of coronavirus disease identified in the community after the patient had spent 14 days in managed isolation and quarantine and had 2 negative test results. By combining genomic sequence analysis and epidemiologic investigations, we identified a multibranched chain of transmission of this virus, including on international and domestic flights, as well as a probable case of aerosol transmission without direct person-to-person contact. These findings show the power of integrating genomic and epidemiologic data to inform outbreak investigations.
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- 2021
47. Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand
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James Hadfield, Matthew Storey, Nigel P. French, Fábio K. Mendes, Andrew Sporle, Sue Huang, David Welch, Shevaun Paine, Xiaoyun Ren, Jemma L. Geoghegan, Colin R Simpson, Michael G Baker, Sebastián Duchêne, Sarah Jefferies, David R. Murdoch, Joep de Ligt, Edward C. Holmes, Lauren Jelley, Jordan Douglas, Alexei J. Drummond, and Jill Sherwood
- Subjects
SARS-CoV-2/classification ,0106 biological sciences ,0301 basic medicine ,Male ,Epidemiology ,General Physics and Astronomy ,01 natural sciences ,law.invention ,law ,Pandemic ,New Zealand/epidemiology ,Child ,Phylogeny ,COVID-19/epidemiology ,Aged, 80 and over ,education.field_of_study ,Multidisciplinary ,Geography ,Genomics ,Middle Aged ,Aotearoa ,Phylogenetics ,Transmission (mechanics) ,Child, Preschool ,Female ,Adult ,medicine.medical_specialty ,Lineage (genetic) ,Adolescent ,Science ,Population ,Genome, Viral ,Disease cluster ,010603 evolutionary biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Young Adult ,Whole Genome Sequencing/methods ,Quarantine ,medicine ,Humans ,Genome, Viral/genetics ,education ,Pandemics ,Aged ,Whole Genome Sequencing ,SARS-CoV-2 ,Public health ,Infant, Newborn ,COVID-19 ,Infant ,General Chemistry ,Genomics/methods ,Genome evolution ,030104 developmental biology ,Demography ,New Zealand - Abstract
New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nationwide ‘lockdown’ of all non-essential services to curb the spread of COVID-19. Here, we generate 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with samples collected during the ‘first wave’, representing 56% of all confirmed cases in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. These data helped to quantify the effectiveness of public health interventions. For example, the effective reproductive number, Re of New Zealand’s largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in ongoing transmission of more than one additional case. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease mitigation., New Zealand implemented stringent COVID-19 control measures early after identification of its first case. Here, the authors perform whole genome sequencing of samples taken until 22 May 2020 and find high viral diversity indicative of multiple separate introductions and limited community transmission.
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- 2020
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48. The power and limitations of genomics to track COVID-19 outbreaks: a case study from New Zealand
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Xiaoyun Ren, Olin K. Silander, Jordan Douglas, Andrew Sporle, Shevaun Paine, Lauren Jelley, Joep de Ligt, Sue Huang, David R. Murdoch, Alexei J. Drummond, David Welch, Jemma L. Geoghegan, Matt Storey, Sarah Jefferies, Nikki E. Freed, Jillian Sherwood, Edward C. Holmes, Nigel P. French, James Hadfield, Michael G Baker, and Colin R Simpson
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Economic growth ,Geography ,Single cluster ,Coronavirus disease 2019 (COVID-19) ,Research council ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Outbreak ,Sample (statistics) ,Genomics ,Track and trace - Abstract
SummaryBackgroundReal-time genomic sequencing has played a major role in tracking the global spread and local transmission of SARS-CoV-2, contributing greatly to disease mitigation strategies. After effectively eliminating the virus, New Zealand experienced a second outbreak of SARS-CoV-2 in August 2020. During this August outbreak, New Zealand utilised genomic sequencing in a primary role to support its track and trace efforts for the first time, leading to a second successful elimination of the virus.MethodsWe generated the genomes of 80% of the laboratory-confirmed samples of SARS-CoV-2 from New Zealand’s August 2020 outbreak and compared these genomes to the available global genomic data.FindingsGenomic sequencing was able to rapidly identify that the new COVID-19 cases in New Zealand belonged to a single cluster and hence resulted from a single introduction. However, successful identification of the origin of this outbreak was impeded by substantial biases and gaps in global sequencing data.InterpretationAccess to a broader and more heterogenous sample of global genomic data would strengthen efforts to locate the source of any new outbreaks.FundingThis work was funded by the Ministry of Health of New Zealand, New Zealand Ministry of Business, Innovation and Employment COVID-19 Innovation Acceleration Fund (CIAF-0470), ESR Strategic Innovation Fund and the New Zealand Health Research Council (20/1018 and 20/1041).
- Published
- 2020
49. Behavioral Responses of Western Flower Thrips (Frankliniella occidentalis) to Visual and Olfactory Cues at Short Distances
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Xu Ruirui, Xiaoyun Ren, Zhongren Lei, Wanzhi Cai, Shengyong Wu, and Zhenlong Xing
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0106 biological sciences ,Thrips ,genetic structures ,Foraging ,Olfactory cues ,Zoology ,food and beverages ,Biology ,biology.organism_classification ,01 natural sciences ,Western flower thrips ,Short distance ,olfactory cue ,010602 entomology ,short distance ,frankliniella occidentalis ,visual cue ,Insect Science ,lcsh:Q ,PEST analysis ,lcsh:Science ,Sensory cue ,trapping efficacy ,010606 plant biology & botany - Abstract
Western flower thrips (WFT), Frankliniella occidentalis (Pergande), is a highly invasive pest, infesting many species of plants worldwide, but few studies have investigated the visual and olfactory cues associated with their foraging behaviors. In this study, the distance traveled by WFT to locate yellow cards using only visual cues and visual cues plus olfactory cues was studied first. Subsequently, preferences for colors (white, red, green, purple, yellow and blue) and patterns (triangle, rectangle, circle and flower-shape) over short distances were assessed with free-choice tests. Finally, as yellow was the most efficient color to catch WFT under laboratory conditions, the yellow flower-shape was used as the visual cue, and preferences between visual and olfactory cues were evaluated with dual choice tests. The results showed that the capture rate of WFT by visual cues decreased as selection distance increased, however capture rate remained higher with the addition of olfactory cues. The flower shape attracted the greatest number of WFT among all shapes tested. The combination of visual cues and extracted volatiles from flowering Medicago sativa L. attracted higher numbers of WFT than to the olfactory cues alone, however these were similar to visual cues alone. The presence of olfactory cues resulted in higher residence times by WFT than did the absence of olfactory cues. These results show the relative effects of visual and olfactory cues on the orientation of WFT to hosts and highlight that visual cues dominate selection behavior at short distances. These findings can be used in the development of efficient trapping products and management strategies for thrips.
- Published
- 2020
50. Cellular rearrangement of the prechordal plate contributes to eye degeneration in the cavefish
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Xiaoyun Ren, Yoshiyuki Yamamoto, Ferenc Müller, and Noémie Hamilton
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Fish Proteins ,0301 basic medicine ,Prechordal plate ,animal structures ,Cavefish ,Nodal signaling ,Optic cup (anatomical) ,Eye ,03 medical and health sciences ,0302 clinical medicine ,Animal physiology - cell ,Animals ,Eye Abnormalities ,Sonic hedgehog ,Molecular Biology ,biology ,Gastrula ,Cell Biology ,Animal structure and function ,Cell biology ,030104 developmental biology ,embryonic structures ,biology.protein ,Eye development ,PAX6 ,Characiformes ,Animal physiology - systems ,Neural plate ,030217 neurology & neurosurgery ,Signal Transduction ,Developmental Biology - Abstract
Astyanax mexicanus consists of two different populations: a sighted surface-dwelling form (surface fish) and a blind cave-dwelling form (cavefish). In the cavefish, embryonic expression of sonic hedgehog a (shha) in the prechordal plate is expanded towards the anterior midline, which has been shown to contribute to cavefish specific traits such as eye degeneration, enhanced feeding apparatus, and specialized brain anatomy. However, it is not clear how this expanded expression is achieved and which signaling pathways are involved.\ud \ud Nodal signaling has a crucial role for expression of shh and formation of the prechordal plate. In this study, we report increased expression of prechordal plate marker genes, nodal-related 2 (ndr2) and goosecoid (gsc) in cavefish embryos at the tailbud stage. To investigate whether Nodal signaling is responsible for the anterior expansion of the prechordal plate, we used an inhibitor of Nodal signaling and showed a decreased anterior expansion of the prechordal plate and increased pax6 expression in the anterior midline in treated cavefish embryos. Later in development, the lens and optic cup of treated embryos were significantly larger than untreated embryos. Conversely, increasing Nodal signaling in the surface fish embryo resulted in the expansion of anterior prechordal plate and reduction of pax6 expression in the anterior neural plate together with the formation of small lenses and optic cups later in development. These results confirmed that Nodal signaling has a crucial role for the anterior expansion of the prechordal plate and plays a significant role in cavefish eye development. We showed that the anterior expansion of the prechordal plate was not due to increased total cell number, suggesting the expansion is achieved by changes in cellular distribution in the prechordal plate. In addition, the distribution of presumptive prechordal plate cells in Spemann's organiser was also altered in the cavefish. These results suggested that changes in the cellular arrangement of Spemann's organiser in early gastrulae could have an essential role in the anterior expansion of the prechordal plate contributing to eye degeneration in the cavefish.
- Published
- 2018
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