Jing-Wen Lin - Academia.edu (original) (raw)

Papers by Jing-Wen Lin

International Journal of Science and Mathematics Education

Science Education Research and Practice in Asia, 2016

The purpose of this book chapter is to investigate the impacts of research articles on conceptual... more The purpose of this book chapter is to investigate the impacts of research articles on conceptual change field via the analysis of citations listed in a set of selected journal articles. According to our screening processes, we found 365 articles in the selected science education journals (Journal of Research in Science Teaching, Science Education, International Journal of Science Education, Research in Science Education, International Journal of Mathematics and Science Education) and 17,919 citations were included in the articles. Out of 365, there were 78 articles that had Asian scholars as either the first author or the corresponding persons. Among them, there were 3710 citations in these Asian studies. From the analyses, we found that Posner et al. (Sci Educ 66(2): 211–227, 1982) was the most cited article across the world, followed by Strike and Posner (Cognitive structure and conceptual change. Academic Press, New York, pp. 211–231, 1992) and Pintrich et al. (Rev Educ Res 63(2): 167–199, 1993). However, there were some differences of the orderings of the cited research articles in Asia except the first one, Posner et al. (Sci Educ 66(2): 211–227, 1982). In terms of the authors, we found Driver as the most influential researcher in the area of conceptual change compared to others across the world. This holds true in Asia as well. However, the orderings of the cited authors were quite different between global and regional aspects. These findings might show specific preferences or impacts of research directions globally and locally. Detailed analyses and implications will be discussed.

Nature Astronomy, 2018

Should science be taught differently? By emphasizing the process, not factual knowledge, students... more Should science be taught differently? By emphasizing the process, not factual knowledge, students will learn how to approach and solve problems and see science as relevant to their careers outside of research.

Chemistry Education and Sustainability in the Global Age, 2012

The aim of this study is to describe a two-tier diagnostic instrument to investigate the types, d... more The aim of this study is to describe a two-tier diagnostic instrument to investigate the types, developmental trends, and sources of Taiwanese high school students’ alternative conceptions of chemical equilibrium and acids/bases. The development of the two-tier diagnostic instrument was guided by Treagust’s framework. Seven common sets of two-tier diagnostic items were designed to compare 6,989 junior and 2,934 senior high school students’ performance. There were six representative alternative conceptions identified. The results showed that, except for the concept of “phase transition between ice and water in an adiabatic condition,” senior high school students had better understanding than junior high students. In addition, high school students were more familiar with science concepts with proper nouns and more conscious of some macro phenomena. Nevertheless, both senior and junior high school students lacked understanding of the mechanism involved in chemical equilibrium and acids/bases ionization. Therefore, the correctness of these items was lower than others. With regard to the sources of these alternative conceptions, the results indicated the main difficulty was the transformation of macro, micro, and symbolic levels. Various alternative conceptions developed. The implications and further suggestions for curriculum designers, teachers, and researchers are discussed.

Journal of Research in Science Teaching, 2005

Abstract: For the past two decades, a growing amount of research has shown that the use of analog... more Abstract: For the past two decades, a growing amount of research has shown that the use of analogies in science teaching and learning promotes meaningful understanding of complex scientific concepts (Gentner, 1983; Glynn, 1989; Harrison & Treagust, 1993; Wong, 1993). ...

Scientific Data, 2021

Hematopoietic stem cells (HSCs) lie at the top of the differentiation hierarchy. Although HSC and... more Hematopoietic stem cells (HSCs) lie at the top of the differentiation hierarchy. Although HSC and their immediate downstream, multipotent progenitors (MPP) have full multilineage differentiation capacity, only long-term (LT-) HSC has the capacity of long-term self-renewal. The heterogeneity within the HSC population is gradually acknowledged with the development of single-cell RNA sequencing and lineage tracing technologies. Transcriptional and post-transcriptional regulations play important roles in controlling the differentiation and self-renewal capacity within HSC population. Here we report a dataset comprising short- and long-read RNA sequencing for mouse long- and short-term HSC and MPP at bulk and single-cell levels. We demonstrate that integrating short- and long-read sequencing can facilitate the identification and quantification of known and unannotated isoforms. Thus, this dataset provides a groundwork for comprehensive and comparative studies on transcriptional diversity...

Signal Transduction and Targeted Therapy, 2021

Pregnant women are generally more susceptible to viral infection. Although the impact of SARS-CoV... more Pregnant women are generally more susceptible to viral infection. Although the impact of SARS-CoV-2 in pregnancy remains to be determined, evidence indicates that the risk factors for severe COVID-19 are similar in pregnancy to the general population. Here we systemically analyzed the clinical characteristics of pregnant and non-pregnant female COVID-19 patients who were hospitalized during the same period and found that pregnant patients developed marked lymphopenia and higher inflammation evident by higher C-reactive protein and IL-6. To elucidate the pathways that might contribute to immunopathology or protective immunity against COVID-19 during pregnancy, we applied single-cell mRNA sequencing to profile peripheral blood mononuclear cells from four pregnant and six non-pregnant female patients after recovery along with four pregnant and three non-pregnant healthy donors. We found normal clonal expansion of T cells in the pregnant patients, heightened activation and chemotaxis in...

Scientific Data, 2020

Malaria is a devastating infectious disease and the immune response is complex and dynamic during... more Malaria is a devastating infectious disease and the immune response is complex and dynamic during a course of a malarial infection. Rodent malaria models allow detailed time-series studies of the host response in multiple organs. Here, we describe two comprehensive datasets containing host transcriptomic data from both the blood and spleen throughout an acute blood stage infection of virulent or avirulent Plasmodium chabaudi infection in C57BL/6 mice. The mRNA expression profiles were generated using Illumina BeadChip microarray. These datasets provide a groundwork for comprehensive and comparative studies on host gene expression in early, acute and recovering phases of a blood stage infection in both the blood and spleen, to explore the interaction between the two, and importantly to investigate whether these responses differ in virulent and avirulent infections.

Nucleic Acids Research, 2020

Alternative splicing is widespread throughout eukaryotic genomes and greatly increases transcript... more Alternative splicing is widespread throughout eukaryotic genomes and greatly increases transcriptomic diversity. Many alternative isoforms have functional roles in developmental processes and are precisely temporally regulated. To facilitate the study of alternative splicing in a developmental context, we created MeDAS, a Metazoan Developmental Alternative Splicing database. MeDAS is an added-value resource that re-analyses publicly archived RNA-seq libraries to provide quantitative data on alternative splicing events as they vary across the time course of development. It has broad temporal and taxonomic scope and is intended to assist the user in identifying trends in alternative splicing throughout development. To create MeDAS, we re-analysed a curated set of 2232 Illumina polyA+ RNA-seq libraries that chart detailed time courses of embryonic and post-natal development across 18 species with a taxonomic range spanning the major metazoan lineages from Caenorhabditis elegans to huma...

Scientific Reports, 2019

Although the spleen is broadly accepted as the major lymphoid organ involved in generating immune... more Although the spleen is broadly accepted as the major lymphoid organ involved in generating immune responses to the erythrocytic stages of the malaria parasite, Plasmodium, human splenic tissue is not readily available in most cases. As a result, most studies of malaria in humans rely on peripheral blood to assess cellular immune responses to malaria. The suitability of peripheral blood as a proxy for splenic immune responses is however unknown. Here, we have simultaneously analysed the transcriptomes of whole blood and spleen over 12 days of erythrocytic stage Plasmodium chabaudi infection in C57BL/6 mice. Using both unsupervised and directed approaches, we compared gene expression between blood and spleen over the course of infection. Taking advantage of publicly available datasets, we used machine learning approaches to infer cell proportions and cell-specific gene expression signatures from our whole tissue transcriptome data. Our findings demonstrate that spleen and blood are qu...

BMC Medicine, 2019

Background: There are over 200 million reported cases of malaria each year, and most children liv... more Background: There are over 200 million reported cases of malaria each year, and most children living in endemic areas will experience multiple episodes of clinical disease before puberty. We set out to understand how frequent clinical malaria, which elicits a strong inflammatory response, affects the immune system and whether these modifications are observable in the absence of detectable parasitaemia. Methods: We used a multi-dimensional approach comprising whole blood transcriptomic, cellular and plasma cytokine analyses on a cohort of children living with endemic malaria, but uninfected at sampling, who had been under active surveillance for malaria for 8 years. Children were categorised into two groups depending on the cumulative number of episodes experienced: high (≥ 8) or low (< 5). Results: We observe that multiple episodes of malaria are associated with modification of the immune system. Children who had experienced a large number of episodes demonstrated upregulation of interferon-inducible genes, a clear increase in circulating levels of the immunoregulatory cytokine IL-10 and enhanced activation of neutrophils, B cells and CD8 + T cells. Conclusion: Transcriptomic analysis together with cytokine and immune cell profiling of peripheral blood can robustly detect immune differences between children with different numbers of prior malaria episodes. Multiple episodes of malaria are associated with modification of the immune system in children. Such immune modifications may have implications for the initiation of subsequent immune responses and the induction of vaccine-mediated protection.

BMC Research Notes, 2018

Objectives: Plasmodium berghei ANKA infection in mice is a model for human cerebral malaria, the ... more Objectives: Plasmodium berghei ANKA infection in mice is a model for human cerebral malaria, the most severe complication of Plasmodium falciparum infection. Responses of brain microglia have been little investigated, and may contribute to the pathogenesis of cerebral malaria. We showed previously that microglia are activated in P. berghei infections, and that Type 1-Interferon signaling is important for activation. This dataset compares transcriptomic profiles of brain microglia of infected mice in the presence and absence of Type 1 interferon signaling, with the aim of identifying genes in microglia in this pathway during experimental cerebral malaria. Data description: We documented global gene expression from microglial RNA from uninfected and P bergheiinfected wild-type C57BL/6 and IFNA Receptor Knockout mice using Illumina Beadarrays. Principal component analysis showed 4 groups of samples corresponding to naïve wild-type, naïve IFNA Receptor knockout , infected wild-type, and IFNA Receptor knockout mice. Differentially-expressed genes of microglia from the two groups of infected mice are documented. Gene set enrichment analysis showing the top 500 genes assigned to Reactome pathways from infected IFNA Receptor knockout versus naïve, and infected WT versus naïve has been generated. These data will be useful for those interested in microglia cells, and in experimental cerebral malaria.

Wellcome Open Research, 2018

Background: Malaria parasite species differ greatly in the harm they do to humans. While P. falci... more Background: Malaria parasite species differ greatly in the harm they do to humans. While P. falciparum kills hundreds of thousands per year, P. vivax kills much less often and P. malariae is relatively benign. Strains of the rodent malaria parasite Plasmodium chabaudi show phenotypic variation in virulence during infections of laboratory mice. This make it an excellent species to study genes which may be responsible for this trait. By understanding the mechanisms which underlie differences in virulence we can learn how parasites adapt to their hosts and how we might prevent disease. Methods: Here we present a complete reference genome sequence for a more virulent P. chabaudi strain, PcCB, and perform a detailed comparison with the genome of the less virulent PcAS strain. Results: We found the greatest variation in the subtelomeric regions, in particular amongst the sequences of the pir gene family, which has been associated with virulence and establishment of chronic infection. Howe...

Molecular and biochemical parasitology, Jan 24, 2018

The transmission-blocking vaccine candidate Pfs48/45 from the human malaria parasite Plasmodium f... more The transmission-blocking vaccine candidate Pfs48/45 from the human malaria parasite Plasmodium falciparum is known to be difficult to express in heterologous systems, either as full-length protein or as correctly folded protein fragments that retain conformational epitopes. In this study we express full-length Pfs48/45 in the rodent parasite P. berghei. Pfs48/45 is expressed as a transgene under control of the strong P. berghei schizont-specific msp1 gene promoter (Pfs48/45@PbMSP1). Pfs48/45@PbMSP1 schizont-infected red blood cells produced full-length Pfs48/45 and the structural integrity of Pfs48/45 was confirmed using a panel of conformation-specific monoclonal antibodies that bind to different Pfs48/45 epitopes. Sera from mice immunized with transgenic Pfs48/45@PbMSP1 schizonts showed strong transmission-reducing activity in mosquitoes infected with P. falciparum using standard membrane feeding. These results demonstrate that transgenic rodent malaria parasites expressing human...

Malaria Journal, 2017

Background: Parasite cytoadherence within the microvasculature of tissues and organs of infected ... more Background: Parasite cytoadherence within the microvasculature of tissues and organs of infected individuals is implicated in the pathogenesis of several malaria syndromes. Multiple host receptors may mediate sequestration. The identity of the host receptor(s), or the parasite ligand(s) responsible for sequestration of Plasmodium species other than Plasmodium falciparum is largely unknown. The rodent malaria parasites may be useful to model interactions of parasite species, which lack the var genes with their respective hosts, as other multigene families are shared between the species. The role of the endothelial receptors ICAM-1 and CD36 in cytoadherence and in the development of pathology was investigated in a Plasmodium chabaudi infection in C57BL/6 mice lacking these receptors. The schizont membrane-associated cytoadherence (SMAC) protein of Plasmodium berghei has been shown to exhibit reduced CD36-associated cytoadherence in P. berghei ANKA-infected mice. Methods: Parasite tissue sequestration and the development of acute stage pathology in P. chabaudi infections of mice lacking CD36 or ICAM-1, their respective wild type controls, and in infections with mutant P. chabaudi parasites lacking the smac gene were compared. Peripheral blood parasitaemia, red blood cell numbers and weight change were monitored throughout the courses of infection. Imaging of bioluminescent parasites in isolated tissues (spleen, lungs, liver, kidney and gut) was used to measure tissue parasite load. Results: This study shows that neither the lack of CD36 nor the deletion of the smac gene from P. chabaudi significantly impacted on acute-stage pathology or parasite sequestration. By contrast, in the absence of ICAM-1, infected animals experience less anaemia and weight loss, reduced parasite accumulation in both spleen and liver and higher peripheral blood parasitaemia during acute stage malaria. The reduction in parasite tissue sequestration in infections of ICAM-1 null mice is maintained after mosquito transmission. Conclusions: These results indicate that ICAM-1-mediated cytoadherence is important in the P. chabaudi model of malaria and suggest that for rodent malarias, as for P. falciparum, there may be multiple host and parasite molecules involved in sequestration.

PLOS Pathogens, 2017

Proteases have been implicated in a variety of developmental processes during the malaria parasit... more Proteases have been implicated in a variety of developmental processes during the malaria parasite lifecycle. In particular, invasion and egress of the parasite from the infected hepatocyte and erythrocyte, critically depend on protease activity. Although falcipain-1 was the first cysteine protease to be characterized in P. falciparum, its role in the lifecycle of the parasite has been the subject of some controversy. While an inhibitor of falcipain-1 blocked erythrocyte invasion by merozoites, two independent studies showed that falcipain-1 disruption did not affect growth of blood stage parasites. To shed light on the role of this protease over the entire Plasmodium lifecycle, we disrupted berghepain-1, its ortholog in the rodent parasite P. berghei. We found that this mutant parasite displays a pronounced delay in blood stage infection after inoculation of sporozoites. Experiments designed to pinpoint the defect of berghepain-1 knockout parasites found that it was not due to alterations in gliding motility, hepatocyte invasion or liver stage development and that injection of berghepain-1 knockout merosomes replicated the phenotype of delayed blood stage growth after sporozoite inoculation. We identified an additional role for berghepain-1 in preparing blood stage merozoites

PLOS Pathogens, 2017

Proteases have been implicated in a variety of developmental processes during the malaria parasit... more Proteases have been implicated in a variety of developmental processes during the malaria parasite lifecycle. In particular, invasion and egress of the parasite from the infected hepatocyte and erythrocyte, critically depend on protease activity. Although falcipain-1 was the first cysteine protease to be characterized in P. falciparum, its role in the lifecycle of the parasite has been the subject of some controversy. While an inhibitor of falcipain-1 blocked erythrocyte invasion by merozoites, two independent studies showed that falcipain-1 disruption did not affect growth of blood stage parasites. To shed light on the role of this protease over the entire Plasmodium lifecycle, we disrupted berghepain-1, its ortholog in the rodent parasite P. berghei. We found that this mutant parasite displays a pronounced delay in blood stage infection after inoculation of sporozoites. Experiments designed to pinpoint the defect of berghepain-1 knockout parasites found that it was not due to alterations in gliding motility, hepatocyte invasion or liver stage development and that injection of berghepain-1 knockout merosomes replicated the phenotype of delayed blood stage growth after sporozoite inoculation. We identified an additional role for berghepain-1 in preparing blood stage merozoites

Scientific reports, Jan 3, 2017

The influence of parasite genetic factors on immune responses and development of severe pathology... more The influence of parasite genetic factors on immune responses and development of severe pathology of malaria is largely unknown. In this study, we performed genome-wide transcriptomic profiling of mouse whole blood during blood-stage infections of two strains of the rodent malaria parasite Plasmodium chabaudi that differ in virulence. We identified several transcriptomic signatures associated with the virulent infection, including signatures for platelet aggregation, stronger and prolonged anemia and lung inflammation. The first two signatures were detected prior to pathology. The anemia signature indicated deregulation of host erythropoiesis, and the lung inflammation signature was linked to increased neutrophil infiltration, more cell death and greater parasite sequestration in the lungs. This comparative whole-blood transcriptomics profiling of virulent and avirulent malaria shows the validity of this approach to inform severity of the infection and provide insight into pathogeni...

Methods in Molecular Biology, 2015

We describe methods for the rapid generation of transgenic rodent Plasmodium berghei (Pb) parasit... more We describe methods for the rapid generation of transgenic rodent Plasmodium berghei (Pb) parasites that express human malaria parasite (HMP) proteins, using the recently developed GIMO-based transfection methodology. Three different genetic modifi cations are described resulting in three types of transgenic parasites. (1) Additional Gene (AG) mutants. In these mutants the HMP gene is introduced as an "additional gene" into a silent/neutral locus of the Pb genome under the control of either a constitutive or stage-specifi c Pb promoter. This method uses the GIMO-transfection protocol and AG mutants are generated by replacing the positive-negative selection marker (SM) h dhfr:: y fcu cassette in a neutral locus of a standard GIMO mother line with the HMP gene expression cassette, resulting in SM free transgenic parasites. (2) Double-step Replacement (DsR) mutants. In these mutants the coding sequence (CDS) of the Pb gene is replaced with the CDS of the HMP ortholog in a two-step GIMO-transfection procedure. This process involves fi rst the replacement of the Pb CDS with the h dhfr:: y fcu SM, followed by insertion of the HMP ortholog at the same locus thereby replacing h dhfr:: y fcu with the HMP CDS. These steps use the GIMO-transfection protocol, which exploits both positive selection for Pb orthologous gene-deletion and negative selection for HMP gene-insertion, resulting in SM free transgenic parasites. (3) Double-step Insertion (DsI) mutants. When a Pb gene is essential for blood stage development the DsR strategy is not possible. In these mutants the HMP expression cassette is fi rst introduced into the neutral locus in a standard GIMO mother line as described for AG mutants but under the control elements of the Pb orthologous gene; subsequently, the Pb ortholog CDS is targeted for deletion through replacement of the Pb CDS with the h dhfr:: y fcu SM, resulting in transgenic parasites with a new GIMO locus permissive for additional gene-insertion modifi cations. The different types of transgenic parasites can be exploited to examine interactions of drugs/inhibitors or immune factors with HMP molecules in vivo. Mice either immunized with HMP-vaccines or treated with specifi c drugs can be infected/challenged with these transgenic mutants to evaluate drug or vaccine effi cacy in vivo.

International Journal of Science and Mathematics Education

Science Education Research and Practice in Asia, 2016

The purpose of this book chapter is to investigate the impacts of research articles on conceptual... more The purpose of this book chapter is to investigate the impacts of research articles on conceptual change field via the analysis of citations listed in a set of selected journal articles. According to our screening processes, we found 365 articles in the selected science education journals (Journal of Research in Science Teaching, Science Education, International Journal of Science Education, Research in Science Education, International Journal of Mathematics and Science Education) and 17,919 citations were included in the articles. Out of 365, there were 78 articles that had Asian scholars as either the first author or the corresponding persons. Among them, there were 3710 citations in these Asian studies. From the analyses, we found that Posner et al. (Sci Educ 66(2): 211–227, 1982) was the most cited article across the world, followed by Strike and Posner (Cognitive structure and conceptual change. Academic Press, New York, pp. 211–231, 1992) and Pintrich et al. (Rev Educ Res 63(2): 167–199, 1993). However, there were some differences of the orderings of the cited research articles in Asia except the first one, Posner et al. (Sci Educ 66(2): 211–227, 1982). In terms of the authors, we found Driver as the most influential researcher in the area of conceptual change compared to others across the world. This holds true in Asia as well. However, the orderings of the cited authors were quite different between global and regional aspects. These findings might show specific preferences or impacts of research directions globally and locally. Detailed analyses and implications will be discussed.

Nature Astronomy, 2018

Should science be taught differently? By emphasizing the process, not factual knowledge, students... more Should science be taught differently? By emphasizing the process, not factual knowledge, students will learn how to approach and solve problems and see science as relevant to their careers outside of research.

Chemistry Education and Sustainability in the Global Age, 2012

The aim of this study is to describe a two-tier diagnostic instrument to investigate the types, d... more The aim of this study is to describe a two-tier diagnostic instrument to investigate the types, developmental trends, and sources of Taiwanese high school students’ alternative conceptions of chemical equilibrium and acids/bases. The development of the two-tier diagnostic instrument was guided by Treagust’s framework. Seven common sets of two-tier diagnostic items were designed to compare 6,989 junior and 2,934 senior high school students’ performance. There were six representative alternative conceptions identified. The results showed that, except for the concept of “phase transition between ice and water in an adiabatic condition,” senior high school students had better understanding than junior high students. In addition, high school students were more familiar with science concepts with proper nouns and more conscious of some macro phenomena. Nevertheless, both senior and junior high school students lacked understanding of the mechanism involved in chemical equilibrium and acids/bases ionization. Therefore, the correctness of these items was lower than others. With regard to the sources of these alternative conceptions, the results indicated the main difficulty was the transformation of macro, micro, and symbolic levels. Various alternative conceptions developed. The implications and further suggestions for curriculum designers, teachers, and researchers are discussed.

Journal of Research in Science Teaching, 2005

Abstract: For the past two decades, a growing amount of research has shown that the use of analog... more Abstract: For the past two decades, a growing amount of research has shown that the use of analogies in science teaching and learning promotes meaningful understanding of complex scientific concepts (Gentner, 1983; Glynn, 1989; Harrison & Treagust, 1993; Wong, 1993). ...

Scientific Data, 2021

Hematopoietic stem cells (HSCs) lie at the top of the differentiation hierarchy. Although HSC and... more Hematopoietic stem cells (HSCs) lie at the top of the differentiation hierarchy. Although HSC and their immediate downstream, multipotent progenitors (MPP) have full multilineage differentiation capacity, only long-term (LT-) HSC has the capacity of long-term self-renewal. The heterogeneity within the HSC population is gradually acknowledged with the development of single-cell RNA sequencing and lineage tracing technologies. Transcriptional and post-transcriptional regulations play important roles in controlling the differentiation and self-renewal capacity within HSC population. Here we report a dataset comprising short- and long-read RNA sequencing for mouse long- and short-term HSC and MPP at bulk and single-cell levels. We demonstrate that integrating short- and long-read sequencing can facilitate the identification and quantification of known and unannotated isoforms. Thus, this dataset provides a groundwork for comprehensive and comparative studies on transcriptional diversity...

Signal Transduction and Targeted Therapy, 2021

Pregnant women are generally more susceptible to viral infection. Although the impact of SARS-CoV... more Pregnant women are generally more susceptible to viral infection. Although the impact of SARS-CoV-2 in pregnancy remains to be determined, evidence indicates that the risk factors for severe COVID-19 are similar in pregnancy to the general population. Here we systemically analyzed the clinical characteristics of pregnant and non-pregnant female COVID-19 patients who were hospitalized during the same period and found that pregnant patients developed marked lymphopenia and higher inflammation evident by higher C-reactive protein and IL-6. To elucidate the pathways that might contribute to immunopathology or protective immunity against COVID-19 during pregnancy, we applied single-cell mRNA sequencing to profile peripheral blood mononuclear cells from four pregnant and six non-pregnant female patients after recovery along with four pregnant and three non-pregnant healthy donors. We found normal clonal expansion of T cells in the pregnant patients, heightened activation and chemotaxis in...

Scientific Data, 2020

Malaria is a devastating infectious disease and the immune response is complex and dynamic during... more Malaria is a devastating infectious disease and the immune response is complex and dynamic during a course of a malarial infection. Rodent malaria models allow detailed time-series studies of the host response in multiple organs. Here, we describe two comprehensive datasets containing host transcriptomic data from both the blood and spleen throughout an acute blood stage infection of virulent or avirulent Plasmodium chabaudi infection in C57BL/6 mice. The mRNA expression profiles were generated using Illumina BeadChip microarray. These datasets provide a groundwork for comprehensive and comparative studies on host gene expression in early, acute and recovering phases of a blood stage infection in both the blood and spleen, to explore the interaction between the two, and importantly to investigate whether these responses differ in virulent and avirulent infections.

Nucleic Acids Research, 2020

Alternative splicing is widespread throughout eukaryotic genomes and greatly increases transcript... more Alternative splicing is widespread throughout eukaryotic genomes and greatly increases transcriptomic diversity. Many alternative isoforms have functional roles in developmental processes and are precisely temporally regulated. To facilitate the study of alternative splicing in a developmental context, we created MeDAS, a Metazoan Developmental Alternative Splicing database. MeDAS is an added-value resource that re-analyses publicly archived RNA-seq libraries to provide quantitative data on alternative splicing events as they vary across the time course of development. It has broad temporal and taxonomic scope and is intended to assist the user in identifying trends in alternative splicing throughout development. To create MeDAS, we re-analysed a curated set of 2232 Illumina polyA+ RNA-seq libraries that chart detailed time courses of embryonic and post-natal development across 18 species with a taxonomic range spanning the major metazoan lineages from Caenorhabditis elegans to huma...

Scientific Reports, 2019

Although the spleen is broadly accepted as the major lymphoid organ involved in generating immune... more Although the spleen is broadly accepted as the major lymphoid organ involved in generating immune responses to the erythrocytic stages of the malaria parasite, Plasmodium, human splenic tissue is not readily available in most cases. As a result, most studies of malaria in humans rely on peripheral blood to assess cellular immune responses to malaria. The suitability of peripheral blood as a proxy for splenic immune responses is however unknown. Here, we have simultaneously analysed the transcriptomes of whole blood and spleen over 12 days of erythrocytic stage Plasmodium chabaudi infection in C57BL/6 mice. Using both unsupervised and directed approaches, we compared gene expression between blood and spleen over the course of infection. Taking advantage of publicly available datasets, we used machine learning approaches to infer cell proportions and cell-specific gene expression signatures from our whole tissue transcriptome data. Our findings demonstrate that spleen and blood are qu...

BMC Medicine, 2019

Background: There are over 200 million reported cases of malaria each year, and most children liv... more Background: There are over 200 million reported cases of malaria each year, and most children living in endemic areas will experience multiple episodes of clinical disease before puberty. We set out to understand how frequent clinical malaria, which elicits a strong inflammatory response, affects the immune system and whether these modifications are observable in the absence of detectable parasitaemia. Methods: We used a multi-dimensional approach comprising whole blood transcriptomic, cellular and plasma cytokine analyses on a cohort of children living with endemic malaria, but uninfected at sampling, who had been under active surveillance for malaria for 8 years. Children were categorised into two groups depending on the cumulative number of episodes experienced: high (≥ 8) or low (< 5). Results: We observe that multiple episodes of malaria are associated with modification of the immune system. Children who had experienced a large number of episodes demonstrated upregulation of interferon-inducible genes, a clear increase in circulating levels of the immunoregulatory cytokine IL-10 and enhanced activation of neutrophils, B cells and CD8 + T cells. Conclusion: Transcriptomic analysis together with cytokine and immune cell profiling of peripheral blood can robustly detect immune differences between children with different numbers of prior malaria episodes. Multiple episodes of malaria are associated with modification of the immune system in children. Such immune modifications may have implications for the initiation of subsequent immune responses and the induction of vaccine-mediated protection.

BMC Research Notes, 2018

Objectives: Plasmodium berghei ANKA infection in mice is a model for human cerebral malaria, the ... more Objectives: Plasmodium berghei ANKA infection in mice is a model for human cerebral malaria, the most severe complication of Plasmodium falciparum infection. Responses of brain microglia have been little investigated, and may contribute to the pathogenesis of cerebral malaria. We showed previously that microglia are activated in P. berghei infections, and that Type 1-Interferon signaling is important for activation. This dataset compares transcriptomic profiles of brain microglia of infected mice in the presence and absence of Type 1 interferon signaling, with the aim of identifying genes in microglia in this pathway during experimental cerebral malaria. Data description: We documented global gene expression from microglial RNA from uninfected and P bergheiinfected wild-type C57BL/6 and IFNA Receptor Knockout mice using Illumina Beadarrays. Principal component analysis showed 4 groups of samples corresponding to naïve wild-type, naïve IFNA Receptor knockout , infected wild-type, and IFNA Receptor knockout mice. Differentially-expressed genes of microglia from the two groups of infected mice are documented. Gene set enrichment analysis showing the top 500 genes assigned to Reactome pathways from infected IFNA Receptor knockout versus naïve, and infected WT versus naïve has been generated. These data will be useful for those interested in microglia cells, and in experimental cerebral malaria.

Wellcome Open Research, 2018

Background: Malaria parasite species differ greatly in the harm they do to humans. While P. falci... more Background: Malaria parasite species differ greatly in the harm they do to humans. While P. falciparum kills hundreds of thousands per year, P. vivax kills much less often and P. malariae is relatively benign. Strains of the rodent malaria parasite Plasmodium chabaudi show phenotypic variation in virulence during infections of laboratory mice. This make it an excellent species to study genes which may be responsible for this trait. By understanding the mechanisms which underlie differences in virulence we can learn how parasites adapt to their hosts and how we might prevent disease. Methods: Here we present a complete reference genome sequence for a more virulent P. chabaudi strain, PcCB, and perform a detailed comparison with the genome of the less virulent PcAS strain. Results: We found the greatest variation in the subtelomeric regions, in particular amongst the sequences of the pir gene family, which has been associated with virulence and establishment of chronic infection. Howe...

Molecular and biochemical parasitology, Jan 24, 2018

The transmission-blocking vaccine candidate Pfs48/45 from the human malaria parasite Plasmodium f... more The transmission-blocking vaccine candidate Pfs48/45 from the human malaria parasite Plasmodium falciparum is known to be difficult to express in heterologous systems, either as full-length protein or as correctly folded protein fragments that retain conformational epitopes. In this study we express full-length Pfs48/45 in the rodent parasite P. berghei. Pfs48/45 is expressed as a transgene under control of the strong P. berghei schizont-specific msp1 gene promoter (Pfs48/45@PbMSP1). Pfs48/45@PbMSP1 schizont-infected red blood cells produced full-length Pfs48/45 and the structural integrity of Pfs48/45 was confirmed using a panel of conformation-specific monoclonal antibodies that bind to different Pfs48/45 epitopes. Sera from mice immunized with transgenic Pfs48/45@PbMSP1 schizonts showed strong transmission-reducing activity in mosquitoes infected with P. falciparum using standard membrane feeding. These results demonstrate that transgenic rodent malaria parasites expressing human...

Malaria Journal, 2017

Background: Parasite cytoadherence within the microvasculature of tissues and organs of infected ... more Background: Parasite cytoadherence within the microvasculature of tissues and organs of infected individuals is implicated in the pathogenesis of several malaria syndromes. Multiple host receptors may mediate sequestration. The identity of the host receptor(s), or the parasite ligand(s) responsible for sequestration of Plasmodium species other than Plasmodium falciparum is largely unknown. The rodent malaria parasites may be useful to model interactions of parasite species, which lack the var genes with their respective hosts, as other multigene families are shared between the species. The role of the endothelial receptors ICAM-1 and CD36 in cytoadherence and in the development of pathology was investigated in a Plasmodium chabaudi infection in C57BL/6 mice lacking these receptors. The schizont membrane-associated cytoadherence (SMAC) protein of Plasmodium berghei has been shown to exhibit reduced CD36-associated cytoadherence in P. berghei ANKA-infected mice. Methods: Parasite tissue sequestration and the development of acute stage pathology in P. chabaudi infections of mice lacking CD36 or ICAM-1, their respective wild type controls, and in infections with mutant P. chabaudi parasites lacking the smac gene were compared. Peripheral blood parasitaemia, red blood cell numbers and weight change were monitored throughout the courses of infection. Imaging of bioluminescent parasites in isolated tissues (spleen, lungs, liver, kidney and gut) was used to measure tissue parasite load. Results: This study shows that neither the lack of CD36 nor the deletion of the smac gene from P. chabaudi significantly impacted on acute-stage pathology or parasite sequestration. By contrast, in the absence of ICAM-1, infected animals experience less anaemia and weight loss, reduced parasite accumulation in both spleen and liver and higher peripheral blood parasitaemia during acute stage malaria. The reduction in parasite tissue sequestration in infections of ICAM-1 null mice is maintained after mosquito transmission. Conclusions: These results indicate that ICAM-1-mediated cytoadherence is important in the P. chabaudi model of malaria and suggest that for rodent malarias, as for P. falciparum, there may be multiple host and parasite molecules involved in sequestration.

PLOS Pathogens, 2017

Proteases have been implicated in a variety of developmental processes during the malaria parasit... more Proteases have been implicated in a variety of developmental processes during the malaria parasite lifecycle. In particular, invasion and egress of the parasite from the infected hepatocyte and erythrocyte, critically depend on protease activity. Although falcipain-1 was the first cysteine protease to be characterized in P. falciparum, its role in the lifecycle of the parasite has been the subject of some controversy. While an inhibitor of falcipain-1 blocked erythrocyte invasion by merozoites, two independent studies showed that falcipain-1 disruption did not affect growth of blood stage parasites. To shed light on the role of this protease over the entire Plasmodium lifecycle, we disrupted berghepain-1, its ortholog in the rodent parasite P. berghei. We found that this mutant parasite displays a pronounced delay in blood stage infection after inoculation of sporozoites. Experiments designed to pinpoint the defect of berghepain-1 knockout parasites found that it was not due to alterations in gliding motility, hepatocyte invasion or liver stage development and that injection of berghepain-1 knockout merosomes replicated the phenotype of delayed blood stage growth after sporozoite inoculation. We identified an additional role for berghepain-1 in preparing blood stage merozoites

PLOS Pathogens, 2017

Proteases have been implicated in a variety of developmental processes during the malaria parasit... more Proteases have been implicated in a variety of developmental processes during the malaria parasite lifecycle. In particular, invasion and egress of the parasite from the infected hepatocyte and erythrocyte, critically depend on protease activity. Although falcipain-1 was the first cysteine protease to be characterized in P. falciparum, its role in the lifecycle of the parasite has been the subject of some controversy. While an inhibitor of falcipain-1 blocked erythrocyte invasion by merozoites, two independent studies showed that falcipain-1 disruption did not affect growth of blood stage parasites. To shed light on the role of this protease over the entire Plasmodium lifecycle, we disrupted berghepain-1, its ortholog in the rodent parasite P. berghei. We found that this mutant parasite displays a pronounced delay in blood stage infection after inoculation of sporozoites. Experiments designed to pinpoint the defect of berghepain-1 knockout parasites found that it was not due to alterations in gliding motility, hepatocyte invasion or liver stage development and that injection of berghepain-1 knockout merosomes replicated the phenotype of delayed blood stage growth after sporozoite inoculation. We identified an additional role for berghepain-1 in preparing blood stage merozoites

Scientific reports, Jan 3, 2017

The influence of parasite genetic factors on immune responses and development of severe pathology... more The influence of parasite genetic factors on immune responses and development of severe pathology of malaria is largely unknown. In this study, we performed genome-wide transcriptomic profiling of mouse whole blood during blood-stage infections of two strains of the rodent malaria parasite Plasmodium chabaudi that differ in virulence. We identified several transcriptomic signatures associated with the virulent infection, including signatures for platelet aggregation, stronger and prolonged anemia and lung inflammation. The first two signatures were detected prior to pathology. The anemia signature indicated deregulation of host erythropoiesis, and the lung inflammation signature was linked to increased neutrophil infiltration, more cell death and greater parasite sequestration in the lungs. This comparative whole-blood transcriptomics profiling of virulent and avirulent malaria shows the validity of this approach to inform severity of the infection and provide insight into pathogeni...

Methods in Molecular Biology, 2015

We describe methods for the rapid generation of transgenic rodent Plasmodium berghei (Pb) parasit... more We describe methods for the rapid generation of transgenic rodent Plasmodium berghei (Pb) parasites that express human malaria parasite (HMP) proteins, using the recently developed GIMO-based transfection methodology. Three different genetic modifi cations are described resulting in three types of transgenic parasites. (1) Additional Gene (AG) mutants. In these mutants the HMP gene is introduced as an "additional gene" into a silent/neutral locus of the Pb genome under the control of either a constitutive or stage-specifi c Pb promoter. This method uses the GIMO-transfection protocol and AG mutants are generated by replacing the positive-negative selection marker (SM) h dhfr:: y fcu cassette in a neutral locus of a standard GIMO mother line with the HMP gene expression cassette, resulting in SM free transgenic parasites. (2) Double-step Replacement (DsR) mutants. In these mutants the coding sequence (CDS) of the Pb gene is replaced with the CDS of the HMP ortholog in a two-step GIMO-transfection procedure. This process involves fi rst the replacement of the Pb CDS with the h dhfr:: y fcu SM, followed by insertion of the HMP ortholog at the same locus thereby replacing h dhfr:: y fcu with the HMP CDS. These steps use the GIMO-transfection protocol, which exploits both positive selection for Pb orthologous gene-deletion and negative selection for HMP gene-insertion, resulting in SM free transgenic parasites. (3) Double-step Insertion (DsI) mutants. When a Pb gene is essential for blood stage development the DsR strategy is not possible. In these mutants the HMP expression cassette is fi rst introduced into the neutral locus in a standard GIMO mother line as described for AG mutants but under the control elements of the Pb orthologous gene; subsequently, the Pb ortholog CDS is targeted for deletion through replacement of the Pb CDS with the h dhfr:: y fcu SM, resulting in transgenic parasites with a new GIMO locus permissive for additional gene-insertion modifi cations. The different types of transgenic parasites can be exploited to examine interactions of drugs/inhibitors or immune factors with HMP molecules in vivo. Mice either immunized with HMP-vaccines or treated with specifi c drugs can be infected/challenged with these transgenic mutants to evaluate drug or vaccine effi cacy in vivo.