Publications by authors named "Alex V Kochetov"
It is widely discussed that eukaryotic mRNAs can encode several functional polypeptides. Recent progress in NGS and proteomics techniques has resulted in a huge volume of information on potential alternative translation initiation sites and open reading frames (altORFs). However, these data are still incomprehensive, and the vast majority of eukaryotic mRNAs annotated in conventional databases (e.
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- Plant surface properties are vital for coping with environmental stresses, and the cuticle's outer layer is made up of diverse waxes influenced by specific gene regulators.
- In this study, researchers used a technique called RNA-guided Cas9 endonuclease to create mutations in four barley genes linked to cuticle properties, identifying one gene responsible for a glossy sheath phenotype due to a deficiency in β-diketones.
- The results indicated that the WIN1 transcription factor plays a crucial role in regulating the biosynthesis of β-diketones in barley by activating certain genes during specific developmental stages and in particular plant organs.
Article Synopsis
- Potatoes are a globally significant crop, and studying their genomic sequences helps understand their diversity and evolutionary variations.
- Researchers sequenced the genomes of 15 Russian potato cultivars and compared them to 12 South American varieties, finding differences in genetic diversity and copy number variations (CNVs).
- Notable discoveries include genes linked to immune responses, tuber development, and a potential new gene related to circadian rhythm regulation in Russian potatoes.
Article Synopsis
- - Autism spectrum disorder (ASD) is a neurodevelopmental condition marked by communication and behavioral difficulties, influenced by both genetic heritability and environmental factors.
- - The review highlights the connection between mTOR signaling and specific gene interactions linked to maternal autoantibodies, suggesting a need for subtyping ASD based on different underlying mechanisms.
- - It emphasizes the importance of developing blood tests to detect antibodies associated with autism-like behavior, which could aid in better understanding and diagnosing ASD.
Article Synopsis
- Autism spectrum disorder (ASD) and autoimmune disorders (AID) both show a high degree of genetic variability and heritability, indicating possible shared genetic factors.
- In analyses of gene sets, significant portions of genes associated with both ASD (59%) and AID (50%) were linked to specific biological pathways related to mTOR signaling and other factors.
- The research suggests that ASD and AID may not be entirely distinct disorders but rather interconnected conditions that share common genetic mechanisms, particularly involving the mTOR signaling pathway, with an emerging hypothesis of an immune subtype of autism.
Article Synopsis
- Globodera rostochiensis is a significant potato pathogen that interacts with host plant roots, with commercial varieties relying on specific resistance genes (R genes) from wild relatives and Andean native potatoes.
- Research on South American Solanum phureja accessions shows that resistant genotypes trigger an active stress response, including gene activation, tissue regeneration, and hypersensitive responses when attacked by G. rostochiensis.
- The study highlights the importance of analyzing gene expression changes in S. phureja to understand resistance mechanisms and suggests that de novo transcriptome assembly can identify new resistance traits.
Article Synopsis
- The naked caryopsis trait in barley results from a loss-of-function mutation in the NUD gene, which is crucial for forming a cementing layer in the grain.
- Researchers used RNA-guided Cas9 to effectively knock out the NUD gene, leading to a 57% conversion rate from hulled to naked barley in transformed plants.
- The development of isogenic lines of hulled and naked barley offers an ideal model for studying the effects of NUD mutations on plant performance and yield, with naked barley having health benefits due to its high β-glucan content.
Choice of the Promoter for Tissue and Developmental Stage-Specific Gene Expression.
Methods Mol Biol
February 2021
Article Synopsis
- Transgenic technologies are key tools in biotechnology, allowing for targeted genetic modifications that can uncover gene functions and alter plant metabolic pathways.
- Proper design of chimeric gene constructs is crucial for effective modification, particularly in the choice of promoters that regulate transgene expression.
- The TGP database has been created to gather information on various noncanonical tissue-specific and developmentally regulated promoters, providing resources for optimizing transgene control in plants.
Article Synopsis
- - Autism spectrum disorder (ASD) is linked to over 1,000 genes, with significant contributions from mTOR-related translation issues, as shown in the SFARI gene database.
- - An analysis identified that 606 out of 1,053 genes (58%) and 179 out of 281 high-confidence genes (64%) are connected to mTOR signaling and other related pathways.
- - The study suggests that both genetic factors and environmental influences, like vitamin D deficiency, may activate mTOR pathways, potentially impacting the severity and symptoms of autism.
Article Synopsis
- - The cultivated potato, an important global crop, relies on the synthesis of anthocyanins for stress resistance and nutritional value, with the gene StAN1 recognized as a key regulator of this process.
- - A study of 36 potato varieties revealed significant variability in the StAN1 gene related to anthocyanin production, while certain other regulatory genes showed inconsistent expression levels across different genotypes.
- - Although StAN1 is crucial for anthocyanin synthesis, current genetic markers for this gene are ineffective at accurately predicting pigmentation patterns in potatoes, indicating that the promoter region of StAN1 may play a significant role in its function.
Article Synopsis
- * A study comparing the root transcriptomes of potato genotypes revealed differentially expressed genes related to resistance against a specific nematode, but limited annotations made it difficult to compile a clear list of candidate R genes.
- * Integrating transcriptomic analysis with data on certain potato genes improved candidate gene identification, suggesting that this combined approach could expedite the discovery of potato R genes for further research and breeding efforts.
Article Synopsis
- The study investigates the role of extracellular RNases in plant defense, focusing on their potential to inhibit viruses like the Cucumber mosaic virus (CMV) in Nicotiana tabacum plants.
- Transgenic plants expressing a non-plant RNase showed suppressed disease symptoms and lower viral levels compared to control plants after CMV infection.
- These findings suggest that boosting extracellular RNase activity can enhance plants' resistance to various RNA viruses, indicating a broader potential for pathogen defense mechanisms in plants.
Article Synopsis
- Protein synthesis is complex, with one gene locus able to create multiple isoforms through mechanisms like alternative start sites in mRNA translation.
- The altORF evaluator (altORFev) is a tool that predicts these alternative open reading frames in eukaryotic mRNA, focusing on efficiently translated altORFs recognized by ribosomal subunits.
- The tool is developed in Java 1.8 using BioJava and is accessible online, with support available through an email contact.
Article Synopsis
- Artificial genetic constructs can create self-replicating RNA molecules, used for gene silencing, bioproduction, and vaccines.
- A less-explored concept involves transgenic organisms, like modified plant cells, that produce foreign replicons such as bacteriophages or insect viruses, termed Alien Replicon-Producing Organisms (ARPOs).
- While ARPOs hold potential for biocontrol and influencing target organisms, they must adhere to strict biosafety standards, and a discussion on their applications could enhance bioengineering strategies.
Article Synopsis
- * The GR gene produces various mRNA species, resulting in different protein isoforms, with GRα being the most prevalent, and distinct translational mechanisms generating several isoforms (A, B, C, D) that control transcription of various genes.
- * The potential mechanism for the translation of GRα isoform C may involve a reinitiation process influenced by the phosphorylation state of eIF2α, suggesting an important link between GR and responses to cellular stress, which warrants further investigation. *
Hidden coding potential of eukaryotic genomes: nonAUG started ORFs.
J Biomol Struct Dyn
October 2013
Article Synopsis
- * Recent studies show that alternative translation from non-AUG codons, as well as weak AUG contexts, is significant in the creation of diverse eukaryotic protein landscapes.
- * This research analyzes mRNA characteristics in yeast and mammals, finding that certain sequence features in upstream ORFs (uORFs) and stable downstream structures may enhance the recognition of non-AUG start codons by ribosomes.
Article Synopsis
- Transgenic plant experiments often need specific promoters to achieve the right gene expression, but the commonly used promoters offer limited options and can cause issues like transgene silencing.
- To tackle these challenges, researchers can utilize various plant gene promoters with proven effects, though this requires extensive literature review.
- The TransGene Promoters (TGP) database provides a centralized resource of genomic DNA segments that deliver specific expression patterns for transgenic plants, complete with an easy-to-use search interface.
Article Synopsis
- * Researchers analyzed mRNA sequences in two plants, Arabidopsis thaliana and Oryza sativa, finding that those with the UGA terminator had more nonsense codons, likely due to weak natural selection.
- * They discovered a correlation between the presence of tandem stop codons and the amino acid composition of proteins, specifically noting that glycine at the protein's C-terminal was linked to higher frequencies of reserve stop signals in UGA-containing mRNAs.
Alternative translation start sites are conserved in eukaryotic genomes.
Nucleic Acids Res
January 2011
Article Synopsis
- Research highlights the role of alternative start codons (AUGs) in generating proteomic diversity, despite ongoing debates about their significance.* -
- Comparative studies show that alternative start codons are negatively selected in various organisms, indicating that their usage is conserved in specific genetic contexts.* -
- Findings suggest that genes with weaker primary start sites and multiple conserved start sites, like transcription factors, utilize alternative starts to enhance translation efficiency and produce diverse protein variants.*
Article Synopsis
- * Recent findings show that nucleotide accessibility in double-stranded DNA is influenced by its sequence context and can be predicted using nearby nucleotide data.
- * The research explores RNA molecules, revealing that certain trinucleotides have varying solvent accessibility, which could play a role in important translational signals and may correlate with codon usage in different genomes.
Article Synopsis
- - The study investigates how the nucleotide context around the AUG start codon affects translation initiation in eukaryotic ribosomes, particularly focusing on the role of specific nucleotides in the +4, +5, and +6 positions.
- - It was found that the presence of guanine (G) in the +4 position is significant for the GnnAUG context, while the context AnnAUG leads to an increased occurrence of serine in the second amino acid position.
- - Overall, the efficiency of the translation initiation process may be influenced by the interaction between both the 5'- and 3'-context regions, as well as the specific amino acids present in the early protein-coding sequence.
Article Synopsis
- Eukaryotic mRNA traditionally believed to have one translation start site, encoding a single protein, but recent findings show multiple start sites exist.
- Studies indicate that eukaryotic ribosomes can recognize these alternative start sites, with many examples confirmed through experimentation.
- The importance of alternative translation events in increasing the complexity of the eukaryotic proteome has been highlighted by computational evaluations.