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1.
Heliyon ; 10(18): e37933, 2024 Sep 30.
Article in English | MEDLINE | ID: mdl-39328527

ABSTRACT

Rice (Oryza sativa L.) is one of the most extensively farmed food crops, but its development and productivity are significantly impacted by cold stress during the budding period. In this study, transcriptome sequencing was conducted on two types of rice: the cold-sensitive indica rice A117 and the substantially cold-tolerant japonica rice B106 under control and cold treatments. Differentially expressed genes between the two materials under cold conditions were analyzed using GO and KEGG enrichment analyses. The results revealed that processes such as the TCA cycle, glycolysis/glycogenesis, oxidative phosphorylation, and glutathione metabolism contribute to B106's cold tolerance. Additionally, an enrichment analysis of cold-induced genes in each material and shared genes identified significant enrichment in pathways such as glutathione metabolism, phenylpropanoid biosynthesis, and photosynthesis-antenna proteins. Initial cold tolerance QTLs at the rice bud stage were collected from published literature, and meta-QTL mapping identified 9 MQTLs. Gene expression profiling led to the identification of 75 potential DEGs within the 9 MQTLs region, from which four candidate genes (Os02g0194100, Os03g0802500, Os05g0129000, and Os07g0462000) were selected using qRT-PCR and gene annotation. These findings provide genetic resources for further research on the molecular mechanisms underlying rice's response to cold stress during the bud stage.

2.
Article in English | MEDLINE | ID: mdl-39222168

ABSTRACT

A recombinant esterase, BaCEm, derived from Bacillus aryabhattai and heterologously expressed in Escherichia coli, was successfully immobilized on polyethyleneimine-impregnated mesoporous silica SBA-15. This immobilization utilized glutaraldehyde as a crosslinker. Optimal conditions were established with a PEI/SBA-15 ratio of 25% (w/w), a pH of 7.5, and a glutaraldehyde concentration of 0.5% (w/w), resulting in a loading capacity of 76.4 mg/g, a recovery activity of 43.5%, and a specific activity of 7917 U/g for BaCEm. The immobilized BaCEm demonstrated high enantioselectivity, with an "E" value of 203.92, in the resolution assay of (R,S)-ethyl indoline-2-carboxylate. Notably, the immobilized enzyme, compared to its free counterpart, exhibited enhanced thermostability, maintaining 95.4% of its activity after 3 h at 30 °C. It also showed significant tolerance to organic solvents, retaining 48.4% and 28.7% residual activity in 10% v/v acetonitrile and acetone, respectively. Moreover, its storage stability was confirmed, with 68.5% residual activity preserved after 30 days at 4 °C. Remarkably, the immobilized BaCEm retained 58.1% of its activity after 10 reuse cycles, underscoring the potential of polyethyleneimine-impregnated mesoporous silica SBA-15 as an effective support for enzyme immobilization, promising for industrial applications.

3.
Mol Ther ; 2024 Jul 31.
Article in English | MEDLINE | ID: mdl-39086133

ABSTRACT

Sickle cell disease (SCD) is a common, severe genetic blood disorder. Current pharmacotherapies are partially effective and allogeneic hematopoietic stem cell transplantation is associated with immune toxicities. Genome editing of patient hematopoietic stem cells (HSCs) to reactivate fetal hemoglobin (HbF) in erythroid progeny offers an alternative potentially curative approach to treat SCD. Although the FDA released guidelines for evaluating genome editing risks, it remains unclear how best to approach pre-clinical assessment of genome-edited cell products. Here, we describe rigorous pre-clinical development of a therapeutic γ-globin gene promoter editing strategy that supported an investigational new drug application cleared by the FDA. We compared γ-globin promoter and BCL11A enhancer targets, identified a potent HbF-inducing lead candidate, and tested our approach in mobilized CD34+ hematopoietic stem progenitor cells (HSPCs) from SCD patients. We observed efficient editing, HbF induction to predicted therapeutic levels, and reduced sickling. With single-cell analyses, we defined the heterogeneity of HbF induction and HBG1/HBG2 transcription. With CHANGE-seq for sensitive and unbiased off-target discovery followed by targeted sequencing, we did not detect off-target activity in edited HSPCs. Our study provides a blueprint for translating new ex vivo HSC genome editing strategies toward clinical trials for treating SCD and other blood disorders.

4.
Genome Res ; 34(7): 1089-1105, 2024 Aug 20.
Article in English | MEDLINE | ID: mdl-38951027

ABSTRACT

Knowledge of locations and activities of cis-regulatory elements (CREs) is needed to decipher basic mechanisms of gene regulation and to understand the impact of genetic variants on complex traits. Previous studies identified candidate CREs (cCREs) using epigenetic features in one species, making comparisons difficult between species. In contrast, we conducted an interspecies study defining epigenetic states and identifying cCREs in blood cell types to generate regulatory maps that are comparable between species, using integrative modeling of eight epigenetic features jointly in human and mouse in our Validated Systematic Integration (VISION) Project. The resulting catalogs of cCREs are useful resources for further studies of gene regulation in blood cells, indicated by high overlap with known functional elements and strong enrichment for human genetic variants associated with blood cell phenotypes. The contribution of each epigenetic state in cCREs to gene regulation, inferred from a multivariate regression, was used to estimate epigenetic state regulatory potential (esRP) scores for each cCRE in each cell type, which were used to categorize dynamic changes in cCREs. Groups of cCREs displaying similar patterns of regulatory activity in human and mouse cell types, obtained by joint clustering on esRP scores, harbor distinctive transcription factor binding motifs that are similar between species. An interspecies comparison of cCREs revealed both conserved and species-specific patterns of epigenetic evolution. Finally, we show that comparisons of the epigenetic landscape between species can reveal elements with similar roles in regulation, even in the absence of genomic sequence alignment.


Subject(s)
Epigenesis, Genetic , Epigenome , Species Specificity , Animals , Mice , Humans , Blood Cells/metabolism , Regulatory Sequences, Nucleic Acid , Gene Expression Regulation , Epigenomics/methods
5.
Bioengineering (Basel) ; 11(5)2024 May 01.
Article in English | MEDLINE | ID: mdl-38790316

ABSTRACT

Optical coherence tomography (OCT) is widely used to probe retinal structure and function. This study investigated the outer retina band (ORB) pattern and reflective intensity for the region between bands 2 and 3 (Dip) in three mouse models of inherited retinal degeneration (Rs1KO, TTLL5KO, RPE65KO) and in human AMD patients from the A2A database. OCT images were manually graded, and reflectivity signals were used to calculate the Dip ratio. Qualitative analyses demonstrated the progressive merging band 2 and band 3 in all three mouse models, leading to a reduction in the Dip ratio compared to wildtype (WT) controls. Gene replacement therapy in Rs1KO mice reverted the ORB pattern to one resembling WT and increased the Dip ratio. The degree of anatomical rescue in these mice was highly correlated with level of transgenic RS1 expression and with the restoration of ERG b-wave amplitudes. While the inner retinal cavity was significantly enlarged in dark-adapted Rs1KO mice, the Dip ratio was not altered. A reduction of the Dip ratio was also detected in AMD patients compared with healthy controls and was also positively correlated with AMD severity on the AMD score. We propose that the ORB and Dip ratio can be used as non-invasive early biomarkers for retina health, which can be used to probe therapeutic gene expression and to evaluate the effectiveness of therapy.

6.
Nature ; 630(8017): 728-735, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38778101

ABSTRACT

Haematopoietic stem cell (HSC) transplantation (HSCT) is the only curative treatment for a broad range of haematological malignancies, but the standard of care relies on untargeted chemotherapies and limited possibilities to treat malignant cells after HSCT without affecting the transplanted healthy cells1. Antigen-specific cell-depleting therapies hold the promise of much more targeted elimination of diseased cells, as witnessed in the past decade by the revolution of clinical practice for B cell malignancies2. However, target selection is complex and limited to antigens expressed on subsets of haematopoietic cells, resulting in a fragmented therapy landscape with high development costs2-5. Here we demonstrate that an antibody-drug conjugate (ADC) targeting the pan-haematopoietic marker CD45 enables the antigen-specific depletion of the entire haematopoietic system, including HSCs. Pairing this ADC with the transplantation of human HSCs engineered to be shielded from the CD45-targeting ADC enables the selective eradication of leukaemic cells with preserved haematopoiesis. The combination of CD45-targeting ADCs and engineered HSCs creates an almost universal strategy to replace a diseased haematopoietic system, irrespective of disease aetiology or originating cell type. We propose that this approach could have broad implications beyond haematological malignancies.


Subject(s)
Hematologic Neoplasms , Hematopoiesis , Immunoconjugates , Leukocyte Common Antigens , Animals , Female , Humans , Male , Mice , Hematologic Neoplasms/drug therapy , Hematologic Neoplasms/therapy , Hematologic Neoplasms/immunology , Hematopoiesis/drug effects , Hematopoietic Stem Cell Transplantation , Hematopoietic Stem Cells/cytology , Hematopoietic Stem Cells/drug effects , Hematopoietic Stem Cells/metabolism , Immunoconjugates/pharmacology , Immunoconjugates/therapeutic use , Leukocyte Common Antigens/immunology , Leukocyte Common Antigens/metabolism , Cell Line, Tumor , Antibody Specificity
7.
Rev Sci Instrum ; 95(4)2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38563715

ABSTRACT

Using a stereo camera system, a new diagnostic for the safety factor of the core plasma based on the pellet ablation trail is applied on the Experimental Advanced Superconducting Tokamak (EAST). In EAST discharge No. 128 874, a shattered pellet injection system is applied to inject a shattered neon pellet into the EAST. Since the strong magnetic field in tokamaks binds the ablated pellet material, the orientation of the pellet ablation trail is the same as the local magnetic field direction. Thus, from the three-dimensional reconstruction result of the pellet ablation trail, the local safety factor q can be obtained. The motional Stark effect (MSE) diagnostic is applied to determine the safety factor q profile in this shot. The determined safety factor q results for this new diagnostic are in quantitative agreement with those from the MSE diagnostic with the mean relative difference of only 6.8%, confirming the effectiveness of this new diagnostic of the safety factor.

8.
BMC Health Serv Res ; 24(1): 469, 2024 Apr 15.
Article in English | MEDLINE | ID: mdl-38622660

ABSTRACT

BACKGROUND: China has piloted Long-Term Care Insurance (LTCI) to address increasing care demand. However, many cities neglected adjusting LTCI premiums since the pilot, risking the long-term sustainability of LTCI. Therefore, using Zhejiang Province as a case, this study simulated mortality-adjusted long-term care demand and the balance of LTCI funds through dynamic financing mechanism under diverse life expectancy and disability scenarios. METHODS: Three-parameter log-quadratic model was used to estimate the mortality from 1990 to 2020. Mortality with predicted interval from 2020 to 2080 was projected by Lee-Carter method extended with rotation. Cohort-component projection model was used to simulate the number of older population with different degrees of disability. Disability data of the older people is sourced from China Health and Retirement Longitudinal Study 2018. The balance of LTCI fund was simulated by dynamic financing actuarial model. RESULTS: Life expectancy of Zhejiang for male (female) is from 80.46 (84.66) years in 2020 to 89.39 [86.61, 91.74] (91.24 [88.90, 93.25]) years in 2080. The number of long-term care demand with severe disability in Zhejiang demonstrates an increasing trend from 285 [276, 295] thousand in 2023 to 1027 [634, 1657] thousand in 2080 under predicted mean of life expectancy. LTCI fund in Zhejiang will become accumulated surplus from 2024 to 2080 when annual premium growth rate is 5.25% [4.20%, 6.25%] under various disability scenarios, which is much higher than the annual growth of unit cost of long-term care services (2.25%). The accumulated balance of LTCI fund is sensitive with life expectancy. CONCLUSIONS: Dynamic growth of LTCI premium is essential in dealing with current deficit around 2050 and realizing Zhejiang's LTCI sustainability in the long-run. The importance of dynamic monitoring disability and mortality information is emphasized to respond immediately to the increase of premiums. LTCI should strike a balance between expanding coverage and controlling financing scale. This study provides implications for developing countries to establish or pilot LTCI schemes.


Subject(s)
Insurance, Long-Term Care , Long-Term Care , Humans , Male , Female , Aged , Longitudinal Studies , Life Expectancy , China
9.
bioRxiv ; 2024 Mar 30.
Article in English | MEDLINE | ID: mdl-38585919

ABSTRACT

Base editors ( BE ) enable programmable conversion of nucleotides in genomic DNA without double-stranded breaks and have substantial promise to become new transformative genome editing medicines. Sensitive and unbiased detection of base editor off-target effects is important for identifying safety risks unique to base editors and translation to human therapeutics, as well as accurate use in life sciences research. However, current methods for understanding the global activities of base editors have limitations in terms of sensitivity or bias. Here we present CHANGE-seq-BE, a novel method to directly assess the off-target profile of base editors that is simultaneously sensitive and unbiased. CHANGE-seq-BE is based on the principle of selective sequencing of adenine base editor modified genomic DNA in vitro , and provides an accessible, rapid, and comprehensive method for identifying genome-wide off-target mutations of base editors.

10.
Toxins (Basel) ; 16(3)2024 Mar 14.
Article in English | MEDLINE | ID: mdl-38535815

ABSTRACT

Microcystin-LR (MC-LR) is a cyanobacterial metabolite produced during cyanobacterial blooms and is toxic to aquatic animals, and the liver is the main targeted organ of MC-LR. To comprehensively understand the toxicity mechanism of chronic exposure to environmental levels of MC-LR on the liver of fish, juvenile Nile tilapia were exposed to 0 µg/L (control), 1 µg/L (M1), 3 µg/L (M3), 10 µg/L (M10), and 30 µg/L (M30) MC-LR for 60 days. Then, the liver hepatotoxicity induced by MC-LR exposure was systematically evaluated via histological and biochemical determinations, and the underlying mechanisms were explored through combining analysis of biochemical parameters, multi-omics (transcriptome and metabolome), and gene expression. The results exhibited that chronic MC-LR exposure caused slight liver minor structural damage and lipid accumulation in the M10 group, while resulting in serious histological damage and lipid accumulation in the M30 group, indicating obvious hepatotoxicity, which was confirmed by increased toxicity indexes (i.e., AST, ALT, and AKP). Transcriptomic and metabolomic analysis revealed that chronic MC-LR exposure induced extensive changes in gene expression and metabolites in six typical pathways, including oxidative stress, apoptosis, autophagy, amino acid metabolism, primary bile acid biosynthesis, and lipid metabolism. Taken together, chronic MC-LR exposure induced oxidative stress, apoptosis, and autophagy, inhibited primary bile acid biosynthesis, and caused fatty deposition in the liver of Nile tilapia.


Subject(s)
Chemical and Drug Induced Liver Injury , Cichlids , Marine Toxins , Microcystins , Animals , Multiomics , Bile Acids and Salts , Lipids
11.
Sci China Life Sci ; 67(4): 817-828, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38217639

ABSTRACT

The Convention on Biological Diversity seeks to conserve at least 30% of global land and water areas by 2030, which is a challenge but also an opportunity to better preserve biodiversity, including flowering plants (angiosperms). Herein, we compiled a large database on distributions of over 300,000 angiosperm species and the key functional traits of 67,024 species. Using this database, we constructed biodiversity-environment models to predict global patterns of taxonomic, phylogenetic, and functional diversity in terrestrial angiosperms and provide a comprehensive mapping of the three diversity facets. We further evaluated the current protection status of the biodiversity centers of these diversity facets. Our results showed that geographical patterns of the three facets of plant diversity exhibited substantial spatial mismatches and nonoverlapping conservation priorities. Idiosyncratic centers of functional diversity, particularly of herbaceous species, were primarily distributed in temperate regions and under weaker protection compared with other biodiversity centers of taxonomic and phylogenetic facets. Our global assessment of multifaceted biodiversity patterns and centers highlights the insufficiency and unbalanced conservation among the three diversity facets and the two growth forms (woody vs. herbaceous), thus providing directions for guiding the future conservation of global plant diversity.


Subject(s)
Magnoliopsida , Phylogeny , Biodiversity , Plants , Ecosystem , Conservation of Natural Resources
12.
Ecotoxicol Environ Saf ; 269: 115775, 2024 Jan 01.
Article in English | MEDLINE | ID: mdl-38070413

ABSTRACT

Geosmin is an environmental pollutant that causes off-flavor in water and aquatic products. The high occurrence of geosmin contamination in aquatic systems and aquaculture raises public awareness, however, few studies have investigated the response pathways of geosmin stress on freshwater fish. In this research, grass carp were exposed to 50 µg/L geosmin for 96 h, liver tissue was sequenced and validated using real-time qPCR. In total of 528 up-regulated genes and 488 down-regulated genes were observed, includes cytochrome P450 and uridine diphosphate (UDP)-glucuronosyltransferase related genes. KEGG analysis showed that chemical carcinogenesis-DNA adducts, metabolism of xenobiotics by cytochrome P450, drug metabolism-cytochrome P450 pathway was enriched. Common genes from the target genes of microRNAs and differential expression genes are enriched in metabolism of xenobiotics cytochrome P450 pathway. Two miRNAs (dre-miR-146a and miR-212-3p) down regulated their target genes (LOC127510138 and adh5, respectively) which are enriched cytochrome P450 related pathway. The results present that geosmin is genetoxic to grass carp and indicate that cytochrome P450 system and UDP-glucuronosyltransferase play essential roles in biotransformation of geosmin. MicroRNAs regulate the biotransformation of geosmin by targeting specific genes, which contributes to the development of strategies to manage its negative impacts in both natural and artificial environments.


Subject(s)
Carps , Fish Diseases , MicroRNAs , Naphthols , Animals , MicroRNAs/genetics , MicroRNAs/metabolism , Carps/genetics , Carps/metabolism , RNA, Messenger , Cytochrome P-450 Enzyme System/genetics , Fresh Water , Glucuronosyltransferase/genetics , Uridine Diphosphate , Fish Proteins/genetics , Fish Proteins/metabolism
13.
bioRxiv ; 2024 Mar 29.
Article in English | MEDLINE | ID: mdl-37066352

ABSTRACT

Knowledge of locations and activities of cis -regulatory elements (CREs) is needed to decipher basic mechanisms of gene regulation and to understand the impact of genetic variants on complex traits. Previous studies identified candidate CREs (cCREs) using epigenetic features in one species, making comparisons difficult between species. In contrast, we conducted an interspecies study defining epigenetic states and identifying cCREs in blood cell types to generate regulatory maps that are comparable between species, using integrative modeling of eight epigenetic features jointly in human and mouse in our V al i dated S ystematic I ntegrati on (VISION) Project. The resulting catalogs of cCREs are useful resources for further studies of gene regulation in blood cells, indicated by high overlap with known functional elements and strong enrichment for human genetic variants associated with blood cell phenotypes. The contribution of each epigenetic state in cCREs to gene regulation, inferred from a multivariate regression, was used to estimate epigenetic state Regulatory Potential (esRP) scores for each cCRE in each cell type, which were used to categorize dynamic changes in cCREs. Groups of cCREs displaying similar patterns of regulatory activity in human and mouse cell types, obtained by joint clustering on esRP scores, harbored distinctive transcription factor binding motifs that were similar between species. An interspecies comparison of cCREs revealed both conserved and species-specific patterns of epigenetic evolution. Finally, we showed that comparisons of the epigenetic landscape between species can reveal elements with similar roles in regulation, even in the absence of genomic sequence alignment.

14.
ACS Omega ; 8(38): 35012-35023, 2023 Sep 26.
Article in English | MEDLINE | ID: mdl-37779930

ABSTRACT

Coal and gas outbursts are a phenomenon whereby broken coal and gas suddenly erupt from the coal body into the mining space under pressure. The Diandong mining area is a group of close-range outburst coal seams in which the gas content is up to 20 m3/t and gas pressure can reach 3 MPa. Research has been conducted on engineering challenges such as advanced detection and prevention of interlayer excavation in close-range coal seam groups, improvement of gas extraction quality and efficiency in low-permeability coal seam groups, and traceability and evaluation of joint extraction of coal seam groups. Through this study, advanced detection technology with full coverage in front of the excavation working face has been constructed as well as advanced pre-extraction technology for adjacent coal seams and this coal seam in ultraclose layers. We have developed a method for achieving the standard of cross-layer fixed-point hole expansion and permeability enhancement for the first mining of coal seams in a coal seam group. A combined process of graded enhanced pre-extraction and segmented regulation and extraction was proposed, which included "fixed-point control section sealing pre-extraction of coal seam groups and secondary sealing and extraction of mining pressure relief orifice."

15.
Materials (Basel) ; 16(20)2023 Oct 11.
Article in English | MEDLINE | ID: mdl-37895616

ABSTRACT

Understanding the infiltration and solidification processes of liquid 5083Al alloy into Al2O3 three-dimensional reticulated porous ceramic (Al2O3(3D) RPC) is essential for optimizing the microstructure and properties of Al2O3(3D)/5083Al interpenetrating phase composites (IPCs) prepared by low-pressure infiltration process (LPIP). This study employs ProCAST software to simulate the infiltration and solidification processes of liquid 5083Al with pouring velocities (PV) of 0.4 m/s infiltrating into Al2O3(3D) RPC preforms with varying porosities at different pouring temperatures (PT) to prepare Al2O3(3D)/5083Al IPCs using LPIP. The results demonstrate that pore diameter of Al2O3(3D) RPC preforms and PT of liquid 5083Al significantly influence the of the infiltration. Solidification process analysis reveals that the Al2O3(3D) RPC preform with smaller pore diameters allows the lower pouring velocity of 5083Al to solidify faster compared to the preform with larger pore diameters. Al2O3(3D)/5083Al IPCs were prepared successfully from Al2O3(3D) RPC porosity of 15 PPI with liquid 5083Al at PV 0.4 m/s and PT 800 °C using LPIP, resulting in nearly fully dense composites, where both Al2O3(3D) RPCs and 5083Al interpenetrate throughout the microstructure. The infiltration and solidification defects were reduced under air pressure of 0.3 MPa (corresponding to PV of 0.4 m/s) during LPIP. Finite volume method simulations are in good agreement with experimental data, validating the suitability of the simplified model for Al2O3(3D) RPCs in the infiltration simulation.

16.
Sci Adv ; 9(43): eadg2555, 2023 10 27.
Article in English | MEDLINE | ID: mdl-37878700

ABSTRACT

Floral symmetry plays an important role in plant-pollinator interactions and may have remarkable impacts on angiosperm diversification. However, spatiotemporal patterns in floral symmetry and drivers of these patterns remain unknown. Here, using newly compiled floral symmetry (actinomorphy versus zygomorphy) data of 279,877 angiosperm species and their distributions and phylogenies, we estimated global geographic patterns and macroevolutionary dynamics of floral symmetry. We found that frequency of actinomorphic species increased with latitude, while that of zygomorphic species decreased. Solar radiation, present-day temperature, and Quaternary temperature change correlated with geographic variation in floral symmetry frequency. Evolutionary transitions from actinomorphy to zygomorphy dominated floral symmetry evolution, although the transition rate decreased with decreasing paleotemperature throughout the Cenozoic. Notably, we found that zygomorphy may not favor diversification of angiosperms as previously observed in some clades. Our study demonstrates the influence of (paleo)climate on spatiotemporal patterns in floral symmetry and challenges previous views about role of flower symmetry in angiosperm diversification.


Subject(s)
Magnoliopsida , Magnoliopsida/genetics , Phylogeny , Flowers/genetics , Climate , Temperature , Biological Evolution
17.
Blood Adv ; 7(18): 5608-5623, 2023 09 26.
Article in English | MEDLINE | ID: mdl-37522715

ABSTRACT

ETS variant 6 (ETV6) encodes a transcriptional repressor expressed in hematopoietic stem and progenitor cells (HSPCs), where it is required for adult hematopoiesis. Heterozygous pathogenic germline ETV6 variants are associated with thrombocytopenia 5 (T5), a poorly understood genetic condition resulting in thrombocytopenia and predisposition to hematologic malignancies. To elucidate how germline ETV6 variants affect HSPCs and contribute to disease, we generated a mouse model harboring an Etv6R355X loss-of-function variant, equivalent to the T5-associated variant ETV6R359X. Under homeostatic conditions, all HSPC subpopulations are present in the bone marrow (BM) of Etv6R355X/+ mice; however, these animals display shifts in the proportions and/or numbers of progenitor subtypes. To examine whether the Etv6R355X/+ mutation affects HSPC function, we performed serial competitive transplantation and observed that Etv6R355X/+ lineage-sca1+cKit+ (LSK) cells exhibit impaired reconstitution, with near complete failure to repopulate irradiated recipients by the tertiary transplant. Mechanistic studies incorporating cleavage under target and release under nuclease assay, assay for transposase accessible chromatin sequencing, and high-throughput chromosome conformation capture identify ETV6 binding at inflammatory gene loci, including multiple genes within the tumor necrosis factor (TNF) signaling pathway in ETV6-sufficient mouse and human HSPCs. Furthermore, single-cell RNA sequencing of BM cells isolated after transplantation reveals upregulation of inflammatory genes in Etv6R355X/+ progenitors when compared to Etv6+/+ counterparts. Corroborating these findings, Etv6R355X/+ HSPCs produce significantly more TNF than Etv6+/+ cells post-transplantation. We conclude that ETV6 is required to repress inflammatory gene expression in HSPCs under conditions of hematopoietic stress, and this mechanism may be critical to sustain HSPC function.


Subject(s)
Hematopoietic Stem Cells , Thrombocytopenia , Animals , Humans , Mice , Bone Marrow , Bone Marrow Cells/metabolism , Hematopoiesis/genetics , Hematopoietic Stem Cells/metabolism , Thrombocytopenia/metabolism , ETS Translocation Variant 6 Protein
18.
Nat Genet ; 55(7): 1210-1220, 2023 07.
Article in English | MEDLINE | ID: mdl-37400614

ABSTRACT

Inducing fetal hemoglobin (HbF) in red blood cells can alleviate ß-thalassemia and sickle cell disease. We compared five strategies in CD34+ hematopoietic stem and progenitor cells, using either Cas9 nuclease or adenine base editors. The most potent modification was adenine base editor generation of γ-globin -175A>G. Homozygous -175A>G edited erythroid colonies expressed 81 ± 7% HbF versus 17 ± 11% in unedited controls, whereas HbF levels were lower and more variable for two Cas9 strategies targeting a BCL11A binding motif in the γ-globin promoter or a BCL11A erythroid enhancer. The -175A>G base edit also induced HbF more potently than a Cas9 approach in red blood cells generated after transplantation of CD34+ hematopoietic stem and progenitor cells into mice. Our data suggest a strategy for potent, uniform induction of HbF and provide insights into γ-globin gene regulation. More generally, we demonstrate that diverse indels generated by Cas9 can cause unexpected phenotypic variation that can be circumvented by base editing.


Subject(s)
Anemia, Sickle Cell , beta-Thalassemia , Mice , Animals , gamma-Globins/genetics , gamma-Globins/metabolism , Gene Editing , Fetal Hemoglobin/genetics , Fetal Hemoglobin/metabolism , Anemia, Sickle Cell/genetics , Antigens, CD34/metabolism , beta-Thalassemia/genetics
19.
PeerJ ; 11: e15733, 2023.
Article in English | MEDLINE | ID: mdl-37483977

ABSTRACT

Faba bean water extract (FBW) and vitamin K3 (VK3) have been demonstrated to improve the muscle textural quality of fish. To better apply these two feed additives in commercial aquaculture setting, four experimental diets (control, commercial feed group; 15% FBW, 15% faba bean water extract group; 2.5% VK3, 2.5% vitamin K3 group; combined group, 15% faba bean water extract + 2.5% vitamin K3 group) were formulated to explore their combined effects of FBW and VK3 on the growth, health status, and muscle textural quality of grass carp. The growth performance, textural quality, intestinal characteristics, and oxidative and immune responses were analyzed on days 40, 80 and 120. The results showed that supplementation with higher doses of FBW and VK3 have no influence on growth-related parameters and immune parameters of grass carp. Notably, compared with the control, fish in the combined group had the highest textural qualities (hardness, chewiness and adhesiveness), followed by those in 15% FBW and 2.5% VK3 groups (P < 0.05). Also, FBW and VK3, to some extent, may lower antioxidative ability of grass carp, as illustrated by lower levels of GSH and CAT in 15% FBW, 2.5% VK3, and combined groups on day 120 (P < 0.05). In addition, enhanced lipase activity was observed in the 15% FBW group. Taken together, the combined supplementation of FBW and VK3 was demonstrated to be a more advanced option than their individual supplementation in a commercial setting owing to the resulting combined effects on both the textural quality and health status of grass carp.


Subject(s)
Carps , Vicia faba , Animals , Vitamin K 3 , Diet , Immunity , Oxidative Stress
20.
Food Chem ; 426: 136590, 2023 Nov 15.
Article in English | MEDLINE | ID: mdl-37331137

ABSTRACT

The present study investigated the effects of chronic heat stress (HS) on the chemical composition, oxidative stability, muscle metabolism, and meat quality of Nile tilapia (Oreochromis niloticus). Compared with the control (26 °C), chronic HS (32 °C) lowered growth performance, the contents of whole-body lipid, muscle protein, and muscle lipid. Also, HS significantly increased the contents of reactive oxygen species (ROS) and decreased antioxidative status, causing a decline in meat quality, including increased lipid and protein oxidation, the centrifugal water loss, and cooking loss as well as decreased the fragmentation index and pH at 24 h, which may be attributed to induced apoptosis by excessive ROS in Nile tilapia meat. Moreover, metabolomic analysis showed HS lowered flavor and nutritional value by affecting amino acid, lipid, and nucleotide metabolism. These results reveal that HS adversely affects oxidative stability, meat quality, flavor, and nutrition, warranting its recognition and prevention.


Subject(s)
Cichlids , Animals , Cichlids/metabolism , Reactive Oxygen Species/metabolism , Muscles/metabolism , Lipids/chemistry , Heat-Shock Response , Meat/analysis , Oxidative Stress , Animal Feed/analysis
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