Chu Hou - Academia.edu (original) (raw)

Papers by Chu Hou

$Research paper thumbnail of The genomic tree of living organisms based on a fractal model$

Physics Letters, Oct 1, 2003

Accumulation of complete genome sequences of living organisms creates new possibilities to discus... more Accumulation of complete genome sequences of living organisms creates new possibilities to discuss the phylogenetic relationships at the genomic level. In the present study, a fractal model is proposed to simulate a kind of visual representation of complete genome. The estimated parameters in the fractal model is used to define the genetic distance between two organisms. Because we take into account all genome content including both coding and non-coding regions, the phylogenetic tree from such an analysis leads to alternate classification of genomes that is called a genomic tree. This method of phylogenetic analysis does not require sequence alignment of homologous genes and relies instead on our fractal analysis, so it can avoid artefacts associated with sequence alignment. The similarity in related organisms based on the fractal model of the complete genome is global. Our result from such an analysis of more than 50 genomes indicates that lateral gene transfer must have been very common in the early history of life and thus constitutes a major source of variations in a substantial proportion of prokaryotic genome.

International Journal of Molecular Sciences, Mar 18, 2010

A shortcoming of most correlation distance methods based on the composition vectors without align... more A shortcoming of most correlation distance methods based on the composition vectors without alignment developed for phylogenetic analysis using complete genomes is that the "distances" are not proper distance metrics in the strict mathematical sense. In this paper we propose two new correlation-related distance metrics to replace the old one in our dynamical language approach. Four genome datasets are employed to evaluate the effects of this replacement from a biological point of view. We find that the two proper distance metrics yield trees with the same or similar topologies as/to those using the old "distance" and agree with the tree of life based on 16S rRNA in a majority of the basic branches. Hence the two proper correlation-related distance metrics proposed here improve our dynamical language approach for phylogenetic analysis.

Journal of Proteomics, Feb 1, 2017

Proteins of the egg perivitelline fluid (PVF) that surrounds the embryo are critical for embryoni... more Proteins of the egg perivitelline fluid (PVF) that surrounds the embryo are critical for embryonic development in many animals, but little is known about their identities. Using an integrated proteomic and transcriptomic approach, we identified 64 proteins from the PVF of Pomacea maculata, a freshwater snail adopting aerial oviposition. Proteins were classified into eight functional groups: major multifunctional perivitellin subunits, immune response, energy metabolism, protein degradation, oxidation-reduction, signaling and binding, transcription and translation, and others. Comparison of gene expression levels between tissues showed that 22 PVF genes were exclusively expressed in albumen gland, the female organ that secretes PVF. Base substitution analysis of PVF and housekeeping genes between P. maculata and its closely related species Pomacea canaliculata showed that the reproductive proteins had a higher mean evolutionary rate. Predicted 3D structures of selected PVF proteins showed that some nonsynonymous substitutions are located at or near the binding regions that may affect protein function. The proteome and sequence divergence analysis revealed a substantial amount of maternal investment in embryonic nutrition and defense, and higher adaptive selective pressure on PVF protein-coding genes when compared with housekeeping genes, providing insight into the adaptations associated with the unusual reproductive strategy in these mollusks. Significance: There has been great interest in studying reproduction-related proteins as such studies may not only answer fundamental questions about speciation and evolution, but also solve practical problems of animal infertility and pest outbreak. Our study has demonstrated the effectiveness of an integrated proteomic and transcriptomic approach in understanding the heavy maternal investment of proteins in the eggs of a nonmodel snail, and how the reproductive proteins may have evolved during the transition from laying underwater eggs to aerial eggs.

BMC Genomics, Apr 30, 2021

Background: The complex life cycle of the coconut crab, Birgus latro, begins when an obligate ter... more Background: The complex life cycle of the coconut crab, Birgus latro, begins when an obligate terrestrial adult female visits the intertidal to hatch zoea larvae into the surf. After drifting for several weeks in the ocean, the postlarval glaucothoes settle in the shallow subtidal zone, undergo metamorphosis, and the early juveniles then subsequently make their way to land where they undergo further physiological changes that prevent them from ever entering the sea again. Here, we sequenced, assembled and analyzed the coconut crab genome to shed light on its adaptation to terrestrial life. For comparison, we also assembled the genomes of the long-tailed marine-living ornate spiny lobster, Panulirus ornatus, and the short-tailed marine-living red king crab, Paralithodes camtschaticus. Our selection of the latter two organisms furthermore allowed us to explore parallel evolution of the crab-like form in anomurans. Results: All three assembled genomes are large, repeat-rich and AT-rich. Functional analysis reveals that the coconut crab has undergone proliferation of genes involved in the visual, respiratory, olfactory and cytoskeletal systems. Given that the coconut crab has atypical mitochondrial DNA compared to other anomurans, we argue that an abundance of kif22 and other significantly proliferated genes annotated with mitochondrial and microtubule functions, point to unique mechanisms involved in providing cellular energy via nuclear proteincoding genes supplementing mitochondrial and microtubule function. We furthermore detected in the coconut crab a significantly proliferated HOX gene, caudal, that has been associated with posterior development in Drosophila, but we could not definitively associate this gene with carcinization in the Anomura since it is also significantly proliferated in the ornate spiny lobster. However, a cuticle-associated coatomer gene, gammacop, that is significantly proliferated in the coconut crab, may play a role in hardening of the adult coconut crab abdomen in order to mitigate desiccation in terrestrial environments.

International Archives of Allergy and Immunology, 2015

Background: Shellfish hypersensitivity is among the most common food allergies. A murine model of... more Background: Shellfish hypersensitivity is among the most common food allergies. A murine model of IgE-mediated shrimp allergy has been established in our laboratory. The aim of this study is to determine the intestinal histological changes and cytokine expression profile of this model sensitized with the major shellfish allergen tropomyosin. Methods: Female Balb/c mice orally sensitized and challenged with recombinant tropomyosin were sacrificed. Continuous sections of duodenum, jejunum and ileum were prepared using the Swiss roll technique for histological and immunological analysis. Duodenal epithelial cell apoptosis and migration were examined. mRNA expression of IL-4, IL-6, IL-10, IL-13, IL-18 and IFN-γ in intestinal tissue was measured via RT-PCR. Results: In tropomyosin-sensitized and challenged mice, an increased number of eosinophils, mast cells and

Frontiers in Cell and Developmental Biology

Cnidarians including sea anemones, corals, hydra, and jellyfishes are a group of animals well kno... more Cnidarians including sea anemones, corals, hydra, and jellyfishes are a group of animals well known for their regeneration capacity. However, how non-coding RNAs such as microRNAs (also known as miRNAs) contribute to cnidarian tissue regeneration is poorly understood. Here, we sequenced and assembled the genome of the sea anemone Exaiptasia pallida collected in Hong Kong waters. The assembled genome size of E. pallida is 229.21 Mb with a scaffold N50 of 10.58 Mb and BUSCO completeness of 91.1%, representing a significantly improved genome assembly of this species. The organization of ANTP-class homeobox genes in this anthozoan further supported the previous findings in jellyfishes, where most of these genes are mainly located on three scaffolds. Tentacles of E. pallida were excised, and both mRNA and miRNA were sequenced at 9 time points (0 h, 6 h, 12 h, 18 h, 1 day, 2, 3, 6, and 8 days) from regenerating tentacles. In addition to the Wnt signaling pathway and homeobox genes that ar...

Journal of Marine Science and Engineering, 2022

The Hong Kong oyster Magallana hongkongensis, previously known as Crassostrea hongkongensis, is a... more The Hong Kong oyster Magallana hongkongensis, previously known as Crassostrea hongkongensis, is a true oyster species native to the estuarine-coast of the Pearl River Delta in southern China. The species—with scientific, ecological, cultural, and nutritional importance—has been farmed for hundreds of years. However, there is only limited information on its genetics, stress adaptation mechanisms, and gut microbiota, restricting the sustainable production and use of oyster resources. Here, we present population structure analysis on M. hongkongensis oysters collected from Deep Bay and Lantau Island in Hong Kong, as well as transcriptome analysis on heat shock responses and the gut microbiota profile of M. hongkongensis oysters collected from Deep Bay. Single nucleotide polymorphisms (SNPs), including those on the homeobox genes and heat shock protein genes, were revealed by the whole genome resequencing. Transcriptomes of oysters incubated at 25 °C and 32 °C for 24 h were sequenced wh...

Molecular Biology and Evolution, 2020

A striking feature of micro-RNAs is that they are often clustered in the genomes of animals. The ... more A striking feature of micro-RNAs is that they are often clustered in the genomes of animals. The functional and evolutionary consequences of this clustering remain obscure. Here, we investigated a micro-RNA cluster miR-6/5/4/286/3/309 that is conserved across drosophilid lineages. Small RNA sequencing revealed expression of this micro-RNA cluster in Drosophila melanogaster leg discs, and conditional overexpression of the whole cluster resulted in leg appendage shortening. Transgenic overexpression lines expressing different combinations of micro-RNA cluster members were also constructed. Expression of individual micro-RNAs from the cluster resulted in a normal wild-type phenotype, but either the expression of several ancient micro-RNAs together (miR-5/4/286/3/309) or more recently evolved clustered micro-RNAs (miR-6-1/2/3) can recapitulate the phenotypes generated by the whole-cluster overexpression. Screening of transgenic fly lines revealed downregulation of leg-patterning gene ca...

International Journal of Molecular Sciences, 2019

Shellfish allergy is one of the most common food allergies, with tropomyosin as the major cross-r... more Shellfish allergy is one of the most common food allergies, with tropomyosin as the major cross-reactive allergen. However, no allergen-specific immunotherapy is clinically available. Recently, we designed two shrimp hypoallergens MEM49 and MED171. This study aimed to examine and compare the efficacy of the MEM49- and MED171-based DNA vaccines (pMEM49 and pMED171) in modulating shrimp allergy in a murine model of shrimp tropomyosin sensitivity. Intradermal immunization of BALB/c mice with pMEM49 or pMED171 effectively down-modulated allergic symptoms, tropomyosin-specific IgE levels, intestinal Th2 cytokines expression, and inflammatory cell infiltration. Both pMEM49 and pMED171 increased the frequency of regulatory T cells, but to a greater extent by pMED171 with upregulation of gut-homing molecules integrin-α4β7. The functionality of the pMED171-induced Treg cells was further illustrated by anti-CD25-mediated depletion of Treg cells and the adoptive transfer of CD4+CD25+Foxp3+Treg...

Journal of Asthma and Allergy, 2018

Seafood allergy is a hypersensitive disorder with increasing prevalence worldwide. Effective and ... more Seafood allergy is a hypersensitive disorder with increasing prevalence worldwide. Effective and accurate diagnostic workup for seafood allergy is essential for clinicians and patients. Parvalbumin and tropomyosin are the most common fish and shellfish allergens, respectively. The diagnosis of seafood allergies is complicated by cross-reactivity among fish allergens and between shellfish allergens and other arthropods. Current clinical diagnosis of seafood allergy is a complex algorithm that includes clinical assessment, skin prick test, specific IgE measurement, and oral food challenges. Emerging diagnostic strategies, such as component-resolved diagnosis (CRD), which uses single allergenic components for assessment of epitope specific IgE, can provide critical information in predicting individualized sensitization patterns and risk of severe allergic reactions. Further understanding of the molecular identities and characteristics of seafood allergens can advance the development of CRD and lead to more precise diagnosis and improved clinical management of seafood allergies.

A striking feature of microRNAs is that they are often clustered in the genomes of animals. The f... more A striking feature of microRNAs is that they are often clustered in the genomes of animals. The functional and evolutionary consequences of this clustering remain obscure. Here, we investigated a microRNA cluster miR-6/5/4/286/3/309 that is conserved across drosophilid lineages. Small RNA sequencing revealed expression of this microRNA cluster in Drosophila melanogaster leg discs, and conditional overexpression of the whole cluster resulted in leg appendage shortening. Transgenic overexpression lines expressing different combinations of microRNA cluster members were also constructed. Expression of individual microRNAs from the cluster resulted in a normal wild-type phenotype, but either the expression of several ancient microRNAs together (miR-5/4/286/3/309) or more recently evolved clustered microRNAs (miR-6-1/2/3) can recapitulate the phenotypes generated by the whole-cluster overexpression. Screening of transgenic fly lines revealed down-regulation of leg patterning gene cassette...

PLoS ONE, 2014

Designer proteins deprived of its IgE-binding reactivity are being sought as a regimen for allerg... more Designer proteins deprived of its IgE-binding reactivity are being sought as a regimen for allergen-specific immunotherapy. Although shrimp tropomyosin (Met e 1) has long been identified as the major shellfish allergen, no immunotherapy is currently available. In this study, we aim at identifying the Met e 1 IgE epitopes for construction of hypoallergens and to determine the IgE inhibitory capacity of the hypoallergens. IgE-binding epitopes were defined by three online computational models, ELISA and dot-blot using sera from shrimp allergy patients. Based on the epitope data, two hypoallergenic derivatives were constructed by site-directed mutagenesis (MEM49) and epitope deletion (MED171). Nine regions on Met e 1 were defined as the major IgE-binding epitopes. Both hypoallergens MEM49 and MED171 showed marked reduction in their in vitro reactivity towards IgE from shrimp allergy patients and Met e 1-sensitized mice, as well as considerable decrease in induction of mast cell degranulation as demonstrated in passive cutaneous anaphylaxis assay. Both hypoallergens were able to induce Met e 1-recognizing IgG antibodies in mice, specifically IgG 2a antibodies, that strongly inhibited IgE from shrimp allergy subjects and Met e 1-sensitized mice from binding to Met e 1. These results indicate that the two designer hypoallergenic molecules MEM49 and MED171 exhibit desirable preclinical characteristics, including marked reduction in IgE reactivity and allergenicity, as well as ability to induce blocking IgG antibodies. This approach therefore offers promises for development of immunotherapeutic regimen for shrimp tropomyosin allergy.

Marine Biotechnology, 2007

Differentially expressed genes were identified in the hepatopancreas of Metapenaeus ensis during ... more Differentially expressed genes were identified in the hepatopancreas of Metapenaeus ensis during ovarian maturation via differential display reverse transcription-polymerase chain reaction (DDRT-PCR). They are G-protein signaling modulator 2 (GPSM2), glutamate carboxypeptide II (GCPII), ligatin, C-type lectin, O-linked N-acetylglucosamine transferase (O-GlcNAc transferase), 1-acylglycerol-3-phosphate O-acyltransferase 4 (AGPAT4), vitellogenin (Vg), and hemocyanin. The hepatopancreas Vg gene identified in this study shows 92% and 49% amino acid sequence homology, respectively, to MeVg1 and MeVg2 previously isolated from this species, suggesting the identification of a new Vg gene in M. ensis. Vg gene expression was highest when the ovary was actively developing. The two metabolic enzymes, O-GlcNAc transferase and AGPAT4, exhibited a similar trend of expression to Vg gene, suggesting their involvement in Vg synthesis. The signal transduction related genes (GPSM2, GCPII, ligatin, and C-type lectin) were highly expressed in the hepatopancreas in the initial phase of maturation. These genes may be important for the signaling in the hepatopancreas for synthesis and mobilization of vitellogenin and nutrients to the developing ovary. The present work provides candidate genes for further investigation on the role of hepatopancreas in shrimp reproduction.

Biochemical Systematics and Ecology, 2004

This study explores the use of amplified fragment length polymorphism (AFLP) technology in specie... more This study explores the use of amplified fragment length polymorphism (AFLP) technology in species identification and phylogenetic analysis of penaeid shrimp. AFLP fingerprinting of six Penaues species, P. monodon, P. chinensis, P. merguiensis, P. latisulcatus, P. canaliculatus and P. japonicus was compared using three sets of selective primers for PCR amplification. A total of 443 bands (size range 80-550 bp) were generated. Eight bands (1.8%) were found in all species, but only three of them (0.7%) were scored in all individuals. Species differed in the levels of genetic diversity among individuals, with 24.6% (in P. canaliculatus) to 60.8% (in P. japonicus) of the bands scored being polymorphic. Speciesspecific markers with potential for genetic identification of species were identified. Average genetic distances among individuals of the same species varied from 0.0023 in P. chinensis to 0.0068 in P. japonicus, while the average distances between species varied from 0.0207 to 0.0324. Phylogenetic analysis shows that the six species could be divided into two major clades. The first clade consisted of P. monodon, P. chinensis and P. merguiensis, with the latter two species more closely related. The other clade comprised P. latisulcatus, P. canaliculatus and P. japonicus. This result based on AFLP is consistent with the segregation of two distinct clades of Penaeus as previously documented by mitochondrial DNA analysis in our laboratory. This study established AFLP technology as a feasible approach in species identification and phylogenetic studies of penaeid shrimp.

Invertebrate Systematics, 2014

The kuruma shrimp Penaeus japonicus Bate, 1888 (Decapoda : Penaeidae) is economically important i... more The kuruma shrimp Penaeus japonicus Bate, 1888 (Decapoda : Penaeidae) is economically important in the global shrimp market. It was regarded as the only species in the subgenus Marsupenaeus. However, our previous molecular analyses revealed two cryptic species (Forms I and II) in this species complex. In this study, we confirm the phylogenetic relatedness between the two cryptic species; revise their taxonomic status; and review their range distribution. The name Penaeus pulchricaudatus Stebbing, 1914 (with type-locality off the eastern coast of South Africa), previously considered as a junior synonym of P. japonicus, is fixed for Form II through a neotype selection. P. japonicus (Form I) is only confined to the East China Sea (including Japan, its type-locality) and the northern South China Sea. P. pulchricaudatus is widely distributed in the South China Sea, Australia, the Red Sea, the Mediterranean, and the western Indian Ocean. Phylogenetic analysis shows that P. japonicus is genetically homogeneous yet P. pulchricaudatus exhibits a strong phylogeographical structure. The Mediterranean stock of P. pulchricaudatus originated from the Red Sea population, supporting the Lessepsian migration hypothesis. The presence of two closely related cryptic species in the P. japonicus species complex provides important insights into fishery management and aquaculture development.

Marine and Freshwater Research, Jan 13, 2022

The lack of information is one of the major impediments to effective conservation of rare, endemi... more The lack of information is one of the major impediments to effective conservation of rare, endemic species. One of which concerns the freshwater atyid shrimp Caridina logemanni known only from three streams in Hong Kong, with an area of occupancy of less than 20 km2, further threatened by harvesting for aquarium trade and potential introgressive hybridisation with a ubiquitous congener C. cantonensis. Here, we delineated the genetic diversity and population structure of C. logemanni, and examined its extent of hybridisation with C. cantonensis, using one mitochondrial (COI), one nuclear (NaK intron) and six microsatellite markers. The two examined populations of C. logemanni exhibited strong genetic differentiation at a spatial scale of <1.5 km apart, and generally low genetic diversity. Historic introgressive hybridisation is evident from the sharing of COI haplotypes between species and the more extensive inter-specific microsatellite admixture than inter-population admixture, such that both C. logemanni populations were of hybrid origin. Future conservation efforts on C. logemanni should aim at (1) minimising waterway modifications to prevent potential anthropogenic hybridisation, (2) fortifying conservation legislations to stop its harvesting, and (3) conducting continuous monitoring in case of stochastic events associated with small population size and linear habitat.

Hydrobiologia, Jul 25, 2018

Fine-scale genetic studies are essential for understanding population connectivity and formulatin... more Fine-scale genetic studies are essential for understanding population connectivity and formulating appropriate conservation measures for freshwater inhabitants. Despite their significance, such studies remain relatively limited in South China and Asia in general. We examined the genetic structure of the predaceous chub Parazacco spilurus in Hong Kong by incorporating genetic data from both mitochondrial (control region and cytochrome b oxidase gene) and nuclear (recombination-activating gene 1) DNA markers. We identified two highly divergent lineages having discrete distribution ranges with limited overlap near two reservoirs located in northeastern (Plover Cove Reservoir) and southeastern (Tai Tam Tuk Reservoir) Hong Kong. Each lineage is further divided into sublineages with geographical association. As such, gene flow is highly restricted at both sublineage and population levels. Despite the presence of sublineages, inter-lineage divergence is far greater than that divergence within lineage. It also exceeds the species divergence in closely related cyprinid genera, suggesting that the two lineages recovered potentially represent two distinct species. Yet genetic analyses based on the nuclear marker indicated a low degree of hybridization between the lineages at two closely situated localities. This study provides insights on the possible direction of conservation plans for P. spilurus in Hong Kong and South China.

Aquatic Conservation-marine and Freshwater Ecosystems, Sep 2, 2019

1. Freshwater fauna is highly threatened owing to various human disturbances and a lack of natura... more 1. Freshwater fauna is highly threatened owing to various human disturbances and a lack of natural connectivity among populations. Immediate conservation actions are vital to save freshwater wildlife from population decline and extinction. Given the paucity of resources, conservation prioritization is essential to guide resource allocation for effective and practical management; however, the incorporation of quantitative ranking approaches in population genetic studies is highly limited. 2. This study scrutinized the genetic diversity and examined the population structure of three invertebrates (the atyid shrimp Caridina cantonensis, the pachychilid snail Sulcospira hainanensis, the palaemonid shrimp Macrobrachium hainanense) and five fishes (the Chinese barb Barbodes semifasciolatus, the paradise fish Marcopodus opercularis, the Hong Kong paradise fish Macropodus hongkongensis, the Beijiang thick-lipped barb Acrossocheilus beijiangensis, and the rosy bitterling Rhodeus ocellatus) in Hong Kong, based on mitochondrial cytochrome c oxidase subunit I gene and control region, respectively. In general, the three fish species of conservation concern (M. hongkongensis, A. beijiangensis, and R. ocellatus) showed low to no genetic diversity while the other species showed high genetic diversity and strong population differentiation. 3. This study also investigated the use of Heightened Evolutionary Distinctiveness (HED) estimation on quantitatively prioritizing the 95 populations for conservation, including three previously studied species (the white cheek goby Rhinogobius duospilus, the sucker-belly loach Pseudogastromyzon myersi, and the striped loach Schistura fasciolata). Only five sites had relatively high normalized HED values (>0.70) for all taxa occurring there, and thus are of relatively higher conservation priority. Many sites harboured evolutionarily distinct populations for only one to three species; therefore, a general plan for all freshwater inhabitants cannot be formulated. 4. This comprehensive comparative study highlights the importance of genetic attributes in conservation decision making and sheds light on plausible conservation management in Hong Kong and other highly developed areas with significant freshwater biodiversity. Wai Yee Wong and Lai Him Chow should be considered joint first authors.

Heredity, Aug 9, 2017

The high biodiversity and strong population structure of freshwater fauna has often been attribut... more The high biodiversity and strong population structure of freshwater fauna has often been attributed to historical geological and climatic alterations. The impact of these historical changes on obligate freshwater species on a small geographical scale has not been well understood due to the lack of fine-scale comparative phylogeographic studies. Strong population structure has been reported in a goby and a caridean shrimp in Hong Kong, a small but highly developed city in South China, but the common drivers of population differentiation in freshwater fauna in this region remain unclear. This study examined the fine-scale phylogeographic patterns of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi in Hong Kong, using sequence data of mitochondrial control region and two nuclear markers (interphotoreceptor retinoid binding protein gene 2 and ribosomal protein S13 gene). Results show that they exhibit pronounced population structure as supported by high and significant Φ ST. Phylogenetic analyses based on the control region reveal six and three distinct lineages in S. fasciolata and P. myersi, respectively. Phylogeographic structure of both species generally follows the paleodrainage pattern, though P. myersi shows a shallower structure on the Mainland, perhaps due to their higher mobility. Most of these lineages diverged during the Pliocene and Late Pleistocene, a period with marked sea-level fluctuations. In a broader context, this suggests that sea-level fluctuation played an important role in shaping even the fine-scale population structure of freshwater fish in South China, implying that the genetic diversity of this fauna may be higher than expected.