2019 Vol. 1, No. 1
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Abstract:
Abstract:
Epigenetic research focuses on heritable changes beyond the DNA sequence, which has led to a revolution in biological studies and benefits in many other fields. The well-known model ciliate, Tetrahymena thermophila offers a unique system for epigenetic studies due to its nuclear dimorphism and special mode of sexual reproduction (conjugation), as well as abundant genomic resources and genetic tools. In this paper, we summarize recent progress made by our research team and collaborators in understanding epigenetic mechanisms using Tetrahymena. This includes: (1) providing the first genome-wide base pair-resolution map of DNA N6-methyladenine (6mA) and revealed it as an integral part of the chromatin landscape; (2) dissecting the relative contribution of cis- and trans- elements to nucleosome distribution by exploring the unique nuclear dimorphism of Tetrahymena; (3) demonstrating the epigenetic controls of RNAi-dependent Polycomb repression pathways on transposable elements, and (4) identifying a new histone monomethyltransferase, TXR1 (Tetrahymena Trithorax 1), that facilitates replication elongation through its substrate histone H3 lysine 27 monomethylation (H3K27me1).
Epigenetic research focuses on heritable changes beyond the DNA sequence, which has led to a revolution in biological studies and benefits in many other fields. The well-known model ciliate, Tetrahymena thermophila offers a unique system for epigenetic studies due to its nuclear dimorphism and special mode of sexual reproduction (conjugation), as well as abundant genomic resources and genetic tools. In this paper, we summarize recent progress made by our research team and collaborators in understanding epigenetic mechanisms using Tetrahymena. This includes: (1) providing the first genome-wide base pair-resolution map of DNA N6-methyladenine (6mA) and revealed it as an integral part of the chromatin landscape; (2) dissecting the relative contribution of cis- and trans- elements to nucleosome distribution by exploring the unique nuclear dimorphism of Tetrahymena; (3) demonstrating the epigenetic controls of RNAi-dependent Polycomb repression pathways on transposable elements, and (4) identifying a new histone monomethyltransferase, TXR1 (Tetrahymena Trithorax 1), that facilitates replication elongation through its substrate histone H3 lysine 27 monomethylation (H3K27me1).
2019, 1(1): 15-21.
doi: 10.1007/s42995-019-00013-2
Abstract:
Many modern biology studies require deep, whole-genome sequencing of hundreds to thousands of samples. Although per-sample costs have dramatically decreased, the total budget for such massive genome sequencing constitutes a significant barrier for poorly funded labs. The costly lab tools required for genomics experiments further hinder such studies. Here, we share two strategies for extensively reducing the costs of massive genomics experiments, including miniaturization of the NEBNext Ultra Ⅱ FS DNA Library Prep Kit for Illumina (reducing the per-sample total costs to ~ 1/6 of that charged by service providers) and in-lab 3D model-designing of genomics tools. These strategies not only dramatically release funding pressure for labs, but also provide students with additional training in hands-on genomics and 3D-model-designing skills, demonstrating the high potential for their application in genomics experiments and science education.
Many modern biology studies require deep, whole-genome sequencing of hundreds to thousands of samples. Although per-sample costs have dramatically decreased, the total budget for such massive genome sequencing constitutes a significant barrier for poorly funded labs. The costly lab tools required for genomics experiments further hinder such studies. Here, we share two strategies for extensively reducing the costs of massive genomics experiments, including miniaturization of the NEBNext Ultra Ⅱ FS DNA Library Prep Kit for Illumina (reducing the per-sample total costs to ~ 1/6 of that charged by service providers) and in-lab 3D model-designing of genomics tools. These strategies not only dramatically release funding pressure for labs, but also provide students with additional training in hands-on genomics and 3D-model-designing skills, demonstrating the high potential for their application in genomics experiments and science education.
Abstract:
Species in the microalgal genus Nannochloropsis are increasingly used as models for theoretical and applied studies. Here we attempt to generate InDel variations in the genome of Nannochloropsis oceanica, and then decipher the genetic basis of its economic and biological traits with bulked mutant analysis modified from bulked segregant analysis. In addition, we describe our efforts to construct site-tagged and gene-traceable mutant libraries to clone its genes through reverse genetic approaches. Currently, more than a half of N. oceanica protein-encoding genes are annotated against databanks. However, no functional gene has been de novo cloned from N. oceanica and no new function has been assigned to any of its annotatable genes. Here, we discuss the possible methods and potential benefits of de novo cloning of N. oceanica genes.
Species in the microalgal genus Nannochloropsis are increasingly used as models for theoretical and applied studies. Here we attempt to generate InDel variations in the genome of Nannochloropsis oceanica, and then decipher the genetic basis of its economic and biological traits with bulked mutant analysis modified from bulked segregant analysis. In addition, we describe our efforts to construct site-tagged and gene-traceable mutant libraries to clone its genes through reverse genetic approaches. Currently, more than a half of N. oceanica protein-encoding genes are annotated against databanks. However, no functional gene has been de novo cloned from N. oceanica and no new function has been assigned to any of its annotatable genes. Here, we discuss the possible methods and potential benefits of de novo cloning of N. oceanica genes.
2019, 1(1): 28-40.
doi: 10.1007/s42995-019-00016-z
Abstract:
Morphogenesis is a process describing how the shapes of living tissues and bodies are created during development. Living and fossil organisms exhibit enormously diverse tissue architecture and body forms, although the functions of organs are evolutionally conserved. Current knowledge reveals that relatively conserved mechanisms are applied to control development among diferent species. However, the regulations of morphogenesis are quite diverse in detail. Animals in the ocean display a wide range of diversity of morphology suitable for their seawater environment. Nevertheless, compared with the intensive studies on terrestrial animals, research on marine animal morphogenesis is still insufcient. The increasing genomic data and the recently available gene editing methods, together with the fast development of imaging techniques, quantitative analyses and biophysical models, provide us the opportunities to have a deeper understanding of the principles that drive the diverse morphogenetic processes in marine animals. In this review, we summarize the recent studies of morphogenesis and evolution at molecular, cellular and tissue levels, with a focus on three model marine animals, namely ascidians, sea urchins and sea anemones.
Morphogenesis is a process describing how the shapes of living tissues and bodies are created during development. Living and fossil organisms exhibit enormously diverse tissue architecture and body forms, although the functions of organs are evolutionally conserved. Current knowledge reveals that relatively conserved mechanisms are applied to control development among diferent species. However, the regulations of morphogenesis are quite diverse in detail. Animals in the ocean display a wide range of diversity of morphology suitable for their seawater environment. Nevertheless, compared with the intensive studies on terrestrial animals, research on marine animal morphogenesis is still insufcient. The increasing genomic data and the recently available gene editing methods, together with the fast development of imaging techniques, quantitative analyses and biophysical models, provide us the opportunities to have a deeper understanding of the principles that drive the diverse morphogenetic processes in marine animals. In this review, we summarize the recent studies of morphogenesis and evolution at molecular, cellular and tissue levels, with a focus on three model marine animals, namely ascidians, sea urchins and sea anemones.
2019, 1(1): 41-49.
doi: 10.1007/s42995-019-00002-5
Abstract:
The diagnosis of bacterial fish diseases has progressed from traditional culture-dependent methods involving the recovery of pathogens on agar-containing media and identification by examination of phenotypic traits. Newer approaches centre on culture-independent approaches. A problem with culturing is that it lacks sensitivity, tends to be slow, and its success depends on the composition of the media and incubation conditions employed. In contrast, culture-independent methods, now centring on molecular methods, are highly specific and sensitive. This raises an important issue that detection of very low numbers of bacterial cells does not necessarily imply the presence of clinical disease. Positivity could reflect background populations of the pathogen that may be present in the aquatic environment.
The diagnosis of bacterial fish diseases has progressed from traditional culture-dependent methods involving the recovery of pathogens on agar-containing media and identification by examination of phenotypic traits. Newer approaches centre on culture-independent approaches. A problem with culturing is that it lacks sensitivity, tends to be slow, and its success depends on the composition of the media and incubation conditions employed. In contrast, culture-independent methods, now centring on molecular methods, are highly specific and sensitive. This raises an important issue that detection of very low numbers of bacterial cells does not necessarily imply the presence of clinical disease. Positivity could reflect background populations of the pathogen that may be present in the aquatic environment.
Abstract:
From the conventional knowledge of protein nutrition to the molecular nutrition of amino acids, our understanding of protein/amino acid nutrition is rapidly increasing. Amino acids control cell growth and metabolism through two amino acid-sensing pathways, i.e. target of rapamycin complex 1 (TORC1) and the general control nonderepressible 2 (GCN2) signaling pathway. In the amino acid-abundant status, TORC1 dominates intracellular signaling and increases protein synthesis and cell growth. In contrast, amino acid deprivation actives GCN2 resulting in repression of general protein synthesis but facilitates the amino acid transport and synthesis process. By integrating and coordinating nutrition and hormone signaling, TORC1 and GCN2 control the switch of the catabolism and anabolism phase in most eukaryotes. Now, we appreciate that the availability of individual amino acids is sensed by intracellular sensors. These cutting-edge findings expand our knowledge of amino acid nutrition. Although the TORC1 and GCN2 were discovered decades ago, the study of molecular amino acid nutrition in aquaculture animals is still at its infancy. The aquaculture industry is highly dependent on the supply of fishmeal, which is the major protein source in aquacultural animal diets. Some concerted efforts were conducted to substitute for fishmeal due to limited supply of it. However, the concomitant issues including the unbalanced amino acid profile of alternative protein sources limited the utilization of those proteins. Continued study of the molecular nutrition of amino acid in aquaculture animals may be expected in the immediate future to expand our knowledge on the utilization of alternative protein sources.
From the conventional knowledge of protein nutrition to the molecular nutrition of amino acids, our understanding of protein/amino acid nutrition is rapidly increasing. Amino acids control cell growth and metabolism through two amino acid-sensing pathways, i.e. target of rapamycin complex 1 (TORC1) and the general control nonderepressible 2 (GCN2) signaling pathway. In the amino acid-abundant status, TORC1 dominates intracellular signaling and increases protein synthesis and cell growth. In contrast, amino acid deprivation actives GCN2 resulting in repression of general protein synthesis but facilitates the amino acid transport and synthesis process. By integrating and coordinating nutrition and hormone signaling, TORC1 and GCN2 control the switch of the catabolism and anabolism phase in most eukaryotes. Now, we appreciate that the availability of individual amino acids is sensed by intracellular sensors. These cutting-edge findings expand our knowledge of amino acid nutrition. Although the TORC1 and GCN2 were discovered decades ago, the study of molecular amino acid nutrition in aquaculture animals is still at its infancy. The aquaculture industry is highly dependent on the supply of fishmeal, which is the major protein source in aquacultural animal diets. Some concerted efforts were conducted to substitute for fishmeal due to limited supply of it. However, the concomitant issues including the unbalanced amino acid profile of alternative protein sources limited the utilization of those proteins. Continued study of the molecular nutrition of amino acid in aquaculture animals may be expected in the immediate future to expand our knowledge on the utilization of alternative protein sources.
Abstract:
Metabolites from marine organisms have proven to be a rich source for the discovery of multiple potent bioactive molecules with diverse structures. In recent years, we initiated a program to investigate the diversity of the secondary metabolites from marine invertebrates and their symbiotic microorganisms collected from the South China Sea. In this review, representative cases are summarized focusing on molecular diversity, mining, and application of natural products from these marine organisms. To provide a comprehensive introduction to the field of marine natural products, we highlight typical molecules including their structures, chemical synthesis, bioactivities and mechanisms, structure-activity relationships as well as biogenesis. The mining of marine-derived microorganisms to produce novel secondary metabolites is also discussed through the OSMAC strategy and via partial chemical epigenetic modification. A broad prospectus has revealed a plethora of bioactive natural products with novel structures from marine organisms, especially from soft corals, gorgonians, sponges, and their symbiotic fungi and bacteria.
Metabolites from marine organisms have proven to be a rich source for the discovery of multiple potent bioactive molecules with diverse structures. In recent years, we initiated a program to investigate the diversity of the secondary metabolites from marine invertebrates and their symbiotic microorganisms collected from the South China Sea. In this review, representative cases are summarized focusing on molecular diversity, mining, and application of natural products from these marine organisms. To provide a comprehensive introduction to the field of marine natural products, we highlight typical molecules including their structures, chemical synthesis, bioactivities and mechanisms, structure-activity relationships as well as biogenesis. The mining of marine-derived microorganisms to produce novel secondary metabolites is also discussed through the OSMAC strategy and via partial chemical epigenetic modification. A broad prospectus has revealed a plethora of bioactive natural products with novel structures from marine organisms, especially from soft corals, gorgonians, sponges, and their symbiotic fungi and bacteria.
Abstract:
Microorganisms play crucial roles in maintaining ecosystem stability. The last two decades have witnessed an upsurge in studies on marine microbial community composition using high-throughput sequencing methods. Extensive mining of the compositional data has provided exciting new insights into marine microbial ecology from a number of perspectives. Both deterministic and stochastic processes contribute to microbial community assembly but their relative importance in structuring subcommunities,that are categorized by traits such as abundance,functional type and activity,difers. Through correlation-based network analysis,signifcant progress has been made in unraveling microbial co-occurrence patterns and dynamics in response to environmental changes. Prediction of ecosystem functioning,based on microbial data,is receiving increasing attention,as closely related microbes often share similar ecological traits and microbial diversity often exhibits signifcant correlations to ecosystem functioning. The ecosystem functioning is likely executed not by the whole community,but rather by an active fraction of a community,which can be inferred from the marker gene transcription level of community members. Furthermore,the huge amount of microbial community data has signifcantly expanded the tree of life and illuminated microbial phylogenetic divergence and evolutionary history. This review summarizes important fndings in microbial assembly,interaction,functioning,activity and diversifcation,highlighting the interacting roles of diferent aspects,derived from community compositional data.
Microorganisms play crucial roles in maintaining ecosystem stability. The last two decades have witnessed an upsurge in studies on marine microbial community composition using high-throughput sequencing methods. Extensive mining of the compositional data has provided exciting new insights into marine microbial ecology from a number of perspectives. Both deterministic and stochastic processes contribute to microbial community assembly but their relative importance in structuring subcommunities,that are categorized by traits such as abundance,functional type and activity,difers. Through correlation-based network analysis,signifcant progress has been made in unraveling microbial co-occurrence patterns and dynamics in response to environmental changes. Prediction of ecosystem functioning,based on microbial data,is receiving increasing attention,as closely related microbes often share similar ecological traits and microbial diversity often exhibits signifcant correlations to ecosystem functioning. The ecosystem functioning is likely executed not by the whole community,but rather by an active fraction of a community,which can be inferred from the marker gene transcription level of community members. Furthermore,the huge amount of microbial community data has signifcantly expanded the tree of life and illuminated microbial phylogenetic divergence and evolutionary history. This review summarizes important fndings in microbial assembly,interaction,functioning,activity and diversifcation,highlighting the interacting roles of diferent aspects,derived from community compositional data.
Abstract:
Production of chitosan and its derivatives by traditional methods involves the excessive use of a reaction solution comprised of sodium hydroxide and hydrochloric acid. Waste water resulting from this process has limited the application of chitosan as a fertilizer as the process causes serious environmental pollution. Specifically, the resulting waste water contains high levels of dissolved nitrogen and minerals from shrimp shells. In this study, an eco-friendly method was established to produce chitooligosaccharides (COS) with different degrees of deacetylation (DDAs) from shrimp shell waste. At a solid-to-solvent ratio of 1:6, the degree of demineralization was above 90% with the treatment of 30 g·L-1 H3PO4, and the degree of deproteinization was above 80% when treated with 30 g·L-1 KOH at 70 ℃. Chitosans with different DDAs were obtained by microwave-assisted KOH metathesis and the COS with Mw approximately 1500 Da were then prepared by oxidative degradation. In summary, 33.73 kg H3PO4, 12.77 kg, and 241.31 kg KOH were supplied during the processes of demineralization, deproteinization, and deacetylation of 100 kg shrimp shell waste, respectively. The process water was totally recycled, demonstrating that the shrimp shell could be wholly transformed into fertilizer. The entire process created a product with the fractions of N:P2O5:K2O:COS=7.94:24.44:10.72:18.27. The test on the germination promotion of wheat seeds revealed that the COS with 72.12% DDA significantly promoted germination. This work demonstrated the use of an eco-friendly preparation method of COS with a specific degree of deacetylation that can be applied as a fertilizer.
Production of chitosan and its derivatives by traditional methods involves the excessive use of a reaction solution comprised of sodium hydroxide and hydrochloric acid. Waste water resulting from this process has limited the application of chitosan as a fertilizer as the process causes serious environmental pollution. Specifically, the resulting waste water contains high levels of dissolved nitrogen and minerals from shrimp shells. In this study, an eco-friendly method was established to produce chitooligosaccharides (COS) with different degrees of deacetylation (DDAs) from shrimp shell waste. At a solid-to-solvent ratio of 1:6, the degree of demineralization was above 90% with the treatment of 30 g·L-1 H3PO4, and the degree of deproteinization was above 80% when treated with 30 g·L-1 KOH at 70 ℃. Chitosans with different DDAs were obtained by microwave-assisted KOH metathesis and the COS with Mw approximately 1500 Da were then prepared by oxidative degradation. In summary, 33.73 kg H3PO4, 12.77 kg, and 241.31 kg KOH were supplied during the processes of demineralization, deproteinization, and deacetylation of 100 kg shrimp shell waste, respectively. The process water was totally recycled, demonstrating that the shrimp shell could be wholly transformed into fertilizer. The entire process created a product with the fractions of N:P2O5:K2O:COS=7.94:24.44:10.72:18.27. The test on the germination promotion of wheat seeds revealed that the COS with 72.12% DDA significantly promoted germination. This work demonstrated the use of an eco-friendly preparation method of COS with a specific degree of deacetylation that can be applied as a fertilizer.
Abstract:
Our previous study evaluated the in vitro and in vivo antioxidant activities of sulfated polysaccharides from a Celluclastassisted extract of Hizikia fusiforme (HFPS). The results indicate that HFPS possesses potent antioxidant activity and suggest the potential use of HFPS to combat photoaging. In this study, we investigated the ultraviolet (UV) protective efect of HFPS in vitro in keratinocytes (HaCaT cells) and in vivo in zebrafsh. The results indicate that HFPS signifcantly reduced the level of intracellular reactive oxygen species (ROS) and improved the viability of UVB-irradiated HaCaT cells. In addition, HFPS remarkably decreased apoptosis formation in UVB-irradiated HaCaT cells in a dose-dependent manner. The in vivo test results also demonstrate that HFPS signifcantly reduced intracellular ROS levels, cell death, NO production, and lipid peroxidation levels in UVB-irradiated zebrafsh in a dose-dependent manner. These results suggest that HFPS possesses strong in vitro and in vivo UV-protective efects, making it a potential ingredient in the cosmeceutical industry.
Our previous study evaluated the in vitro and in vivo antioxidant activities of sulfated polysaccharides from a Celluclastassisted extract of Hizikia fusiforme (HFPS). The results indicate that HFPS possesses potent antioxidant activity and suggest the potential use of HFPS to combat photoaging. In this study, we investigated the ultraviolet (UV) protective efect of HFPS in vitro in keratinocytes (HaCaT cells) and in vivo in zebrafsh. The results indicate that HFPS signifcantly reduced the level of intracellular reactive oxygen species (ROS) and improved the viability of UVB-irradiated HaCaT cells. In addition, HFPS remarkably decreased apoptosis formation in UVB-irradiated HaCaT cells in a dose-dependent manner. The in vivo test results also demonstrate that HFPS signifcantly reduced intracellular ROS levels, cell death, NO production, and lipid peroxidation levels in UVB-irradiated zebrafsh in a dose-dependent manner. These results suggest that HFPS possesses strong in vitro and in vivo UV-protective efects, making it a potential ingredient in the cosmeceutical industry.
