Arabidopsis thaliana transcriptomes have been extensively studied and characterized under differe... more Arabidopsis thaliana transcriptomes have been extensively studied and characterized under different conditions. However, most of the current 'RNAsequencing' technologies produce a relatively short read length and demand a reverse-transcription step, preventing effective characterization of transcriptome complexity. Here, we performed Direct RNA Sequencing (DRS) using the latest Oxford Nanopore Technology (ONT) with exceptional read length. We demonstrate that the complexity of the A. thaliana transcriptomes has been substantially underestimated. The ONT direct RNA sequencing identified novel transcript isoforms at both the vegetative (14-day old seedlings, stage 1.04) and reproductive stages (stage 6.00-6.10) of development. Using in-house software called TrackCluster, we determined alternative transcription initiation (ATI), alternative polyadenylation (APA), alternative splicing (AS), and fusion transcripts. More than 38 500 novel transcript isoforms were identified, including six categories of fusion-transcripts that may result from differential RNA processing mechanisms. Aided by the Tombo algorithm, we found an enrichment of m5C modifications in the mobile mRNAs, consistent with a recent finding that m5C modification in mRNAs is crucial for their long-distance movement. In summary , ONT DRS offers an advantage in the identification and functional characterization of novel RNA isoforms and RNA base modifications, significantly improving annotation of the A. thaliana genome.
Relative of Early Flowing 6 (REF6) is a DNA-sequence-specific H3K27me3/2 demethylase that contain... more Relative of Early Flowing 6 (REF6) is a DNA-sequence-specific H3K27me3/2 demethylase that contains four zinc finger (ZnF) domains and targets several thousand genes in Arabidopsis thaliana. The ZnF domains are essential for binding target genes, but the structural basis remains unclear. Here, we determined crystal structures of the ZnF domains and REF6-DNA complex, revealing a unique REF6-family-specific half-cross-braced ZnF (RCZ) domain and two C2H2-type ZnFs. DNA-binding induces a profound conformational change in the hinge region of REF6. Each REF6 recognizes six bases and DNA methylation reduces the binding affinity. Both the acidic region and basic region are important for the self-association of REF6. The REF6 DNA-binding affinity is determined by the sequence-dependent conformations of DNA and also the cooperativity in different target motifs. The conformational plasticity enables REF6 to function as a global transcriptional regulator that directly binds to many diverse genes, revealing the structural basis for the epigenetic modification recognition.
A cDNA clone (OsRHC1) was obtained, which encodes a novel RING zinc finger protein sharing simila... more A cDNA clone (OsRHC1) was obtained, which encodes a novel RING zinc finger protein sharing similar structural features (multiple transmembrane domains at the N-half; a unique RING zinc finger consensus Cys-X 2-Cys-X 11-Cys-X-His-X 3-Cys-X 2-Cys-X 6-Cys-X 2-Cys at the C terminus) to a group of closely related annotated proteins from both monocots and dicots. OsRHC1 was found to be localized on plasma membrane of rice cells and induced by wounding in rice lines containing Xa loci. Ecotopic expression of the OsRHC1 cDNA from rice (a monocot) in transgenic Arabidopsis thaliana (a dicot) enhanced the defence response toward Pseudomonas syringae pv. tomato DC3000, suggesting that OsRHC1 may confer broadspectrum disease resistance. The protective effects were neutralized in the presence of MG132 or in an npr1-3 mutation background, indicating that the function of OsRHC1 is dependent on the ubiquitin-mediated protein degradation via the 26S proteasome and the presence of the key defence response regulator NPR1.
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
By using differential hybridization, Misrahi et al. isolated a rabbit cDNA clone that corresponds... more By using differential hybridization, Misrahi et al. isolated a rabbit cDNA clone that corresponds to a novel progesterone-induced mRNA in rabbit and human endometria (1). Unfortunately, sequence analysis of the cDNA clone failed to identify the protein encoded by the hormone-induced mRNA.
Proceedings of the National Academy of Sciences of the United States of America, Nov 10, 1998
PII is a protein allosteric effector in Escherichia coli and other bacteria that indirectly regul... more PII is a protein allosteric effector in Escherichia coli and other bacteria that indirectly regulates glutamine synthetase at the transcriptional and post-translational levels in response to nitrogen availability. Data supporting the notion that plants have a nitrogen regulatory system(s) includes previous studies showing that the levels of mRNA for plant nitrogen assimilatory genes such as glutamine synthetase (GLN) and asparagine synthetase (ASN) are modulated by carbon and organic nitrogen metabolites. Here, we have characterized a PII homolog (GLB1) in two higher plants, Arabidopsis thaliana and Ricinus communis (Castor bean). Each plant PII-like protein has high overall identity to E. coli PII (50%). Western blot analyses reveal that the plant PII-like protein is a nuclear-encoded chloroplast protein. The PII-like protein of plants appears to be regulated at the transcriptional level in that levels of GLB1 mRNA are affected by light and metabolites. To initiate studies of the in vivo function of the Arabidopsis PII-like protein, we have constructed transgenic lines in which PII expression is uncoupled from its native regulation. Analyses of these transgenic plants support the notion that the plant PII-like protein may serve as part of a complex signal transduction network involved in perceiving the status of carbon and organic nitrogen. Thus, the PII protein found in archaea, bacteria, and now in higher eukaryotes (plants) is one of the most widespread regulatory proteins known, providing evidence for an ancestral metabolic regulatory mechanism that may have existed before the divergence of these three domains of life. The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked ''advertisement'' in accordance with 18 U.S.C. §1734 solely to indicate this fact.
In wild-type Arabidopsis, levels of ASN1 mRNA and asparagine (Asn) are tightly regulated by envir... more In wild-type Arabidopsis, levels of ASN1 mRNA and asparagine (Asn) are tightly regulated by environmental factors and metabolites. Because Asn serves as an important nitrogen storage and transport compound used to allocate nitrogen resources between source and sink organs, we tested whether overexpression of the major expressed gene for Asn synthetase, ASN1, would lead to changes in nitrogen status in the ultimate storage organ for metabolites-seeds. Transgenic Arabidopsis constitutively overexpressing ASN1 under the cauliflower mosaic virus 35S promoter were constructed (35S-ASN1). In seeds of the 35S-ASN1 lines, three observations support the notion that the nitrogen status was enhanced: (a) elevations of soluble seed protein contents, (b) elevations of total protein contents from acid-hydrolyzed seeds, and (c) higher tolerance of young seedlings when grown on nitrogen-limiting media. Besides quantitative differences, changes in the relative composition of the seed amino acid were also observed. The change in seed nitrogen status was accompanied by an increase of total free amino acids (mainly Asn) allocated to flowers and developing siliques. In 35S-ASN1 lines, sink tissues such as flowers and developing siliques exhibit a higher level of free Asn than source tissues such as leaves and stems, despite significantly higher levels of ASN1 mRNA observed in the source tissues. This was at least partially due to an enhanced transport of Asn from source to sink via the phloem, as demonstrated by the increased levels of Asn in phloem exudates of the 35S-ASN1 plants.
Abiotic stresses, such as drought, salinity, heat, cold, and heavy metals, are associated with gl... more Abiotic stresses, such as drought, salinity, heat, cold, and heavy metals, are associated with global climate change and hamper plant growth and development, affecting crop yields and quality. However, the negative effects of abiotic stresses can be mitigated through exogenous treatments using small biomolecules. For example, the foliar application of melatonin provides the following: it protects the photosynthetic apparatus; it increases the antioxidant defenses, osmoprotectant, and soluble sugar levels; it prevents tissue damage and reduces electrolyte leakage; it improves reactive oxygen species (ROS) scavenging; and it increases biomass, maintains the redox and ion homeostasis, and improves gaseous exchange. Glutathione spray upregulates the glyoxalase system, reduces methylglyoxal (MG) toxicity and oxidative stress, decreases hydrogen peroxide and malondialdehyde accumulation, improves the defense mechanisms, tissue repairs, and nitrogen fixation, and upregulates the phytochela...
MotivationSynteny analysis is a widely used framework in comparative genomics studies, which prov... more MotivationSynteny analysis is a widely used framework in comparative genomics studies, which provides valuable information to reveal chromosome collinearity in both intra-species and inter-species. Most analysis pipelines, however, are command line-based, making it challenging for biologists to run the algorithms and visualize the results. Existing visualization tools either provide static plots or can only be run on web-based servers and lack efficient visualization methods for associating macro-synteny blocks with individual gene pairs in a micro-synteny region.ResultsWe developed ShinySyn, a Shiny/R application built on the MCscan framework that provides an easy-to-use graphic interface for synteny analyses without requiring any programming skills, to reduce technical barriers. ShinySyn not only provides interactive visualization for macro-synteny, micro-synteny and genome-level dot views, but it also creates an intuitive representation with a dynamic zooming feature from macro-s...
Food production is one of the main contributors to greenhouse gas emissions and climate change. C... more Food production is one of the main contributors to greenhouse gas emissions and climate change. China, as a rapidly developing economy, contributes to an unsustainable food system as its consumption of animal products and meat has continued to grow in recent decades. Using the extended theory of planned behavior as the conceptual framework, this paper examines factors influencing consumers' intention to purchase sustainable food in China. To this end, a population‐based face‐to‐face survey was conducted with 2422 respondents in five provinces spanning the north and south of China. The results showed that the traditional constructs of behavioral attitude, subjective norms, perceived behavioral control, and the additional construct of perceived quality are significant in inducing such intentions. This paper suggests that to enhance consumers' willingness to shift to sustainable food consumption, appropriate regulation and monitoring framework is needed to increase consumers...
The number of annotated and newly predicted R-genes in each legume species. Annotated: the R-gene... more The number of annotated and newly predicted R-genes in each legume species. Annotated: the R-genes annotated from original gene models; Predicted: the R-genes predicted based on the R proteins from our self-curated database. (PDF 249 kb)
Chromosomal distributions of R-genes in the legume family. The different colors represent differe... more Chromosomal distributions of R-genes in the legume family. The different colors represent different species, and the Y-axis denotes the number of R-genes on each chromosome. Note that the legumes have different chromosomes and some genome assembly was not anchored to chromosomes. (PDF 591 kb)
Arbuscular mycorrhiza (AM) is a widespread symbiosis between roots of the majority of land plants... more Arbuscular mycorrhiza (AM) is a widespread symbiosis between roots of the majority of land plants and Glomeromycotina fungi. AM is important for ecosystem health and functioning as the fungi critically support plant performance by providing essential mineral nutrients, particularly the poorly accessible phosphate, in exchange for organic carbon. AM fungi colonize the inside of roots and this is promoted at low but inhibited at high plant phosphate status, while the mechanistic basis for this phosphate-dependence remained obscure. Here we demonstrate that a major transcriptional regulator of phosphate starvation responses in rice PHOSPHATE STARVATION RESPONSE 2 (PHR2) regulates AM. Root colonization of phr2 mutants is drastically reduced, and PHR2 is required for root colonization, mycorrhizal phosphate uptake, and yield increase in field soil. PHR2 promotes AM by targeting genes required for pre-contact signaling, root colonization, and AM function. Thus, this important symbiosis is...
Soybean is an important crop as both human food and animal feed. However, the yield of soybean is... more Soybean is an important crop as both human food and animal feed. However, the yield of soybean is heavily impacted by biotic stresses including insect attack and pathogen infection. Insect bites usually make the plants vulnerable to pathogen infection, which causes diseases. Fungi, oomycetes, bacteria, viruses, and nematodes are major soybean pathogens. The infection by pathogens and the defenses mounted by soybean are an interactive and dynamic process. Using fungi, oomycetes, and bacteria as examples, we will discuss the recognition of pathogens by soybean at the molecular level. In this review, we will discuss both the secretory peptides for soybean plant infection and those for pathogen inhibition. Pathogenic secretory peptides and peptides secreted by soybean and its associated microbes will be included. We will also explore the possible use of externally applied antimicrobial peptides identical to those secreted by soybean and its associated microbes as biopesticides.
Bedbugs (Cimex spp.) are a nuisance public-health pest that is on the rise globally, particularly... more Bedbugs (Cimex spp.) are a nuisance public-health pest that is on the rise globally, particularly in crowded cities such as Hong Kong. To investigate the health impacts of bedbug infestations among bedbug victims, online surveys were distributed in Hong Kong between June 2019 to July 2020. Data on sociodemographics, self-rated health, average hours of sleep per day, and details of bedbug infestation were collected. Bivariate and multivariable analysis were performed using logistic regression. The survey identified 422 bedbug victims; among them, 223 (52.9%) experienced ≥five bites in the past month; most bites occurred on the arms (n = 202, 47.8%) and legs (n = 215, 51%), and the most common reaction to bites were itchiness (n = 322, 76.3%), redness, and swelling of the skin (n = 246, 58.1%), and difficulties sleeping or restlessness (n = 125, 29.6%). Bites usually occurred during sleep (n = 230, 54.5%). For impact on daily life in the past month, most bedbug victims reported modera...
Arbuscular mycorrhiza (AM) is a widespread symbiosis between roots of the majority of land plants... more Arbuscular mycorrhiza (AM) is a widespread symbiosis between roots of the majority of land plants and Glomeromycotina fungi. AM is important for ecosystem health and functioning as the fungi critically support plant performance by providing essential mineral nutrients, particularly the poorly accessible phosphate, in exchange for organic carbon. AM fungi colonize the inside of roots and this is promoted at low but inhibited at high plant phosphate status, while the mechanistic basis for this phosphate-dependence remained obscure. Here we demonstrate that a major transcriptional regulator of phosphate starvation responses in rice PHOSPHATE STARVATION RESPONSE 2 (PHR2) regulates AM. Root colonization of phr2 mutants is drastically reduced, and PHR2 is required for root colonization, mycorrhizal phosphate uptake, and yield increase in field soil. PHR2 promotes AM by targeting genes required for pre-contact signaling, root colonization, and AM function. Thus, this important symbiosis is...
Journal of Housing and the Built Environment, 2021
In the original publication, the figure-5 legends were incorrectly published. The correct Fig. 5 ... more In the original publication, the figure-5 legends were incorrectly published. The correct Fig. 5 is given below, And the appendix 1, 2 and 3 were incorrectly published in the article PDF, however, it should be treated as the Electronic Supplementary Materials. The original article has been corrected.
Arabidopsis thaliana transcriptomes have been extensively studied and characterized under differe... more Arabidopsis thaliana transcriptomes have been extensively studied and characterized under different conditions. However, most of the current ‘RNA-sequencing’ technologies produce a relatively short read length and demand a reverse-transcription step, preventing effective characterization of transcriptome complexity. Here, we performed Direct RNA Sequencing (DRS) using the latest Oxford Nanopore Technology (ONT) with exceptional read length. We demonstrate that the complexity of the A. thaliana transcriptomes has been substantially under-estimated. The ONT direct RNA sequencing identified novel transcript isoforms at both the vegetative (14-day old seedlings, stage 1.04) and reproductive stages (stage 6.00–6.10) of development. Using in-house software called TrackCluster, we determined alternative transcription initiation (ATI), alternative polyadenylation (APA), alternative splicing (AS), and fusion transcripts. More than 38 500 novel transcript isoforms were identified, including s...
To investigate the risk factors associated with bedbug infestations among Hong Kong households, s... more To investigate the risk factors associated with bedbug infestations among Hong Kong households, self-reported questionnaires in Chinese were distributed online between June 2019 to July 2020. The questionnaire collected data on participants’ sociodemographics, history of bedbug infestation, and housing situation. Among the 663 participants who completed the questionnaire, 422 (63.7%) have experienced bedbug infestations in the past year, they were concentrated around the Kowloon region. Weighted bivariate and multivariate binary logistic regression were performed to identify the statistically significant (p-value <0.05) factors associated with bedbug infestations. Bivariate analysis shows a positive correlation between the number of reported dilapidated housing features and bedbug infestation. For multivariate analysis, those aged 45-64 (OR=2.53, 95% CI 1.30-4.91), have primary education or below (OR=9.43, 95% CI 3.12-28.44), and monthly household income ≤HKD30,000 (OR=1.69, 95% ...
Arabidopsis thaliana transcriptomes have been extensively studied and characterized under differe... more Arabidopsis thaliana transcriptomes have been extensively studied and characterized under different conditions. However, most of the current 'RNAsequencing' technologies produce a relatively short read length and demand a reverse-transcription step, preventing effective characterization of transcriptome complexity. Here, we performed Direct RNA Sequencing (DRS) using the latest Oxford Nanopore Technology (ONT) with exceptional read length. We demonstrate that the complexity of the A. thaliana transcriptomes has been substantially underestimated. The ONT direct RNA sequencing identified novel transcript isoforms at both the vegetative (14-day old seedlings, stage 1.04) and reproductive stages (stage 6.00-6.10) of development. Using in-house software called TrackCluster, we determined alternative transcription initiation (ATI), alternative polyadenylation (APA), alternative splicing (AS), and fusion transcripts. More than 38 500 novel transcript isoforms were identified, including six categories of fusion-transcripts that may result from differential RNA processing mechanisms. Aided by the Tombo algorithm, we found an enrichment of m5C modifications in the mobile mRNAs, consistent with a recent finding that m5C modification in mRNAs is crucial for their long-distance movement. In summary , ONT DRS offers an advantage in the identification and functional characterization of novel RNA isoforms and RNA base modifications, significantly improving annotation of the A. thaliana genome.
Relative of Early Flowing 6 (REF6) is a DNA-sequence-specific H3K27me3/2 demethylase that contain... more Relative of Early Flowing 6 (REF6) is a DNA-sequence-specific H3K27me3/2 demethylase that contains four zinc finger (ZnF) domains and targets several thousand genes in Arabidopsis thaliana. The ZnF domains are essential for binding target genes, but the structural basis remains unclear. Here, we determined crystal structures of the ZnF domains and REF6-DNA complex, revealing a unique REF6-family-specific half-cross-braced ZnF (RCZ) domain and two C2H2-type ZnFs. DNA-binding induces a profound conformational change in the hinge region of REF6. Each REF6 recognizes six bases and DNA methylation reduces the binding affinity. Both the acidic region and basic region are important for the self-association of REF6. The REF6 DNA-binding affinity is determined by the sequence-dependent conformations of DNA and also the cooperativity in different target motifs. The conformational plasticity enables REF6 to function as a global transcriptional regulator that directly binds to many diverse genes, revealing the structural basis for the epigenetic modification recognition.
A cDNA clone (OsRHC1) was obtained, which encodes a novel RING zinc finger protein sharing simila... more A cDNA clone (OsRHC1) was obtained, which encodes a novel RING zinc finger protein sharing similar structural features (multiple transmembrane domains at the N-half; a unique RING zinc finger consensus Cys-X 2-Cys-X 11-Cys-X-His-X 3-Cys-X 2-Cys-X 6-Cys-X 2-Cys at the C terminus) to a group of closely related annotated proteins from both monocots and dicots. OsRHC1 was found to be localized on plasma membrane of rice cells and induced by wounding in rice lines containing Xa loci. Ecotopic expression of the OsRHC1 cDNA from rice (a monocot) in transgenic Arabidopsis thaliana (a dicot) enhanced the defence response toward Pseudomonas syringae pv. tomato DC3000, suggesting that OsRHC1 may confer broadspectrum disease resistance. The protective effects were neutralized in the presence of MG132 or in an npr1-3 mutation background, indicating that the function of OsRHC1 is dependent on the ubiquitin-mediated protein degradation via the 26S proteasome and the presence of the key defence response regulator NPR1.
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
By using differential hybridization, Misrahi et al. isolated a rabbit cDNA clone that corresponds... more By using differential hybridization, Misrahi et al. isolated a rabbit cDNA clone that corresponds to a novel progesterone-induced mRNA in rabbit and human endometria (1). Unfortunately, sequence analysis of the cDNA clone failed to identify the protein encoded by the hormone-induced mRNA.
Proceedings of the National Academy of Sciences of the United States of America, Nov 10, 1998
PII is a protein allosteric effector in Escherichia coli and other bacteria that indirectly regul... more PII is a protein allosteric effector in Escherichia coli and other bacteria that indirectly regulates glutamine synthetase at the transcriptional and post-translational levels in response to nitrogen availability. Data supporting the notion that plants have a nitrogen regulatory system(s) includes previous studies showing that the levels of mRNA for plant nitrogen assimilatory genes such as glutamine synthetase (GLN) and asparagine synthetase (ASN) are modulated by carbon and organic nitrogen metabolites. Here, we have characterized a PII homolog (GLB1) in two higher plants, Arabidopsis thaliana and Ricinus communis (Castor bean). Each plant PII-like protein has high overall identity to E. coli PII (50%). Western blot analyses reveal that the plant PII-like protein is a nuclear-encoded chloroplast protein. The PII-like protein of plants appears to be regulated at the transcriptional level in that levels of GLB1 mRNA are affected by light and metabolites. To initiate studies of the in vivo function of the Arabidopsis PII-like protein, we have constructed transgenic lines in which PII expression is uncoupled from its native regulation. Analyses of these transgenic plants support the notion that the plant PII-like protein may serve as part of a complex signal transduction network involved in perceiving the status of carbon and organic nitrogen. Thus, the PII protein found in archaea, bacteria, and now in higher eukaryotes (plants) is one of the most widespread regulatory proteins known, providing evidence for an ancestral metabolic regulatory mechanism that may have existed before the divergence of these three domains of life. The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked ''advertisement'' in accordance with 18 U.S.C. §1734 solely to indicate this fact.
In wild-type Arabidopsis, levels of ASN1 mRNA and asparagine (Asn) are tightly regulated by envir... more In wild-type Arabidopsis, levels of ASN1 mRNA and asparagine (Asn) are tightly regulated by environmental factors and metabolites. Because Asn serves as an important nitrogen storage and transport compound used to allocate nitrogen resources between source and sink organs, we tested whether overexpression of the major expressed gene for Asn synthetase, ASN1, would lead to changes in nitrogen status in the ultimate storage organ for metabolites-seeds. Transgenic Arabidopsis constitutively overexpressing ASN1 under the cauliflower mosaic virus 35S promoter were constructed (35S-ASN1). In seeds of the 35S-ASN1 lines, three observations support the notion that the nitrogen status was enhanced: (a) elevations of soluble seed protein contents, (b) elevations of total protein contents from acid-hydrolyzed seeds, and (c) higher tolerance of young seedlings when grown on nitrogen-limiting media. Besides quantitative differences, changes in the relative composition of the seed amino acid were also observed. The change in seed nitrogen status was accompanied by an increase of total free amino acids (mainly Asn) allocated to flowers and developing siliques. In 35S-ASN1 lines, sink tissues such as flowers and developing siliques exhibit a higher level of free Asn than source tissues such as leaves and stems, despite significantly higher levels of ASN1 mRNA observed in the source tissues. This was at least partially due to an enhanced transport of Asn from source to sink via the phloem, as demonstrated by the increased levels of Asn in phloem exudates of the 35S-ASN1 plants.
Abiotic stresses, such as drought, salinity, heat, cold, and heavy metals, are associated with gl... more Abiotic stresses, such as drought, salinity, heat, cold, and heavy metals, are associated with global climate change and hamper plant growth and development, affecting crop yields and quality. However, the negative effects of abiotic stresses can be mitigated through exogenous treatments using small biomolecules. For example, the foliar application of melatonin provides the following: it protects the photosynthetic apparatus; it increases the antioxidant defenses, osmoprotectant, and soluble sugar levels; it prevents tissue damage and reduces electrolyte leakage; it improves reactive oxygen species (ROS) scavenging; and it increases biomass, maintains the redox and ion homeostasis, and improves gaseous exchange. Glutathione spray upregulates the glyoxalase system, reduces methylglyoxal (MG) toxicity and oxidative stress, decreases hydrogen peroxide and malondialdehyde accumulation, improves the defense mechanisms, tissue repairs, and nitrogen fixation, and upregulates the phytochela...
MotivationSynteny analysis is a widely used framework in comparative genomics studies, which prov... more MotivationSynteny analysis is a widely used framework in comparative genomics studies, which provides valuable information to reveal chromosome collinearity in both intra-species and inter-species. Most analysis pipelines, however, are command line-based, making it challenging for biologists to run the algorithms and visualize the results. Existing visualization tools either provide static plots or can only be run on web-based servers and lack efficient visualization methods for associating macro-synteny blocks with individual gene pairs in a micro-synteny region.ResultsWe developed ShinySyn, a Shiny/R application built on the MCscan framework that provides an easy-to-use graphic interface for synteny analyses without requiring any programming skills, to reduce technical barriers. ShinySyn not only provides interactive visualization for macro-synteny, micro-synteny and genome-level dot views, but it also creates an intuitive representation with a dynamic zooming feature from macro-s...
Food production is one of the main contributors to greenhouse gas emissions and climate change. C... more Food production is one of the main contributors to greenhouse gas emissions and climate change. China, as a rapidly developing economy, contributes to an unsustainable food system as its consumption of animal products and meat has continued to grow in recent decades. Using the extended theory of planned behavior as the conceptual framework, this paper examines factors influencing consumers' intention to purchase sustainable food in China. To this end, a population‐based face‐to‐face survey was conducted with 2422 respondents in five provinces spanning the north and south of China. The results showed that the traditional constructs of behavioral attitude, subjective norms, perceived behavioral control, and the additional construct of perceived quality are significant in inducing such intentions. This paper suggests that to enhance consumers' willingness to shift to sustainable food consumption, appropriate regulation and monitoring framework is needed to increase consumers...
The number of annotated and newly predicted R-genes in each legume species. Annotated: the R-gene... more The number of annotated and newly predicted R-genes in each legume species. Annotated: the R-genes annotated from original gene models; Predicted: the R-genes predicted based on the R proteins from our self-curated database. (PDF 249 kb)
Chromosomal distributions of R-genes in the legume family. The different colors represent differe... more Chromosomal distributions of R-genes in the legume family. The different colors represent different species, and the Y-axis denotes the number of R-genes on each chromosome. Note that the legumes have different chromosomes and some genome assembly was not anchored to chromosomes. (PDF 591 kb)
Arbuscular mycorrhiza (AM) is a widespread symbiosis between roots of the majority of land plants... more Arbuscular mycorrhiza (AM) is a widespread symbiosis between roots of the majority of land plants and Glomeromycotina fungi. AM is important for ecosystem health and functioning as the fungi critically support plant performance by providing essential mineral nutrients, particularly the poorly accessible phosphate, in exchange for organic carbon. AM fungi colonize the inside of roots and this is promoted at low but inhibited at high plant phosphate status, while the mechanistic basis for this phosphate-dependence remained obscure. Here we demonstrate that a major transcriptional regulator of phosphate starvation responses in rice PHOSPHATE STARVATION RESPONSE 2 (PHR2) regulates AM. Root colonization of phr2 mutants is drastically reduced, and PHR2 is required for root colonization, mycorrhizal phosphate uptake, and yield increase in field soil. PHR2 promotes AM by targeting genes required for pre-contact signaling, root colonization, and AM function. Thus, this important symbiosis is...
Soybean is an important crop as both human food and animal feed. However, the yield of soybean is... more Soybean is an important crop as both human food and animal feed. However, the yield of soybean is heavily impacted by biotic stresses including insect attack and pathogen infection. Insect bites usually make the plants vulnerable to pathogen infection, which causes diseases. Fungi, oomycetes, bacteria, viruses, and nematodes are major soybean pathogens. The infection by pathogens and the defenses mounted by soybean are an interactive and dynamic process. Using fungi, oomycetes, and bacteria as examples, we will discuss the recognition of pathogens by soybean at the molecular level. In this review, we will discuss both the secretory peptides for soybean plant infection and those for pathogen inhibition. Pathogenic secretory peptides and peptides secreted by soybean and its associated microbes will be included. We will also explore the possible use of externally applied antimicrobial peptides identical to those secreted by soybean and its associated microbes as biopesticides.
Bedbugs (Cimex spp.) are a nuisance public-health pest that is on the rise globally, particularly... more Bedbugs (Cimex spp.) are a nuisance public-health pest that is on the rise globally, particularly in crowded cities such as Hong Kong. To investigate the health impacts of bedbug infestations among bedbug victims, online surveys were distributed in Hong Kong between June 2019 to July 2020. Data on sociodemographics, self-rated health, average hours of sleep per day, and details of bedbug infestation were collected. Bivariate and multivariable analysis were performed using logistic regression. The survey identified 422 bedbug victims; among them, 223 (52.9%) experienced ≥five bites in the past month; most bites occurred on the arms (n = 202, 47.8%) and legs (n = 215, 51%), and the most common reaction to bites were itchiness (n = 322, 76.3%), redness, and swelling of the skin (n = 246, 58.1%), and difficulties sleeping or restlessness (n = 125, 29.6%). Bites usually occurred during sleep (n = 230, 54.5%). For impact on daily life in the past month, most bedbug victims reported modera...
Arbuscular mycorrhiza (AM) is a widespread symbiosis between roots of the majority of land plants... more Arbuscular mycorrhiza (AM) is a widespread symbiosis between roots of the majority of land plants and Glomeromycotina fungi. AM is important for ecosystem health and functioning as the fungi critically support plant performance by providing essential mineral nutrients, particularly the poorly accessible phosphate, in exchange for organic carbon. AM fungi colonize the inside of roots and this is promoted at low but inhibited at high plant phosphate status, while the mechanistic basis for this phosphate-dependence remained obscure. Here we demonstrate that a major transcriptional regulator of phosphate starvation responses in rice PHOSPHATE STARVATION RESPONSE 2 (PHR2) regulates AM. Root colonization of phr2 mutants is drastically reduced, and PHR2 is required for root colonization, mycorrhizal phosphate uptake, and yield increase in field soil. PHR2 promotes AM by targeting genes required for pre-contact signaling, root colonization, and AM function. Thus, this important symbiosis is...
Journal of Housing and the Built Environment, 2021
In the original publication, the figure-5 legends were incorrectly published. The correct Fig. 5 ... more In the original publication, the figure-5 legends were incorrectly published. The correct Fig. 5 is given below, And the appendix 1, 2 and 3 were incorrectly published in the article PDF, however, it should be treated as the Electronic Supplementary Materials. The original article has been corrected.
Arabidopsis thaliana transcriptomes have been extensively studied and characterized under differe... more Arabidopsis thaliana transcriptomes have been extensively studied and characterized under different conditions. However, most of the current ‘RNA-sequencing’ technologies produce a relatively short read length and demand a reverse-transcription step, preventing effective characterization of transcriptome complexity. Here, we performed Direct RNA Sequencing (DRS) using the latest Oxford Nanopore Technology (ONT) with exceptional read length. We demonstrate that the complexity of the A. thaliana transcriptomes has been substantially under-estimated. The ONT direct RNA sequencing identified novel transcript isoforms at both the vegetative (14-day old seedlings, stage 1.04) and reproductive stages (stage 6.00–6.10) of development. Using in-house software called TrackCluster, we determined alternative transcription initiation (ATI), alternative polyadenylation (APA), alternative splicing (AS), and fusion transcripts. More than 38 500 novel transcript isoforms were identified, including s...
To investigate the risk factors associated with bedbug infestations among Hong Kong households, s... more To investigate the risk factors associated with bedbug infestations among Hong Kong households, self-reported questionnaires in Chinese were distributed online between June 2019 to July 2020. The questionnaire collected data on participants’ sociodemographics, history of bedbug infestation, and housing situation. Among the 663 participants who completed the questionnaire, 422 (63.7%) have experienced bedbug infestations in the past year, they were concentrated around the Kowloon region. Weighted bivariate and multivariate binary logistic regression were performed to identify the statistically significant (p-value <0.05) factors associated with bedbug infestations. Bivariate analysis shows a positive correlation between the number of reported dilapidated housing features and bedbug infestation. For multivariate analysis, those aged 45-64 (OR=2.53, 95% CI 1.30-4.91), have primary education or below (OR=9.43, 95% CI 3.12-28.44), and monthly household income ≤HKD30,000 (OR=1.69, 95% ...
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