Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants

Plant Communications, Journal Year: 2023, Volume and Issue: 4(4), P. 100558 - 100558

Published: Feb. 9, 2023

With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design construct biological parts, modules, circuits, even whole systems. To overcome limitations native promoters in controlling gene expression, promoter aims synthesize short, inducible, conditionally controlled coordinate expression multiple genes diverse plant metabolic signaling pathways. Synthetic are versatile can drive accurately with smart responses; they show potential for enhancing desirable traits crops, thereby improving crop yield, nutritional quality, food security. This review first illustrates importance synthetic promoters, then introduces architecture thoroughly summarizes advances construction. Restrictions future applications such improvement also discussed.

Language: Английский

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Differentially Expressed Genes and Molecular Susceptibility to Human Age-Related Diseases

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(4), P. 3996 - 3996

Published: Feb. 16, 2023

Mainstream transcriptome profiling of susceptibility versus resistance to age-related diseases (ARDs) is focused on differentially expressed genes (DEGs) specific gender, age, and pathogeneses. This approach fits in well with predictive, preventive, personalized, participatory medicine helps understand how, why, when, what ARDs one can develop depending their genetic background. Within this mainstream paradigm, we wanted find out whether the known ARD-linked DEGs available PubMed reveal a molecular marker that will serve purpose anyone’s any tissue at time. We sequenced periaqueductal gray (PAG) tame aggressive rats, identified rat-behavior-related DEGs, compared them homologous animal DEGs. analysis yielded statistically significant correlations between behavior-related ARD-susceptibility-related fold changes (log2 values) expression these DEG homologs. found principal components, PC1 PC2, corresponding half-sum half-difference log2 values, respectively. With linked ARD humans used as controls, verified components. only common for ARDs: an excess Fcγ receptor IIb suppressing immune cell hyperactivation.

Language: Английский

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Russian Science Foundation grant No. 20-14-00140 supported this study. The authors are thankful to the multi-access Center “Bioinformatics” for the use of computational resources as supported by Russian government project FWNR-2022-0020 and the Russian Federal Science and Technology Program for the Development of Genetic Technologies.

Vavilov Journal of Genetics and Breeding, Journal Year: 2023, Volume and Issue: 26(8), P. 798 - 805

Published: Jan. 4, 2023

It is generally accepted that during the domestication of food plants, selection was focused on their productivity, ease technological processing into food, and resistance to pathogens environmental stressors. Besides, palatability plant foods health benefits could also be subjected by humans in past. Nonetheless, it unclear whether antiquity, aside from positive for beneficial properties simultaneously selected against such detrimental as allergenicity. This topic becoming increasingly relevant allergization population grows, being a major challenge modern medicine. That why intensive research breeders already underway creating hypoallergenic forms plants. Accordingly, this paper, albumin, globulin, β-amylase common wheat Triticum aestivum L. (1753) are analyzed, which have been identified earlier targets attacks human class E immunoglobulins. At genomic level, we wanted find signs past negative allergenicity these three proteins (albumin, β-amylase) ancestral We search TATA-binding protein (TBP)-binding site because located within narrow region (between positions -70 -20 relative corresponding transcription start sites), most conserved, necessary primary initiation, best-studied regulatory signal eukaryotes. Our previous studies presented our publicly available Web service Plant_SNP_TATA_Z-tester, makes possible estimate equilibrium dissociation constant (KD) TBP complexes with proximal promoters (as output data) using 90 bp DNA sequences input data). In work, means bioinformatics tool, 363 gene promoter representing 43 species were analyzed. found compared non-food plants characterized significantly weaker affinity genes homologous common-wheat (food allergens) (p < 0.01, Fisher's Z-test). evidence suggests carried out selective breeding reduce expression encoding allergenic proteins.Принято считать, что при доместикации пищевых растений отбор шел на урожайность, технологичность переработки в продукты питания, устойчивость к патогенам и стрессовым воздействиям окружающей среды. При этом также могли оцениваться вкусовые качества продуктов питания растительного происхождения их ценность для здоровья. Однако неясно, проводил ли человек прошлом наряду с положительным отбором полезные свойства одновременно против таких вредоносных свойств, как способность вызывать аллергические реакции. Этот вопрос становится все более актуальным по мере роста аллергизации населения вызова современной медицине. В связи этим селекционерами уже ведутся интенсивные исследования созданию гипоаллергенных форм растений. этой работе рассмотрены альбумин, глобулин β-амилаза мягкой пшеницы (1753), идентифицированные ранее мишени атак иммуноглобулинов класса Е человека. Нашей целью было найти геномном уровне следы отрицательного отбора гипераллергенности трех белков (альбумин, β-амилаза) одомашнивании предковых современных Для этого мы сфокусировали поиск сайте связывания ТАТА-связывающего белка (ТВР) локализованном узком районе [–70; –20] относительно старта транскрипции, консервативном, необходимом первичной инициации транскрипции наиболее изученном регуляторном сигнале геномах эукариот. Ранее нами был создан свободно доступный веб-сервис Plant_SNP_TATA_Z-tester оценки величин равновесной константы диссоциации комплексов ТВР проксимальными промоторами генов последовательностям ДНК длиной п. о. настоящей его помощью проанализированы последовательности промоторов видов Обнаружено, пищевые растения, сравнении непищевыми, характеризуются достоверно низкой аффинностью ТBP проксимальным промоторам генов, гомологичных генам глобулина, альбумина β-амилазы аллергенов ( p Z-критерий Фишера). Это свидетельствует об отборе снижение уровня данных аллергенных белков.

Language: Русский

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Research Topics of the Bioinformatics of Gene Regulation

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(10), P. 8774 - 8774

Published: May 15, 2023

The study of gene expression regulation raises the challenge developing bioinformatics tools and algorithms, demanding data integration [...]

Language: Английский

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Candidate SNP Markers Significantly Altering the Affinity of TATA-Binding Protein for the Promoters of Human Hub Genes for Atherogenesis, Atherosclerosis and Atheroprotection

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(10), P. 9010 - 9010

Published: May 19, 2023

Atherosclerosis is a systemic disease in which focal lesions arteries promote the build-up of lipoproteins and cholesterol they are transporting. The development atheroma (atherogenesis) narrows blood vessels, reduces supply leads to cardiovascular diseases. According World Health Organization (WHO), diseases leading cause death, has been especially boosted since COVID-19 pandemic. There variety contributors atherosclerosis, including lifestyle factors genetic predisposition. Antioxidant diets recreational exercises act as atheroprotectors can retard atherogenesis. search for molecular markers atherogenesis atheroprotection predictive, preventive personalized medicine appears be most promising direction study atherosclerosis. In this work, we have analyzed 1068 human genes associated with atherogenesis, atherosclerosis atheroprotection. hub regulating these processes found ancient. silico analysis all 5112 SNPs their promoters revealed 330 candidate SNP markers, statistically significantly change affinity TATA-binding protein (TBP) promoters. These made us confident that natural selection acts against underexpression At same time, upregulation one promotes health.

Language: Английский

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AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(1), P. 607 - 607

Published: Jan. 3, 2024

The mainstream of the post-genome target-assisted breeding in crop plant species includes biofortification such as high-throughput phenotyping along with genome-based selection. Therefore, this work, we used Web-service Plant_SNP_TATA_Z-tester, which have previously developed, to run a uniform silico analysis transcriptional alterations 54,013 protein-coding transcripts from 32,833 Arabidopsis thaliana L. genes caused by 871,707 SNPs located proximal promoter region. identified 54,993 significantly decreasing or increasing gene expression through changes TATA-binding protein affinity promoters. existence these highly conserved promoters may be explained intraspecific diversity kept stabilizing natural To support this, hand-annotated papers on some possessing their orthologs other and demonstrated effects expressions vital traits. We integrated estimates TBP-promoter AtSNP_TATAdb knowledge base showed significant correlations independent vivo experimental data. These appeared robust variations statistical criteria, genomic environment TATA box regions, plants growing conditions.

Language: Английский

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Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(2), P. 1011 - 1011

Published: Jan. 13, 2024

Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) is a central genome-wide method for in vivo analyses of DNA-protein interactions various cellular conditions. Numerous studies have demonstrated the complex contextual organization ChIP-seq peak sequences and presence binding sites transcription factors them. We assessed dependence score on different signals analyzing these from several experiments using our fully enumerative GPU-based de novo motif discovery method, Argo_CUDA. Analysis revealed sets significant IUPAC motifs corresponding to target partner factors. For experiments, multiple regression models were constructed, demonstrating scores not only highly but also less A correlation was shown between FOXA2 HNF4G, which found experimental confirmation scientific literature, important contribution factor and, consequently, their score.

Language: Английский

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CRISPR/Cas Systems for Enhancing Photosynthesis: Climate Resilience and Food Production

Published: Jan. 1, 2024

To achieve the Sustainable Development Goal 2 (SDG 2) established by UN, there is a need to produce 15–20% more food from recent trends of production. Biotechnological advances in late twentieth century paved path for creation genetically engineered crop species enhance agricultural Recently programmable gene editing tools such as zinc-finger nucleases (ZFN), transcription activator-like effector (TALE) nucleases, clustered regularly interspaced short palindromic repeat (CRISPR) systems, and base editors have been developed edit any genome desirable traits. Furthermore, plant organelle genomes are distinct, encoding numerous genes crucial photosynthesis respiration. Any alteration photosynthetic functionality can directly impact Photosynthesis enzymes evolutionarily conserved green plants. There huge scope CRISPR genomics transform routine crops into superfoods. Chloroplast-targeting with magic cut allows engineering higher expression useful traits increased specific types oil content seeds or inclusion all essential vitamins plant-based diets. Knock-out knock-in genes, especially those related photosystem small subunits key CO2-fixing enzyme Rubisco (SSU-encoded rbcS) disease—resistance other intermediate metabolites plants facilitate high productivity even under climate change scenario. CRISPR-Cas9 enables multiple polyploid which remained challenging long time. Supercharging C3 advancement process production calories limited land area fertilizer. In this review, we address CRISPR-Cas9-based uses, challenges improve targeted efficiency

Language: Английский

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Developmental Biology: Computational and Experimental Approaches

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(13), P. 10435 - 10435

Published: June 21, 2023

Developmental biology studies ontogenesis, the individual development of an organism from time fertilization in sexual reproduction or its expelling maternal asexual to end organism's life, with all phenotypical characters typical this biological species and supporting normal course biochemical processes morphogenesis [...].

Language: Английский

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Diagnostic and prognostic implications of non-high-density lipoprotein cholesterol and homocysteine levels for cognitive impairment in thalamic infarction

World Journal of Psychiatry, Journal Year: 2023, Volume and Issue: 13(12), P. 985 - 994

Published: Dec. 19, 2023

BACKGROUND Patients with thalamic infarction experience abnormal blockages of multinucleated vessels, affecting the body and thereby thalamus. Most patients have an adverse prognosis, which seriously affects their safety. Therefore, it is essential to analyze independent risk factors that influence prognosis develop corresponding preventive measures. AIM To explore effect non-high-density lipoprotein cholesterol (non-HDL-C) Homocysteine (Hcy) levels in cognitive impairment infarction. METHODS From March 2019 2022, 80 were divided into a group [Montreal Cognitive Assessment (MoCA) score < 26; 35 patients] normal function (MoCA 26-30; 45 patients) according MoCA score. In addition, 50 healthy people same period selected as control group. A correlation between non-HDL-C Hcy receiver operating characteristic curve was observed, serum analyzed for diagnosis According Modified Rankin Scale (MRS) score, good (MRS ≤ 2) poor >2). RESULTS The significantly higher than (P 0.05). There no significant difference level > scores lower those correlated 0.05), [areas under (AUC) = 0.709, 95% confidence interval (95%CI): 0.599-0.816], level, could predict (AUC 0.738, 95%CI: 0.618-0.859). combined can 0.769, 0.721-0.895). 30 Compared group, National Institutes Health Stroke (NIHSS) large-area cerebral infarction, atrial fibrillation, activated partial prothrombin time statistically NIHSS extensive serum, fibrillation may all be CONCLUSION Non-HDL-C are positively used detection better. main fibrillation. Clinically, measures formulated based on above prevent reduce mortality.

Language: Английский

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