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1.
Nat Prod Res ; : 1-6, 2021 May 05.
Artigo em Inglês | MEDLINE | ID: mdl-33949250

RESUMO

Two new terragine analogs (1‒2) with special succinimide and aminopentane moieties were isolated from the fermentation broth of Bacillus sp. SH-1.2-ROOT-18, an endophyte previously discovered from the root of Dendrobium officinale. The structures were elucidated base on comprehensive 1 D/2D NMR and MS data analysis. Complete NMR assignments for the first reported naturally occurring metabolite 3 was also provided.

2.
J Am Soc Mass Spectrom ; 32(5): 1180-1188, 2021 May 05.
Artigo em Inglês | MEDLINE | ID: mdl-33822609

RESUMO

Mass spectrometry imaging is well-suited to characterizing sample surfaces for their chemical content in a spatially resolved manner. However, when the surface contains small objects with significant empty spaces between them, more efficient approaches to sample acquisition are possible. Image-guided mass spectrometry (MS) enables high-throughput analysis of a diverse range of sample types, such as microbial colonies, liquid microdroplets, and others, by recognizing and analyzing selected location targets in an image. Here, we describe an imaging protocol and macroMS, an online software suite that can be used to enhance MS measurements of macroscopic samples that are imaged by a camera or a flatbed scanner. The web-based tool enables users to find and filter targets from the optical images, correct optical distortion issues for improved spatial location of selected targets, input the custom geometry files into an MS device to acquire spectra at the selected locations, and finally, perform limited data analysis and use visualization tools to aid locating samples containing compounds of interest. Using the macroMS suite, an enzyme mutant library of Saccharomyces cerevisiae and nL droplet arrays of Escherichia coli and Pseudomonas fluorescens have been assayed at a rate of ∼2 s/sample.

3.
Science ; 372(6540): 371-378, 2021 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-33888635

RESUMO

The temporal order of DNA replication [replication timing (RT)] is correlated with chromatin modifications and three-dimensional genome architecture; however, causal links have not been established, largely because of an inability to manipulate the global RT program. We show that loss of RIF1 causes near-complete elimination of the RT program by increasing heterogeneity between individual cells. RT changes are coupled with widespread alterations in chromatin modifications and genome compartmentalization. Conditional depletion of RIF1 causes replication-dependent disruption of histone modifications and alterations in genome architecture. These effects were magnified with successive cycles of altered RT. These results support models in which the timing of chromatin replication and thus assembly plays a key role in maintaining the global epigenetic state.


Assuntos
Período de Replicação do DNA , Epigênese Genética , Epigenoma , Proteínas de Ligação a Telômeros/metabolismo , Linhagem Celular , Cromatina/metabolismo , Montagem e Desmontagem da Cromatina , Replicação do DNA , Expressão Gênica , Técnicas de Inativação de Genes , Genoma Humano , Heterocromatina/metabolismo , Código das Histonas , Histonas/metabolismo , Humanos , Proteínas de Ligação a Telômeros/genética
4.
Science ; 372(6541): 512-516, 2021 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-33926954

RESUMO

DNA modifications vary in form and function but generally do not alter Watson-Crick base pairing. Diaminopurine (Z) is an exception because it completely replaces adenine and forms three hydrogen bonds with thymine in cyanophage S-2L genomic DNA. However, the biosynthesis, prevalence, and importance of Z genomes remain unexplored. Here, we report a multienzyme system that supports Z-genome synthesis. We identified dozens of globally widespread phages harboring such enzymes, and we further verified the Z genome in one of these phages, Acinetobacter phage SH-Ab 15497, by using liquid chromatography with ultraviolet and mass spectrometry. The Z genome endows phages with evolutionary advantages for evading the attack of host restriction enzymes, and the characterization of its biosynthetic pathway enables Z-DNA production on a large scale for a diverse range of applications.

5.
Asia Pac J Clin Nutr ; 30(1): 87-98, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33787044

RESUMO

BACKGROUND AND OBJECTIVES: PUFAs play critical roles in the development of nonalcoholic fatty liver disease (NAFLD). This study examined the associations between dietary n-3 and n-6 PUFA intake and NAFLD risk in a US population. METHODS AND STUDY DESIGN: Data from the National Health and Nutrition Examination Survey (NHANES) 2007-2014 was used in this cross-sectional study. Data on dietary n-3 and n-6 PUFAs were extracted through two 24-h dietary recall interviews, and the dietary n-3 and n-6 PUFA intakes were adjusted by weight. NAFLD was defined based on the US fatty liver index (FLI) value ≥30. Multivariable logistic regression models and restricted cubic spline models were applied to investigate the associations between dietary n-3 and n-6 PUFA intakes and NAFLD risk. RESULTS: Dietary n-3 and n-6 PUFA intakes were inversely associated with NAFLD risk. The multivariable-adjusted OR (95% CI) of NAFLD for the highest versus lowest quartile of dietary n-3 and n-6 PUFA intakes was 0.24 (0.17-0.35) and 0.18 (0.13-0.26), respectively. In stratified analyses by sex and age, the negative associations between dietary n-3 and n-6 PUFA intakes and NAFLD risk were significant in men, women, and individuals younger and older than 45 years. Dose-response analyses indicated that NAFLD risk was associated with dietary n-3 and n-6 PUFA intakes in a nonlinear manner. CONCLUSIONS: Dietary n-3 and n-6 PUFA intakes were inversely associated with NAFLD risk in US adults.

6.
BMJ Open ; 11(3): e041578, 2021 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-33664069

RESUMO

OBJECTIVES: To assess the prevalence of frailty and identify predictors of frailty among Chinese community-dwelling older adults with type 2 diabetes. DESIGN: A cross-sectional design. SETTING: Two community health centres in central China. PARTICIPANTS: 291 community-dwelling older adults aged ≥65 years with type 2 diabetes. MAIN OUTCOME MEASURES: Data were collected via face-to-face interviews, anthropometric measurements, laboratory tests and community health files. The main outcome measure was frailty, as assessed by the frailty phenotype criteria. The multivariate logistic regression model was used to identify the predictors of frailty. RESULTS: The prevalence of prefrailty and frailty were 51.5% and 19.2%, respectively. The significant predictors of frailty included alcohol drinking (ex-drinker) (OR 4.461, 95% CI 1.079 to 18.438), glycated haemoglobin (OR 1.434, 95% CI 1.045 to 1.968), nutritional status (malnutrition risk/malnutrition) (OR 8.062, 95% CI 2.470 to 26.317), depressive symptoms (OR 1.438, 95% CI 1.166 to 1.773) and exercise behaviour (OR 0.796, 95% CI 0.716 to 0.884). CONCLUSIONS: A high prevalence of frailty was found among older adults with type 2 diabetes in the Chinese community. Frailty identification and multifaceted interventions should be developed for this population, taking into consideration proper glycaemic control, nutritional instruction, depressive symptoms improvement and enhancement of self-care behaviours.

7.
Mol Genet Genomic Med ; : e1640, 2021 Mar 03.
Artigo em Inglês | MEDLINE | ID: mdl-33656256

RESUMO

BACKGROUND: Creatine transporter deficiency is an inborn error of metabolism caused by a deficiency in the creatine transporter protein encoded by the SLC6A8 gene. Previous treatment with creatine supplementation, either alone or in combination with creatine precursors (arginine or glycine), has been attempted; the efficacy of therapy, however, remains controversial. METHODS AND RESULTS: To analyze the treatment efficacy of high-dose creatine supplementation on creatine transporter deficiency, we reported a child diagnosed with creatine transporter deficiency, who was treated with a conventional dose of creatine (400 mg/kg/d) for 1 month, then twice the dose (800 mg/kg/d) for 2 months, and finally 3 times the dose (1200 mg/kg/d) for 3 months. The patient tolerated the treatment well and showed improvements in muscle mass and strength when the creatine dose was gradually increased to 1200 mg/kg/d. However, when assessed by proton magnetic resonance spectroscopy (H-MRS), the brain creatine concentration did not increase, and there was no improvement in speech and neurodevelopmental symptoms. CONCLUSION: We conclude that high-dose creatine supplementation (1200 mg/kg/d) alone improved muscular symptoms, but did not improve cognitive symptoms and brain creatine concentration assessed using H-MRS. Therefore, new treatment strategies are required for the management of creatine transporter deficiency.

8.
Metab Eng ; 2021 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-33713797

RESUMO

S-Adenosyl-L-methionine (SAM) is an important intracellular metabolite and widely used for treatment of various diseases. Although high level production of SAM had been achieved in yeast, novel metabolic engineering strategies are needed to further enhance SAM production for industrial applications. Here genome-scale engineering (GSE) was performed to identify new targets for SAM overproduction using the multi-functional genome-wide CRISPR (MAGIC) system, and the effects of these newly identified targets were further validated in industrial yeast strains. After 3 rounds of FACS screening and characterization, numerous novel targets for enhancing SAM production were identified. In addition, transcriptomic and metabolomic analyses were performed to investigate the molecular mechanisms for enhanced SAM accumulation. The best combination (upregulation of SNZ3, RFC4, and RPS18B) improved SAM productivity by 2.2-fold and 1.6-fold in laboratory and industrial yeast strains, respectively. Using GSE of laboratory yeast strains to guide industrial yeast strain engineering presents an effective approach to design microbial cell factories for industrial applications.

9.
Adv Biol (Weinh) ; 5(3): e2000252, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33729696

RESUMO

The construction of a host-orthogonal genetic system can not only minimize the impact of host-specific nuances on fine-tuning of gene expression, but also expand cellular functions such as in vivo continuous evolution of genes based on an error-prone DNA polymerase. It represents an emerging powerful approach for making biology easier to engineer. In this review, the recent advances are described on the design of genetic systems that can be stably inherited in the host cells and are responsible for important biological processes including DNA replication, RNA transcription, protein translation, and gene regulation. Their applications in synthetic biology are summarized and the future challenges and opportunities are discussed in developing such systems.

10.
Soft comput ; : 1-9, 2021 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-33613098

RESUMO

The severe situation caused by THE COVID-19 epidemic has not only hindered the steady development of social economy, but also had a great impact on the development of e-commerce logistics. For e-commerce enterprises, logistics cost is an important factor that affects the operation effect and consumer experience. Based on this, this study proposes cost control methods for e-commerce logistics in the prevention and control of COVID-19 environment. In this study, based on the actual environment of COVID-19 prevention and control, the logistics cost algorithm during the epidemic period is designed on the basis of the analysis of the influencing factors of e-commerce logistics cost, and the cross-border logistics strategy that conforms to the background of COVID-19 prevention and control and the demand of e-commerce logistics cost control is developed to better reduce the operating cost of logistics enterprises. The e-commerce logistics cost control method proposed in this article is effective in the prevention and control of new crown pneumonia, and the overall actual cost is within the budgeted cost range. The experimental results prove that the e-commerce logistics cost control method designed in this paper can help e-commerce companies achieve good economic benefits and proves that it has higher application advantages.

11.
CRISPR J ; 4(1): 13-15, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33616444
12.
Curr Opin Biotechnol ; 67: iii-v, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33581998

Assuntos
Biotecnologia
13.
Curr Med Sci ; 41(1): 31-38, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33582902

RESUMO

The outbreak of coronavirus disease 2019 (COVID-19) posed an unprecedented threat to health care providers (HCPs) in Wuhan, China, especially for nurses who were frequently exposed to infected or suspected patients. Limited information was available about the working experience of nurses in fighting against the pandemic. To learn the physical and psychological responses of nurses during the pandemic and explore the potential determinants, we conducted a large-scale survey in Wuhan. This multicenter cross-sectional study enrolled 5521 nurses who worked in designated hospitals, mobile cabins, or shelters during the pandemic. A structured online questionnaire was distributed to assess the physical discomforts, emotional distress and cognitive reactions of nurses at work, and the log-binomial regression analysis was performed to explore potential determinants. A considerable proportion of nurses had symptoms of physical discomforts [3677 (66.6%)] and emotional distress [4721 (85.5%)]. Nurses who were directly involved in the care of patients (i.e., care for severe patients: RR, 2.35; 95% CI, 1.95-2.84), with irregular work schedules (RR, 2.36; 95% CI, 1.95-2.87), and working overtime (RR, 1.34; 95% CI, 1.08-1.65) were at a higher risk for physical discomforts. Nurses who were directly involved in the care of patients (i.e., care for severe patients: RR, 1.78; 95% CI, 1.40-2.29), with irregular work schedules (RR, 3.39; 95% CI, 2.43-4.73), and working overtime (RR, 1.51; 95% CI, 1.12-2.04) were at a higher risk for emotional distress. Therefore, formulating reasonable work schedules and improving workforce systems are necessary to alleviate the physical and emotional distress of nurses during the pandemic.


Assuntos
/enfermagem , Enfermeiras e Enfermeiros/psicologia , Estresse Ocupacional/psicologia , Carga de Trabalho/psicologia , Adulto , China , Estudos Transversais , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Inquéritos e Questionários
14.
J Colloid Interface Sci ; 590: 365-374, 2021 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-33549895

RESUMO

Present work reports preparation of colloidal single/few layer Ti3C2Tx MXene flakes using minimally intensive layer delamination (MILD) method for rapid electroanalytical screening of carbamate pesticides. Lithium fluoride salt and hydrochloric acid (7.5 M LiF/9M HCl) was used to produce in-situ generated HF as etchant to remove Al successfully from Ti3AlC2 MAX phase. Unlike the clay method (5 M LiF/6M HCl), this methodology simplified Ti3C2Tx synthesis protocol resulting in Li+ ions intercalated Ti3C2Tx which was delaminated without further sonication. The delaminated Ti3C2Tx flakes were found to be single/few layered sheets with mostly -OH and -O terminated surface groups. The characteristic 002 peak observed in X-ray diffraction (XRD) at 2θ = 6.4° with interplaner distance of 1.1137 nm suggested broadening of the peak attributed to the presence of Li+ ions between Ti3C2Tx flakes. Delaminated Ti3C2Tx flakes were utilized as working electrode which demonstrated simultaneous and selective detection of carbamate pesticides methiocarb and diethofencarb by voltammetry. The oxidation peaks of the two pesticides were well separated by a potential difference of 0.35 V in 0.5 M H2SO4 and DPV detection limits were calculated as 0.19 µg mL-1 and 0.46 µg mL-1 for methiocarb and diethofencarb respectively. Ti3C2Tx flakes as electrochemical sensor exhibited long term stability and acceptable recoveries in real sample for environmental applications.

15.
ACS Synth Biol ; 10(3): 429-446, 2021 03 19.
Artigo em Inglês | MEDLINE | ID: mdl-33596056

RESUMO

Inserting custom designed DNA sequences into the mammalian genome plays an essential role in synthetic biology. In particular, the ability to introduce foreign DNA in a site-specific manner offers numerous advantages over random DNA integration. In this review, we focus on two mechanistically distinct systems that have been widely adopted for targeted DNA insertion in mammalian cells, the CRISPR/Cas9 system and site-specific recombinases. The CRISPR/Cas9 system has revolutionized the genome engineering field thanks to its high programmability and ease of use. However, due to its dependence on linearized DNA donor and endogenous cellular pathways to repair the induced double-strand break, CRISPR/Cas9-mediated DNA insertion still faces limitations such as small insert size, and undesired editing outcomes via error-prone repair pathways. In contrast, site-specific recombinases, in particular the Serine integrases, demonstrate large-cargo capability and no dependence on cellular repair pathways for DNA integration. Here we first describe recent advances in improving the overall efficacy of CRISPR/Cas9-based methods for DNA insertion. Moreover, we highlight the advantages of site-specific recombinases over CRISPR/Cas9 in the context of targeted DNA integration, with a special focus on the recent development of programmable recombinases. We conclude by discussing the importance of protein engineering to further expand the current toolkit for targeted DNA insertion in mammalian cells.

16.
Nat Commun ; 12(1): 1171, 2021 02 19.
Artigo em Inglês | MEDLINE | ID: mdl-33608525

RESUMO

Direct cloning represents the most efficient strategy to access the vast number of uncharacterized natural product biosynthetic gene clusters (BGCs) for the discovery of novel bioactive compounds. However, due to their large size, repetitive nature, or high GC-content, large-scale cloning of these BGCs remains an overwhelming challenge. Here, we report a scalable direct cloning method named Cas12a-assisted precise targeted cloning using in vivo Cre-lox recombination (CAPTURE) which consists of Cas12a digestion, a DNA assembly approach termed T4 polymerase exo + fill-in DNA assembly, and Cre-lox in vivo DNA circularization. We apply this method to clone 47 BGCs ranging from 10 to 113 kb from both Actinomycetes and Bacilli with ~100% efficiency. Heterologous expression of cloned BGCs leads to the discovery of 15 previously uncharacterized natural products including six cyclic head-to-tail heterodimers with a unique 5/6/6/6/5 pentacyclic carbon skeleton, designated as bipentaromycins A-F. Four of the bipentaromycins show strong antimicrobial activity to both Gram-positive and Gram-negative bacteria such as methicillin-resistant Staphylococcus aureus, vancomycinresistant Enterococcus faecium, and bioweapon Bacillus anthracis. Due to its robustness and efficiency, our direct cloning method coupled with heterologous expression provides an effective strategy for large-scale discovery of novel natural products.


Assuntos
Proteínas de Bactérias/genética , Proteínas Associadas a CRISPR/genética , Clonagem Molecular/métodos , Endodesoxirribonucleases/genética , Integrases/genética , Recombinação Genética , Actinobacteria/genética , Actinobacteria/metabolismo , Produtos Biológicos/metabolismo , Vias Biossintéticas/genética , DNA Bacteriano , Enterococcus faecium/genética , Bactérias Gram-Negativas/genética , Bactérias Gram-Negativas/metabolismo , Bactérias Gram-Positivas/genética , Bactérias Gram-Positivas/metabolismo , Staphylococcus aureus Resistente à Meticilina/genética , Família Multigênica , Streptomyces/genética
17.
Nat Struct Mol Biol ; 28(2): 152-161, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33398174

RESUMO

The CCCTC-binding factor (CTCF) works together with the cohesin complex to drive the formation of chromatin loops and topologically associating domains, but its role in gene regulation has not been fully defined. Here, we investigated the effects of acute CTCF loss on chromatin architecture and transcriptional programs in mouse embryonic stem cells undergoing differentiation to neural precursor cells. We identified CTCF-dependent enhancer-promoter contacts genome-wide and found that they disproportionately affect genes that are bound by CTCF at the promoter and are dependent on long-distance enhancers. Disruption of promoter-proximal CTCF binding reduced both long-range enhancer-promoter contacts and transcription, which were restored by artificial tethering of CTCF to the promoter. Promoter-proximal CTCF binding is correlated with the transcription of over 2,000 genes across a diverse set of adult tissues. Taken together, the results of our study show that CTCF binding to promoters may promote long-distance enhancer-dependent transcription at specific genes in diverse cell types.


Assuntos
Fator de Ligação a CCCTC/metabolismo , Cromatina/metabolismo , Células-Tronco Embrionárias Murinas/metabolismo , Células-Tronco Neurais/metabolismo , Animais , Sítios de Ligação , Linhagem Celular , Elementos Facilitadores Genéticos , Regulação da Expressão Gênica , Camundongos , Células-Tronco Embrionárias Murinas/citologia , Células-Tronco Neurais/citologia , Regiões Promotoras Genéticas , Ligação Proteica , Ativação Transcricional
18.
Cell Rep ; 34(1): 108594, 2021 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-33406419

RESUMO

Skeletal muscle regeneration after injury is essential for maintaining muscle function throughout aging. ARHGEF3, a RhoA/B-specific GEF, negatively regulates myoblast differentiation through Akt signaling independently of its GEF activity in vitro. Here, we report ARHGEF3's role in skeletal muscle regeneration revealed by ARHGEF3-KO mice. These mice exhibit indiscernible phenotype under basal conditions. Upon acute injury, however, ARHGEF3 deficiency enhances the mass/fiber size and function of regenerating muscles in both young and regeneration-defective middle-aged mice. Surprisingly, these effects occur independently of Akt but via the GEF activity of ARHGEF3. Consistently, overexpression of ARHGEF3 inhibits muscle regeneration in a Rho-associated kinase-dependent manner. We further show that ARHGEF3 KO promotes muscle regeneration through activation of autophagy, a process that is also critical for maintaining muscle strength. Accordingly, ARHGEF3 depletion in old mice prevents muscle weakness by restoring autophagy. Taken together, our findings identify a link between ARHGEF3 and autophagy-related muscle pathophysiology.

19.
Environ Pollut ; 271: 116316, 2021 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-33385893

RESUMO

Large amounts of antibiotics/disinfectants are used in the farming of ornamental fish so as to prevent and treat bacterial infection. This may exert considerable selection pressures on the prevalence and propagation of antibiotic resistance genes (ARGs). However, the levels of ARGs and their potential prevalence mechanism in the wastewater of the ornamental fish industry remains unclear. In this work, wastewater is collected from a representative ornamental fish market (OFM) that is located at the northern China to study the occurrence and abundance of 21 ARGs and 2 integrase genes. Results indicated that 15 different ARGs and 2 integrase genes are existent and prevalent in the wastewater of OFM, whereby concentrations range from 2.01 to 10.34 copies/L. Proteobacteria, Bacteroidetes, Verrucomicrobia, and Firmicutes are the predominant phyla in the wastewater samples. 17 species of human opportunistic pathogens are present with relative abundance of up to 0.01%, which suggests a considerable risk of pathogens acquiring and disseminating ARGs. Moreover, oxytetracycline, ciprofloxacin, norfloxacin, sulfadiazine, and chloramphenicol are most frequently detected in wastewater, with concentrations of up to 1150, 877, 514, 1970, and 1700 ng/L, respectively. Notably, good correlations have been determined among ARGs and antibiotics, non-antibiotic environmental factors in wastewater of OFM. This current study reveals, for the first time, that OFM is a previously unperceived reservoir for ARG prevalence in aquatic environment and water environmental factors (particularly antibiotics), and their induced shifts in the microbial communities are the key factors for distribution of ARGs in OFM.


Assuntos
Antibacterianos , Águas Residuárias , Animais , Antibacterianos/farmacologia , China , Resistência Microbiana a Medicamentos/genética , Genes Bacterianos , Humanos , Prevalência
20.
Nat Commun ; 12(1): 606, 2021 01 27.
Artigo em Inglês | MEDLINE | ID: mdl-33504770

RESUMO

Genome editing critically relies on selective recognition of target sites. However, despite recent progress, the underlying search mechanism of genome-editing proteins is not fully understood in the context of cellular chromatin environments. Here, we use single-molecule imaging in live cells to directly study the behavior of CRISPR/Cas9 and TALEN. Our single-molecule imaging of genome-editing proteins reveals that Cas9 is less efficient in heterochromatin than TALEN because Cas9 becomes encumbered by local searches on non-specific sites in these regions. We find up to a fivefold increase in editing efficiency for TALEN compared to Cas9 in heterochromatin regions. Overall, our results show that Cas9 and TALEN use a combination of 3-D and local searches to identify target sites, and the nanoscopic granularity of local search determines the editing outcomes of the genome-editing proteins. Taken together, our results suggest that TALEN is a more efficient gene-editing tool than Cas9 for applications in heterochromatin.


Assuntos
Proteína 9 Associada à CRISPR/metabolismo , Edição de Genes , Heterocromatina/metabolismo , Nucleases dos Efetores Semelhantes a Ativadores de Transcrição/metabolismo , Proteínas de Ligação a DNA/metabolismo , Células HEK293 , Células HeLa , Humanos , Imagem Individual de Molécula
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