Current status and trends in forest genomics

Forests are not only the most predominant of the Earth\u27s terrestrial ecosystems, but are also the core supply for essential products for human use. However, global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest degradation. Forest genomics has great potential of increasing forest productivity and adaptation to the changing climate. In the last two decades, the field of forest genomics has advanced quickly owing to the advent of multiple high-throughput sequencing technologies, single cell RNA-seq, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing, and spatial transcriptomes, as well as bioinformatics analysis technologies, which have led to the generation of multidimensional, multilayered, and spatiotemporal gene expression data. These technologies, together with basic technologies routinely used in plant biotechnology, enable us to tackle many important or unique issues in forest biology, and provide a panoramic view and an integrative elucidation of molecular regulatory mechanisms underlying phenotypic changes and variations. In this review, we recapitulated the advancement and current status of 12 research branches of forest genomics, and then provided future research directions and focuses for each area. Evidently, a shift from simple biotechnology-based research to advanced and integrative genomics research, and a setup for investigation and interpretation of many spatiotemporal development and differentiation issues in forest genomics have just begun to emerge

Current advances in seagrass research: A review from Viet Nam

Seagrass meadows provide valuable ecosystem services but are fragile and threatened ecosystems all over the world. This review highlights the current advances in seagrass research from Viet Nam. One goal is to support decision makers in developing science-based conservation strategies. In recent years, several techniques were applied to estimate the size of seagrass meadows. Independent from the method used, there is an alarming decline in the seagrass area in almost all parts of Viet Nam. Since 1990, a decline of 46.5% or 13,549 ha was found. Only in a few protected and difficult-to-reach areas was an increase observed. Conditions at those sites could be investigated in more detail to make suggestions for conservation and recovery of seagrass meadows. Due to their lifestyle and morphology, seagrasses take up compounds from their environment easily. Phytoremediation processes of Thalassia hemprichii and Enhalus acoroides are described exemplarily. High accumulation of heavy metals dependent on their concentration in the environment in different organs can be observed. On the one hand, seagrasses play a role in phytoremediation processes in polluted areas; on the other hand, they might suffer at high concentrations, and pollution will contribute to their overall decline. Compared with the neighboring countries, the total Corg stock from seagrass beds in Viet Nam was much lower than in the Philippines and Indonesia but higher than that of Malaysia and Myanmar. Due to an exceptionally long latitudinal coastline of 3,260 km covering cool to warm water environments, the seagrass species composition in Viet Nam shows a high diversity and a high plasticity within species boundaries. This leads to challenges in taxonomic issues, especially with the Halophila genus, which can be better deduced from genetic diversity/population structures of members of Hydrocharitaceae. Finally, the current seagrass conservation and management efforts in Viet Nam are presented and discussed. Only decisions based on the interdisciplinary cooperation of scientists from all disciplines mentioned will finally lead to conserve this valuable ecosystem for mankind and biodiversity

Pichia pastoris versus Saccharomyces cerevisiae:a case study on the recombinant production of human granulocyte-macrophage colony-stimulating factor

BACKGROUND: Recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) is a glycoprotein that has been approved by the FDA for the treatment of neutropenia and leukemia in combination with chemotherapies. Recombinant hGM-CSF is produced industrially using the baker's yeast, Saccharomyces cerevisiae, by large-scale fermentation. The methylotrophic yeast, Pichia pastoris, has emerged as an alternative host cell system due to its shorter and less immunogenic glycosylation pattern together with higher cell density growth and higher secreted protein yield than S. cerevisiae. In this study, we compared the pipeline from gene to recombinant protein in these two yeasts. RESULTS: Codon optimization in silico for both yeast species showed no difference in frequent codon usage. However, rhGM-CSF expressed from S. cerevisiae BY4742 showed a significant discrepancy in molecular weight from those of P. pastoris X33. Analysis showed purified rhGM-CSF species with molecular weights ranging from 30 to more than 60 kDa. Fed-batch fermentation over 72 h showed that rhGM-CSF was more highly secreted from P. pastoris than S. cerevisiae (285 and 64 mg total secreted protein/L, respectively). Ion exchange chromatography gave higher purity and recovery than hydrophobic interaction chromatography. Purified rhGM-CSF from P. pastoris was 327 times more potent than rhGM-CSF from S. cerevisiae in terms of proliferative stimulating capacity on the hGM-CSF-dependent cell line, TF-1. CONCLUSION: Our data support a view that the methylotrophic yeast P. pastoris is an effective recombinant host for heterologous rhGM-CSF production

Drought-stress-related reprogramming of gene expression in barley involves differential histone modifications at ABA-related genes

Plants respond to drought by the major reprogramming of gene expression, enabling the plant to survive this threatening environmental condition. The phytohormone abscisic acid (ABA) serves as a crucial upstream signal, inducing this multifaceted process. This report investigated the drought response in barley plants (Hordeum vulgare, cv. Morex) at both the epigenome and transcriptome levels. After a ten-day drought period, during which the soil water content was reduced by about 35%, the relative chlorophyll content, as well as the photosystem II efficiency of the barley leaves, decreased by about 10%. Furthermore, drought-related genes such as HvS40 and HvA1 were already induced compared to the well-watered controls. Global ChIP-Seq analysis was performed to identify genes in which histones H3 were modified with euchromatic K4 trimethylation or K9 acetylation during drought. By applying stringent exclusion criteria, 129 genes loaded with H3K4me3 and 2008 genes loaded with H3K9ac in response to drought were identified, indicating that H3K9 acetylation reacts to drought more sensitively than H3K4 trimethylation. A comparison with differentially expressed genes enabled the identification of specific genes loaded with the euchromatic marks and induced in response to drought treatment. The results revealed that a major proportion of these genes are involved in ABA signaling and related pathways. Intriguingly, two members of the protein phosphatase 2C family (PP2Cs), which play a crucial role in the central regulatory machinery of ABA signaling, were also identified through this approach

Nanocarrier systems loaded with IR780, iron oxide nanoparticles and chlorambucil for cancer theragnostics

Theragnostics has become a popular term nowadays, since it enables both diagnosis and therapy at the same time while only using one carrier platform. Therefore, formulating a nanocarrier system that could serve as theragnostic agent by using simple techniques would be an advantage during production. In this project, we aimed to develop a nanocarrier that can be loaded with the chemotherapeutic medication chlorambucil and magnetic resonance imaging agents (e.g., iron oxide nanoparticles and near-infrared fluorophore IR780) for theragnostics. Poly(lactic-co-glycolic acid) was combined with the aforementioned ingredients to generate poly(vinyl alcohol)-based nanoparticles (NPs) using the single emulsion technique. Then the NPs were coated with F127 and F127-folate by simple incubation for five days. The nanoparticles have the hydrodynamic size of approx. 250 nm with negative charge. Similar to chlorambucil and IR780, iron oxide loadings were observed for all three kinds of NPs. The release of chlorambucil was quicker at pH 5.4 than at pH 7.4 at 37 °C. The F127@NPs and F127-folate@NPs demonstrated much greater cell uptake and toxicity up to 72 h after incubation. Our in vitro results of F127@NPs and F127-folate@NPs have demonstrated the ability of these systems to serve as medication and imaging agent carriers for cancer treatment and diagnostics, respectively

Current status and trends in forest genomics

Forests are not only the most predominant of the Earth's terrestrial ecosystems, but are also the core supply for essential products for human use. However, global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest degradation. Forest genomics has great potential of increasing forest productivity and adaptation to the changing climate. In the last two decades, the field of forest genomics has advanced quickly owing to the advent of multiple high-throughput sequencing technologies, single cell RNA-seq, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing, and spatial transcriptomes, as well as bioinformatics analysis technologies, which have led to the generation of multidimensional, multilayered, and spatiotemporal gene expression data. These technologies, together with basic technologies routinely used in plant biotechnology, enable us to tackle many important or unique issues in forest biology, and provide a panoramic view and an integrative elucidation of molecular regulatory mechanisms underlying phenotypic changes and variations. In this review, we recapitulated the advancement and current status of 12 research branches of forest genomics, and then provided future research directions and focuses for each area. Evidently, a shift from simple biotechnology-based research to advanced and integrative genomics research, and a setup for investigation and interpretation of many spatiotemporal development and differentiation issues in forest genomics have just begun to emerge

Medical-Waste Chain: A Medical Waste Collection, Classification and Treatment Management by Blockchain Technology

To prevent the spread of the COVID-19 pandemic, 2019 has seen unprecedented demand for medical equipment and supplies. However, the problem of waste treatment has not yet been given due attention, i.e., the traditional waste treatment process is done independently, and it is not easy to share the necessary information. Especially during the COVID-19 pandemic, the interaction between parties is minimized to limit infections. To evaluate the current system at medical centers, we also refer to the traditional waste treatment processes of four hospitals in Can Tho and Ho Chi Minh cities (Vietnam). Almost all hospitals are handled independently, lacking any interaction between the stakeholders. In this article, we propose a decentralized blockchain-based system for automating waste treatment processes for medical equipment and supplies after usage among the relevant parties, named Medical-Waste Chain. It consists of four components: medical equipment and supplies, waste centers, recycling plants, and sorting factories. Medical-Waste Chain integrates blockchain-based Hyperledger Fabric technology with decentralized storage of medical equipment and supply information, and securely shares related data with stakeholders. We present the system design, along with the interactions among the stakeholders, to ensure the minimization of medical waste generation. We evaluate the performance of the proposed solution using system-wide timing and latency analysis based on the Hyperledger Caliper engine. Our system is developed based on the hybrid-blockchain system, so it is fully scalable for both on-chain and off-chain-based extensions. Moreover, the participants do not need to pay any fees to use and upgrade the system. To encourage future use of Medical-Waste Chain, we also share a proof-of-concept on our Github repository

Medical-Waste Chain: A Medical Waste Collection, Classification and Treatment Management by Blockchain Technology

To prevent the spread of the COVID-19 pandemic, 2019 has seen unprecedented demand for medical equipment and supplies. However, the problem of waste treatment has not yet been given due attention, i.e., the traditional waste treatment process is done independently, and it is not easy to share the necessary information. Especially during the COVID-19 pandemic, the interaction between parties is minimized to limit infections. To evaluate the current system at medical centers, we also refer to the traditional waste treatment processes of four hospitals in Can Tho and Ho Chi Minh cities (Vietnam). Almost all hospitals are handled independently, lacking any interaction between the stakeholders. In this article, we propose a decentralized blockchain-based system for automating waste treatment processes for medical equipment and supplies after usage among the relevant parties, named Medical-Waste Chain. It consists of four components: medical equipment and supplies, waste centers, recycling plants, and sorting factories. Medical-Waste Chain integrates blockchain-based Hyperledger Fabric technology with decentralized storage of medical equipment and supply information, and securely shares related data with stakeholders. We present the system design, along with the interactions among the stakeholders, to ensure the minimization of medical waste generation. We evaluate the performance of the proposed solution using system-wide timing and latency analysis based on the Hyperledger Caliper engine. Our system is developed based on the hybrid-blockchain system, so it is fully scalable for both on-chain and off-chain-based extensions. Moreover, the participants do not need to pay any fees to use and upgrade the system. To encourage future use of Medical-Waste Chain, we also share a proof-of-concept on our Github repository