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1.
Nucleic Acids Res ; 52(12): 7367-7383, 2024 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-38808673

RESUMO

Temperature is an important control factor for biologics biomanufacturing in precision fermentation. Here, we explored a highly responsive low temperature-inducible genetic system (LowTempGAL) in the model yeast Saccharomyces cerevisiae. Two temperature biosensors, a heat-inducible degron and a heat-inducible protein aggregation domain, were used to regulate the GAL activator Gal4p, rendering the leaky LowTempGAL systems. Boolean-type induction was achieved by implementing a second-layer control through low-temperature-mediated repression on GAL repressor gene GAL80, but suffered delayed response to low-temperature triggers and a weak response at 30°C. Application potentials were validated for protein and small molecule production. Proteomics analysis suggested that residual Gal80p and Gal4p insufficiency caused suboptimal induction. 'Turbo' mechanisms were engineered through incorporating a basal Gal4p expression and a galactose-independent Gal80p-supressing Gal3p mutant (Gal3Cp). Varying Gal3Cp configurations, we deployed the LowTempGAL systems capable for a rapid stringent high-level induction upon the shift from a high temperature (37-33°C) to a low temperature (≤30°C). Overall, we present a synthetic biology procedure that leverages 'leaky' biosensors to deploy highly responsive Boolean-type genetic circuits. The key lies in optimisation of the intricate layout of the multi-factor system. The LowTempGAL systems may be applicable in non-conventional yeast platforms for precision biomanufacturing.


Assuntos
Regulação Fúngica da Expressão Gênica , Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae , Fatores de Transcrição , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Fatores de Transcrição/metabolismo , Fatores de Transcrição/genética , Proteínas Repressoras/metabolismo , Proteínas Repressoras/genética , Proteínas de Ligação a DNA/metabolismo , Proteínas de Ligação a DNA/genética , Temperatura Baixa , Galactose/metabolismo , Técnicas Biossensoriais
2.
Artigo em Inglês | MEDLINE | ID: mdl-38719166

RESUMO

OBJECTIVE: To investigate the effects of physiotherapeutic scoliosis-specific exercises (PSSE) on coronal, horizontal, and sagittal deformities of the spine in adolescent idiopathic scoliosis (AIS) as well as how curve severity, intervention duration, and intervention type could modify these effects. DATA SOURCES: Data sources included PubMed, Web of Science, Embase, Cochrane Library, and Scopus databases, which were searched from their inception to September 5, 2023. STUDY SELECTION: Clinical controlled trials reporting the effects of PSSE on the Cobb angle, angle of trunk rotation (ATR), thoracic kyphosis (TK), or lumbar lordosis in patients with AIS aged 10-18 years. The experimental groups received PSSE; the control groups received standard care (observation or bracing) or conventional exercise such as core stabilization exercise, Pilates, proprioceptive neuromuscular facilitation, and other nonspecific exercises. DATA EXTRACTION: Two researchers independently extracted key information from eligible studies. The quality of the studies was assessed using the Cochrane Handbook version 5.1.0 risk of bias assessment and the JBI Center for Evidence-Based Health Care (2016) of quasi-experimental research authenticity assessment tool. The level and certainty of evidence were rated according to the Grading of Recommendations, Assessment, Development, and Evaluation framework. We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. The protocol for this study was registered in PROSPERO (CRD42023404996). DATA SYNTHESIS: Twelve randomized controlled trials (RCTs) and 5 non-RCTs were meta-analyzed separately. The results indicated that compared with other nonsurgical management, PSSE significantly improved the Cobb angle, ATR, and TK, whereas the lumbar lordosis improvement was not statistically significant. Additionally, the efficacy of PSSE on Cobb angle was not significant in patients with curve severity ≥30° compared with controls. Nevertheless, the pooled effect of PSSE on Cobb angle was not significantly modified by intervention duration and intervention type and that on ATR was not significantly modified by intervention duration. The overall quality of evidence according to Grading of Recommendations, Assessment, Development, and Evaluation was moderate to low for RCT and very low for non-RCT. CONCLUSIONS: PSSE exhibited positive benefits on the Cobb angle, ATR, and TK in patients with AIS compared with other nonsurgical therapies. In addition, the effectiveness of PSSE may be independent of intervention duration and intervention type but may be influenced by the initial Cobb angle. However, more RCTs are needed in the future to validate the efficacy of PSSE in moderate AIS with a mean Cobb angle ≥30°. Current evidence is limited by inconsistent control group interventions and small sample size of the studies.

3.
Metab Eng ; 77: 143-151, 2023 05.
Artigo em Inglês | MEDLINE | ID: mdl-36990382

RESUMO

The end-to-end fusion of enzymes that catalyse successive steps in a reaction pathway is a metabolic engineering strategy that has been successfully applied in a variety of pathways and is particularly common in terpene bioproduction. Despite its popularity, limited work has been done to interrogate the mechanism of metabolic enhancement from enzyme fusion. We observed a remarkable >110-fold improvement in nerolidol production upon translational fusion of nerolidol synthase (a sesquiterpene synthase) to farnesyl diphosphate synthase. This delivered a titre increase from 29.6 mg/L up to 4.2 g/L nerolidol in a single engineering step. Whole-cell proteomic analysis revealed that nerolidol synthase levels in the fusion strains were greatly elevated compared to the non-fusion control. Similarly, the fusion of nerolidol synthase to non-catalytic domains also produced comparable increases in titre, which coincided with improved enzyme expression. When farnesyl diphosphate synthase was fused to other terpene synthases, we observed more modest improvements in terpene titre (1.9- and 3.8-fold), corresponding with increases of a similar magnitude in terpene synthase levels. Our data demonstrate that increased in vivo enzyme levels - resulting from improved expression and/or improved protein stability - is a major driver of catalytic enhancement from enzyme fusion.


Assuntos
Alquil e Aril Transferases , Sesquiterpenos , Geraniltranstransferase/genética , Proteômica , Sesquiterpenos/metabolismo , Alquil e Aril Transferases/genética , Terpenos
4.
Microb Ecol ; 86(4): 3111-3127, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-37878052

RESUMO

Intestinal microbiota plays an important role in promoting digestion, metabolism, and immunity. Intestinal microbiota and fatty acids are important indicators to evaluate the health and nutritional composition of Procambarus clarkii. They have been shown to be strongly influence by environmental and genetic factors. However, it is not clear whether environmental factors have a greater impact on the intestinal microbiota and fatty acid composition of crayfish. The link between the intestinal microbial communities and fatty acid (FA) compositions of red swamp crayfish from different geographical has not yet been studied. Thus, the current paper focuses on the influence of different environments on the fatty acids in muscles of crayfish and the possible existence between gut microbiota and fatty acids. Therefore, in this study, we compared the fatty acid compositions and intestinal microbiota of five crayfish populations from different geographical locations. The results were further analyzed to determine whether there is a relationship between geographical location, fatty acid compositions and intestinal microbiota. The gut microbial communities of the crayfish populations were characterized using 16S rRNA high-throughput gene sequencing. The results showed that there were significant differences in FA compositions of crayfish populations from different geographical locations. A similar trend was observed in the gut microbiome, which also varied significantly according to geographic location. Interestingly, the analysis revealed that there was a relationship between fatty acid compositions and intestinal microbes, revealed by alpha diversity analysis and cluster analysis. However, further studies of the interactions between the P. clarkii gut microbiota and biochemical composition are needed, which will ultimately reveal the complexity of microbial ecosystems with potential applications in aquaculture and species conservation.


Assuntos
Microbioma Gastrointestinal , Microbiota , Animais , Astacoidea/genética , RNA Ribossômico 16S/genética , Ácidos Graxos
5.
Plant Cell Rep ; 42(5): 859-877, 2023 May.
Artigo em Inglês | MEDLINE | ID: mdl-36788135

RESUMO

SINA (Seven in absentia) proteins in the subtype of E3 ubiquitin ligase family play a crucial role in plant growth and development. However, their functions in response to salt and osmotic stresses in oil crops are still largely unknown. In this study, a total number of 23 BnaSINAs were identified in the rapeseed genome. Chromosome location and collinear relationship analyses revealed that they were unevenly distributed on 13 chromosomes, and have gone through 22 segmental duplication events under purifying selection. Phylogenetic and gene structural analyses indicated that they belonged to five main groups, and those in the same subgroup showed similar gene structure. All BnaSINAs were predicted to form homo- or heterodimers. Except BnaSINA7, BnaSINA11, BnaSINA17 and BnaSINA18, which lacked the N-terminal RING finger, all BnaSINAs contained a conserved C-terminal SINA domain, a typical structural feature of the RING-type E3 ligase family. Transcriptional expression analyses demonstrated that most BnaSINAs were ubiquitously expressed in roots, stems, leaves, flowers, pods and seeds, and all were responsive to salt and osmotic stresses. Further, yeast two-hybrid and Arabidopsis mutant complementation analyses demonstrated that BnaSINA4 interacted with BnaSINA17 to form heterodimer, and expression of BnaSINA17 in the Arabidopsis sina2 mutant restored its growth resistance to salt and osmotic stresses. Our findings provide an important genetic foundation for the functional elucidation of BnaSINAs and a novel gene resource for the breeding of new oil crop cultivars with improved abiotic stress resistance.


Assuntos
Arabidopsis , Brassica napus , Ubiquitina-Proteína Ligases/genética , Ubiquitina-Proteína Ligases/metabolismo , Arabidopsis/genética , Brassica napus/genética , Brassica napus/metabolismo , Pressão Osmótica , Ubiquitina/genética , Ubiquitina/metabolismo , Filogenia , Melhoramento Vegetal , Cloreto de Sódio/farmacologia , Cloreto de Sódio/metabolismo , Estresse Fisiológico/genética , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/metabolismo
6.
Int J Mol Sci ; 24(13)2023 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-37446297

RESUMO

Raffinose synthase (Rafs) is an important enzyme in the synthesis pathway of raffinose from sucrose and galactinol in higher plants and is involved in the regulation of seed development and plant responses to abiotic stresses. In this study, we analyzed the Rafs families and profiled their alternative splicing patterns at the genome-wide scale from 10 grass species representing crops and grasses. A total of 73 Rafs genes were identified from grass species such as rice, maize, foxtail millet, and switchgrass. These Rafs genes were assigned to six groups based the phylogenetic analysis. We compared the gene structures, protein domains, and expression patterns of Rafs genes, and also unraveled the alternative transcripts of them. In addition, different conserved sequences were observed at these putative splice sites among grass species. The subcellular localization of PvRafs5 suggested that the Rafs gene was expressed in the cytoplasm or cell membrane. Our findings provide comprehensive knowledge of the Rafs families in terms of genes and proteins, which will facilitate further functional characterization in grass species in response to abiotic stress.


Assuntos
Processamento Alternativo , Setaria (Planta) , Humanos , Filogenia , Galactosiltransferases/genética , Galactosiltransferases/metabolismo , Estresse Fisiológico/genética , Setaria (Planta)/genética , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo
7.
Biochemistry ; 56(21): 2747-2757, 2017 05 30.
Artigo em Inglês | MEDLINE | ID: mdl-28459538

RESUMO

Ras/Rap1-specific endopeptidase (RRSP) is a cytotoxic effector domain of the multifunctional autoprocessing repeats-in-toxin (MARTX) toxin of highly virulent strains of Vibrio vulnificus. RRSP blocks RAS-MAPK kinase signaling by cleaving Ras and Rap1 within the switch I region between Y32 and D33. Although the RRSP processing site is highly conserved among small GTPases, only Ras and Rap1 have been identified as proteolytic substrates. Here we report that residues Y32 and D33 at the scissile bond play an important role in RRSP substrate recognition, while the nucleotide state of Ras has an only minimal effect. In addition, substrate specificity is generated by residues across the entire switch I region. Indeed, swapping the Ras switch I region into either RalA or RhoA, GTPases that are not recognized by RRSP, generated chimeras that are substrates of RRSP. However, a difference in the processing efficiency of Ras switch I in the context of Ras, RalA, or RhoA indicates that protein regions outside Ras switch I also contribute to efficient RRSP substrate recognition. Moreover, we show that synthetic peptides corresponding to the Ras and Rap1, but not RalA, switch I regions are cleaved by RRSP, demonstrating sequence-specific substrate recognition. In conclusion, this work demonstrates that the GTPase recognition of RRSP is independent of the nucleotide state and is mainly driven by the Ras and Rap1 switch I loop and also influenced by additional protein-protein interactions, increasing the substrate specificity of RRSP.


Assuntos
Toxinas Bacterianas/química , Toxinas Bacterianas/metabolismo , Endopeptidases/química , Endopeptidases/metabolismo , Vibrio vulnificus/enzimologia , Proteínas rap1 de Ligação ao GTP/metabolismo , Proteínas ras/metabolismo , Humanos , Modelos Moleculares , Especificidade por Substrato , Proteínas rap1 de Ligação ao GTP/química , Proteínas ras/química
8.
Molecules ; 21(5)2016 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-27213305

RESUMO

To solve the problem of transfection efficiency vs. cytotoxicity and tumor-targeting ability when polyethylenimine (PEI) was used as a nonviral gene delivery vector, new degradable PEI polymers were synthesized via cross-linking low-molecular-weight PEI with Pluronic P123 and then further coupled with a targeting peptide R4 (RGD) and a bifunctional R11 (RGD-NLS), which were termed as P123-PEI-R4 and P123-PEI-R11, respectively. Agarose gel electrophoresis showed that both P123-PEI-R4 and P123-PEI-R11 efficaciously condense plasmid DNA at a polymer-to-pDNA w/w ratio of 3.0 and 0.4, respectively. The polyplexes were stable in the presence of serum and could protect plasmid DNA against DNaseI. They had uniform spherical nanoparticles with appropriate sizes around 100-280 nm and zeta-potentials about +40 mV. Furthermore, in vitro experiments showed that these polyplexes had lower cytotoxicity at any concentration compared with PEI 25 kDa, thus giving promise to high transfection efficiency as compared with another P123-PEI derivate conjugated with trifunctional peptide RGD-TAT-NLS (P123-PEI-R18). More importantly, compared with the other polymers, P123-PEI-R11 showed the highest transfection efficiency with relatively lower cytotoxicity at any concentration, indicating that the new synthetic polymer P123-PEI-R11 could be used as a safe and efficient gene deliver vector.


Assuntos
Técnicas de Transferência de Genes , Terapia Genética/métodos , Sinais de Localização Nuclear/genética , Oligopeptídeos/genética , Polietilenoimina/química , DNA , Eletroforese em Gel de Ágar , Proteínas de Fluorescência Verde , Células HeLa , Humanos , Peso Molecular , Nanopartículas/química , Nanopartículas/uso terapêutico , Sinais de Localização Nuclear/química , Sinais de Localização Nuclear/uso terapêutico , Oligopeptídeos/química , Oligopeptídeos/uso terapêutico , Plasmídeos/química , Plasmídeos/genética , Polietilenoimina/uso terapêutico , Polímeros/química , Polímeros/uso terapêutico , Transfecção/métodos
9.
bioRxiv ; 2024 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-38895220

RESUMO

BIT is a novel Bayesian hierarchical model capable of predicting transcriptional regulators (TRs) from the input of user-provided epigenomic regions. TRs are critical molecules in transcriptional regulation. Many diseases and cancers are linked to the dysfunction of TRs. Knowing TRs in certain biological process can help find new biomarkers or therapeutic targets. Thus, BIT formulates a novel Bayesian hierarchical model with the Pólya-gamma data augmentation strategy. Based on collected ChIP-seq datasets, BIT can identify TRs responsible for the genome-wide binding pattern within the user-provided epigenomic regions. BIT has been validated by using a simulation study and three applications.

10.
iScience ; 27(6): 109841, 2024 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-38765249

RESUMO

In recent years, two-dimensional (2D) materials have been extensively studied and applied in the field of catalysis on account of their high specific surface areas, high exposure of metal active sites, and readily tunable structures. This article introduces various 2D materials (including materials composed of a few atomic layers) and the related synthesis methods and discusses their catalytic performances for hydrogen fuel cells, in particular, for oxygen reduction reaction and hydrogen oxidation reaction. At the end of this review, the advantages and current challenges of 2D materials are summarized, and the prospects of 2D electrocatalytic materials are proposed.

11.
bioRxiv ; 2024 Mar 22.
Artigo em Inglês | MEDLINE | ID: mdl-38562775

RESUMO

This article provides an in-depth review of computational methods for predicting transcriptional regulators with query gene sets. Identification of transcriptional regulators is of utmost importance in many biological applications, including but not limited to elucidating biological development mechanisms, identifying key disease genes, and predicting therapeutic targets. Various computational methods based on next-generation sequencing (NGS) data have been developed in the past decade, yet no systematic evaluation of NGS-based methods has been offered. We classified these methods into two categories based on shared characteristics, namely library-based and region-based methods. We further conducted benchmark studies to evaluate the accuracy, sensitivity, coverage, and usability of NGS-based methods with molecular experimental datasets. Results show that BART, ChIP-Atlas, and Lisa have relatively better performance. Besides, we point out the limitations of NGS-based methods and explore potential directions for further improvement. Key points: An introduction to available computational methods for predicting functional TRs from a query gene set.A detailed walk-through along with practical concerns and limitations.A systematic benchmark of NGS-based methods in terms of accuracy, sensitivity, coverage, and usability, using 570 TR perturbation-derived gene sets.NGS-based methods outperform motif-based methods. Among NGS methods, those utilizing larger databases and adopting region-centric approaches demonstrate favorable performance. BART, ChIP-Atlas, and Lisa are recommended as these methods have overall better performance in evaluated scenarios.

12.
Materials (Basel) ; 17(3)2024 Feb 02.
Artigo em Inglês | MEDLINE | ID: mdl-38591570

RESUMO

Hydration plays a crucial role in cement composites, but the traditional methods for measuring hydration heat face several limitations. In this study, we propose a machine learning-based approach to predict hydration heat at specific time points for three types of cement composites: ordinary Portland cement pastes, fly ash cement pastes, and fly ash-metakaolin cement composites. By adjusting the model architecture and analyzing the datasets, we demonstrate that the optimized artificial neural network model not only performs well during the learning process but also accurately predicts hydration heat for various cement composites from an extra dataset. This approach offers a more efficient way to measure hydration heat for cement composites, reducing the need for labor- and time-intensive sample preparation and testing. Furthermore, it opens up possibilities for applying similar machine learning approaches to predict other properties of cement composites, contributing to efficient cement research and production.

13.
Front Neurol ; 15: 1325960, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38721119

RESUMO

Objective: Inflammation is a central driver of atherogenesis and eventual plaque rupture. This study aimed to evaluate the association between residual inflammatory risk (RIR) and vulnerable plaques in the carotid artery in patients with ischemic stroke. Methods: Patients with acute ischemic stroke were enrolled from January 2021 to July 2022. They were divided into four groups: RIR only (LDL-C <2.6 mmol/L and hsCRP ≥2 mg/L), residual cholesterol risk (RCR) only (LDL-C ≥2.6 mmol/L and hsCRP <2 mg/L), both risk or residual cholesterol and inflammatory risk (RCIR) (LDL-C ≥2.6 mmol/L and hsCRP ≥2 mg/L), and neither risk (LDL-C <2.6 mmol/L and hsCRP <2 mg/L). Vulnerable plaques were determined if it had a low attenuated plaque CT value of <35 Hounsfield Units (HU) and a remodeling index of >1.1, which indicated a positive remodeling. Results: Out of the 468 enrolled patients, 157 (33.5%) were detected to have vulnerable plaques. The proportion of patients with neither risk, RIR, RCR, and RCIR were 32.9%, 28.6%, 18.8%, and 19.7%, respectively. Patients with vulnerable plaques exhibited a higher prevalence of hyperlipidemia (P = 0.026), higher proportion of RIR (P = 0.015), a higher ratio of stroke subtypes of large artery atherosclerosis (P = 0.012), and high leukocyte counts (P < 0.001). The logistic regression analysis detected that RIR was associated with vulnerable plaques after adjusted for major confounding factors (OR 1.98, 95% CI 1.13-3.45, P = 0.016), especially in the large artery atherosclerosis subtype (OR 2.71, 95% CI 1.08-6.77, P = 0.034). Conclusions: In patients with ischemic stroke, RIR is associated with the vulnerability of carotid plaques, especially for those with the large artery atherosclerosis subtype. Therefore, further studies investigating the interventions to modulate inflammation in these patients may be warranted.

14.
J Med Chem ; 67(5): 3764-3777, 2024 Mar 14.
Artigo em Inglês | MEDLINE | ID: mdl-38385325

RESUMO

Hepatocellular carcinoma (HCC) is a frequent malignancy that has a high death rate and a high rate of recurrence following surgery, owing to insufficient surgical resection. Furthermore, HCC is prone to peritoneal metastasis (HCC-PM), resulting in a significant number of tiny cancer lesions, making surgical removal more challenging. As a potential imaging target, FGFR4 is highly expressed in tumors, especially in HCC, but is less expressed in the normal liver. In this study, we used computational simulation approaches to develop peptide I0 derived from FGF19, a particular ligand of FGFR4, and labeled it with the NIRF dye, MPA, for HCC detection. In surgical navigation, the TBR was 9.31 ± 1.36 and 8.57 ± 1.15 in HepG2 in situ tumor and HCC-PM models, respectively, indicating considerable tumor uptake. As a result, peptide I0 is an excellent clinical diagnostic reagent for HCC, as well as a tool for surgically resecting HCC peritoneal metastases.


Assuntos
Carcinoma Hepatocelular , Neoplasias Hepáticas , Cirurgia Assistida por Computador , Humanos , Carcinoma Hepatocelular/diagnóstico por imagem , Carcinoma Hepatocelular/cirurgia , Neoplasias Hepáticas/diagnóstico , Neoplasias Hepáticas/cirurgia , Neoplasias Hepáticas/patologia , Receptor Tipo 4 de Fator de Crescimento de Fibroblastos , Fatores de Crescimento de Fibroblastos , Linhagem Celular Tumoral
15.
Gene ; 915: 148396, 2024 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-38552750

RESUMO

Family with sequence similarity 20 member C (FAM20C) is a Golgi casein kinase that phosphorylates extracellularly-secreted regulatory proteins involved in bone development and mineralization, but its specific role in bone development is still largely unknown. In this study, to examine the specific mechanisms that FAM20C influences bone development, we cross-bred Osx-Cre with FAM20Cflox/flox mice to establish a Osx-Cre; FAM20Cflox/flox knockout (oKO) mouse model; FAM20C was KO in pre-osteoblasts. oKO development was examined at 1-10 weeks, in which compared to control FAM20Cflox/flox, they had lower body weights and bone tissue mineralization. Furthermore, oKO had lower bone volume fractions, thickness, and trabecular numbers, along with higher degrees of trabecular separation. These mice also had decreased femoral metaphyseal cartilage proliferation layer, along with thickened hypertrophic layer and increased apoptotic cell counts. Transcriptomic analysis found that differentially-expressed genes in oKO were concentrated in the osteoclast differentiation pathway, in line with increased osteoclast presence. Additionally, up-regulation of osteoclast-related, and down-regulation of osteogenesis-related genes, were identified, in which the most up-regulated genes were signal regulatory protein ß-1 family (Sirpb1a-c) and mitogen-activated protein kinase 13. Overall, FAM20C KO in pre-osteoblasts leads to abnormal long bone development, likely due to subsequent up-regulation of osteoclast differentiation-associated genes.


Assuntos
Desenvolvimento Ósseo , Proteínas de Ligação ao Cálcio , Caseína Quinase I , Diferenciação Celular , Camundongos Knockout , Osteoblastos , Osteoclastos , Osteogênese , Regulação para Cima , Animais , Camundongos , Desenvolvimento Ósseo/genética , Caseína Quinase I/metabolismo , Caseína Quinase I/genética , Proteínas da Matriz Extracelular/genética , Proteínas da Matriz Extracelular/metabolismo , Osteoblastos/metabolismo , Osteoclastos/metabolismo , Osteogênese/genética , Masculino , Feminino
16.
ACS Synth Biol ; 13(1): 141-156, 2024 Jan 19.
Artigo em Inglês | MEDLINE | ID: mdl-38084917

RESUMO

The variability in phenotypic outcomes among biological replicates in engineered microbial factories presents a captivating mystery. Establishing the association between phenotypic variability and genetic drivers is important to solve this intricate puzzle. We applied a previously developed auxin-inducible depletion of hexokinase 2 as a metabolic engineering strategy for improved nerolidol production in Saccharomyces cerevisiae, and biological replicates exhibit a dichotomy in nerolidol production of either 3.5 or 2.5 g L-1 nerolidol. Harnessing Oxford Nanopore's long-read genomic sequencing, we reveal a potential genetic cause─the chromosome integration of a 2µ sequence-based yeast episomal plasmid, encoding the expression cassettes for nerolidol synthetic enzymes. This finding was reinforced through chromosome integration revalidation, engineering nerolidol and valencene production strains, and generating a diverse pool of yeast clones, each uniquely fingerprinted by gene copy numbers, plasmid integrations, other genomic rearrangements, protein expression levels, growth rate, and target product productivities. Τhe best clone in two strains produced 3.5 g L-1 nerolidol and ∼0.96 g L-1 valencene. Comparable genotypic and phenotypic variations were also generated through the integration of a yeast integrative plasmid lacking 2µ sequences. Our work shows that multiple factors, including plasmid integration status, subchromosomal location, gene copy number, sesquiterpene synthase expression level, and genome rearrangement, together play a complicated determinant role on the productivities of sesquiterpene product. Integration of yeast episomal/integrative plasmids may be used as a versatile method for increasing the diversity and optimizing the efficiency of yeast cell factories, thereby uncovering metabolic control mechanisms.


Assuntos
Saccharomyces cerevisiae , Sesquiterpenos , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Plasmídeos/genética , Sesquiterpenos/metabolismo , Engenharia Metabólica/métodos
17.
Protein Expr Purif ; 92(2): 190-4, 2013 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-24084005

RESUMO

Iron-dependent regulators (IdeRs) control the transcription of a variety of genes associated with iron homeostasis in Gram-positive bacteria. In this study we report the cloning of a putative IdeR gene from the moderate thermophile Thermobifida fusca into the pET-21a(+) expression vector. The expressed protein, Tf-IdeR, was purified using immobilized metal affinity and size-exclusion chromatography, and yielded approximately 12-16 mg of protein per liter of culture. The purified Tf-IdeR protein binds the tox operator sequence in the presence of divalent metal ions. Two Tf-IdeR binding sites were identified in the T. fusca genome upstream of a putative enterobactin exporter and a putative ABC-type multidrug transporter.


Assuntos
Actinomycetales/genética , Proteínas de Bactérias/metabolismo , Proteínas de Ligação a DNA/metabolismo , Proteínas Recombinantes/metabolismo , Proteínas Repressoras/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/isolamento & purificação , Clonagem Molecular , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/isolamento & purificação , Escherichia coli/genética , Escherichia coli/metabolismo , Dados de Sequência Molecular , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Repressoras/química , Proteínas Repressoras/genética , Proteínas Repressoras/isolamento & purificação , Alinhamento de Sequência
18.
Heliyon ; 9(3): e13786, 2023 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-36915517

RESUMO

A cross-sectional census was conducted on all students at the campus of Inner Mongolia Medical University using a self-administered questionnaire. This study aimed to investigate their love from psychological pressure, behavioral characteristics, social cognition, etc. Our results show that all students cultivate feelings and become lifelong partners as their motivation for love. Among the population with various demographic characteristics, the prevalence of love among disadvantaged groups is low; that is, women are lower than men, and those from rural are lower than those from cities. After balancing areas and gender, mental working families have a high prevalence of love. Instead, students whose parents' high expectations pressure their children to have a high love prevalence. This is due to China's specific historical perspective. Our results suggested that although China has been deeply integrated with the world and has more frequent ideological and cultural exchanges, college students still inherit China's traditional outlook on love.

19.
Genome Biol ; 24(1): 262, 2023 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-37974276

RESUMO

Recently, many analysis tools have been devised to offer insights into data generated via cytometry by time-of-flight (CyTOF). However, objective evaluations of these methods remain absent as most evaluations are conducted against real data where the ground truth is generally unknown. In this paper, we develop Cytomulate, a reproducible and accurate simulation algorithm of CyTOF data, which could serve as a foundation for future method development and evaluation. We demonstrate that Cytomulate can capture various characteristics of CyTOF data and is superior in learning overall data distributions than single-cell RNA-seq-oriented methods such as scDesign2, Splatter, and generative models like LAMBDA.


Assuntos
Algoritmos , Análise de Célula Única , Simulação por Computador , Análise de Célula Única/métodos , Citometria de Fluxo/métodos
20.
IEEE Trans Biomed Circuits Syst ; 17(5): 1050-1061, 2023 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-37812554

RESUMO

Brain-machine Interface (BMI) with implantable bioelectronics systems can provide an alternative way to cure neural diseases, while a power management system plays an important role in providing a stable voltage supply for the implanted chip. a prototype system of power management integrated circuit (PMIC) with heavy load capability supplying artifacts tolerable neural recording integrated circuit (ATNR-IC) is presented in this work. A reverse nested miller compensation (RNMC) low dropout regulator (LDO) with a transient enhancer is proposed for the PMIC. The power consumption is 0.55 mW and 22.5 mW at standby (SB) and full stimulation (ST) load, respectively. For a full load transition, the overshoot and downshoot of the LDO are 110 mV and 71 mV, respectively, which help improve the load transient response during neural stimulation. With the load current peak-to-peak range is about 560 µA supplied by a 4-channel stimulator, the whole PMIC can output a stable 3.3 V supply voltage, which indicates that this PMIC can be extended for more stimulating channels' scenarios. When the ATNR-IC is supplied for presented PMIC through a voltage divider network, it can amplify the signal consisting of 1 mVpp simulated neural signal and 20 mVpp simulated artifact by 28 dB with no saturation.


Assuntos
Interfaces Cérebro-Computador , Próteses e Implantes , Fontes de Energia Elétrica , Eletrodos
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