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Waste Management (New York, N.Y.) Jun 2024In a world with a population exceeding 8 billion people and continuing to grow, pollution from food and plastic waste is causing long-term issues in ecosystems....
In a world with a population exceeding 8 billion people and continuing to grow, pollution from food and plastic waste is causing long-term issues in ecosystems. Potential solutions may be found by exploiting insect-based bioconversion. In this context, we investigated the impact of polyvinyl chloride microparticles (PVC-MPs) on the development of Hermetia illucens (black soldier fly; BSF) and its midgut bacterial and fungal microbiota. The impact of PVC-MPs was evaluated feeding BSF larvae with a PVC-MPs-supplemented diet. The larvae exposed to different PVC-MPs concentrations (2.5%, 5%, 10% and 20% w/w) developed into adults with no significant increase in pupal mortality. Faster development and smaller pupae were observed when 20% PVC-MPs was provided. The BSF larvae ingest PVC-MPs, resulting in a reduction in MPs size. Larvae exposed to PVC-MPs did not exhibit differences in gut morphology. Regarding the impact of PVC-MPs on the structure of both bacterial and fungal communities, the overall alpha- and beta-diversity did not exhibit significant changes. However, the presence of PVC-MPs significantly affected the relative abundances of Enterobacteriaceae and Paenibacillaceae among the bacteria and of Dipodascaceae and Plectospharellaceae among the fungi (including yeast and filamentous life forms), suggesting that PVC-MP contamination has a taxa-dependent impact. These results indicate that BSF larvae can tolerate PVC-MPs in their diet, supporting the potential use of these insects in organic waste management, even in the presence of high levels of PVC-MP contamination.
PubMed: 38943817
DOI: 10.1016/j.wasman.2024.06.021 -
Virology Jun 2024The increasing prevalence of drug-resistant Escherichia coli (E. coli) resulting from the excessive utilization of antibiotics necessitates the immediate exploration of...
The increasing prevalence of drug-resistant Escherichia coli (E. coli) resulting from the excessive utilization of antibiotics necessitates the immediate exploration of alternative approaches to counteract pathogenic E. coli. Phages, with their unique antibacterial mechanisms, are considered promising candidates for treating bacterial infections. Herein, we isolated a lytic Escherichia phage Tequatrovirus YZ2 (phage YZ2), which belongs to the genus Tequatrovirus. The genome of phage YZ2 consists of 168,356 base pairs with a G + C content of 35.34% and 269 putative open reading frames (ORFs). Of these, 146 ORFs have been annotated as functional proteins associated with nucleotide metabolism, structure, transcription, DNA replication, translation, and lysis. In the mouse model of a skin wound infected by E. coli, phage YZ2 therapy significantly promoted the wound healing. Furthermore, histopathological analysis revealed reductions in IL-1β and TNF-α and increased VEGF levels, indicating the potential of phages as effective antimicrobial agents against E. coli infection.
PubMed: 38943783
DOI: 10.1016/j.virol.2024.110155 -
Psychoneuroendocrinology Jun 2024Brain-Derived Neurotrophic Factor (BDNF) is implicated in extinction learning, which is a primary mechanism of exposure therapy for posttraumatic stress disorder (PTSD)....
Brain-Derived Neurotrophic Factor (BDNF) is implicated in extinction learning, which is a primary mechanism of exposure therapy for posttraumatic stress disorder (PTSD). Brief aerobic exercise has been shown to promote BDNF release and augment extinction learning. On the premise that the Val allele of the BDNF Val66Met polymorphism facilitates greater release of BDNF, this study examined the extent to which the Val allele of the BDNF polymorphism predicted treatment response in PTSD patients who underwent exposure therapy combined with aerobic exercise or passive stretching. PTSD patients (N = 85) provided saliva samples in order to extract genomic DNA to identify Val/Val and Met carriers of the BDNF Val66Met genotype, and were assessed for PTSD severity prior to and following a 9-week course of exposure therapy combined with aerobic exercise or stretching. The sample comprised 52 Val/Val carriers and 33 Met carriers. Patients with the BDNF high-expression Val allele display greater reduction of PTSD symptoms at posttreatment than Met carriers. Hierarchical regression analysis indicated that greater PTSD reduction was specifically observed in Val/Val carriers who received exposure therapy in combination with the aerobic exercise. This finding accords with animal and human evidence that the BDNF Val allele promotes greater extinction learning, and that these individuals may benefit more from exercise-augmented extinction. Although preliminary, this result represents a possible avenue for augmented exposure therapy in patients with the BDNF Val allele.
PubMed: 38943720
DOI: 10.1016/j.psyneuen.2024.107106 -
Journal of the American Chemical Society Jun 2024Methylation, a widely occurring natural modification serving diverse regulatory and structural functions, is carried out by a myriad of -adenosyl-l-methionine...
Methylation, a widely occurring natural modification serving diverse regulatory and structural functions, is carried out by a myriad of -adenosyl-l-methionine (AdoMet)-dependent methyltransferases (MTases). The AdoMet cofactor is produced from l-methionine (Met) and ATP by a family of multimeric methionine adenosyltransferases (MAT). To advance mechanistic and functional studies, strategies for repurposing the MAT and MTase reactions to accept extended versions of the transferable group from the corresponding precursors have been exploited. Here, we used structure-guided engineering of mouse MAT2A to enable biocatalytic production of an extended AdoMet analogue, Ado-6-azide, from a synthetic methionine analogue, -(6-azidohex-2-ynyl)-l-homocysteine (N-Met). Three engineered MAT2A variants showed catalytic proficiency with the extended analogues and supported DNA derivatization in cascade reactions with M.I and an engineered variant of mouse DNMT1 both in the absence and presence of competing Met. We then installed two of the engineered variants as MAT2A-DNMT1 cascades in mouse embryonic stem cells by using CRISPR-Cas genome editing. The resulting cell lines maintained normal viability and DNA methylation levels and showed Dnmt1-dependent DNA modification with extended azide tags upon exposure to N-Met in the presence of physiological levels of Met. This for the first time demonstrates a genetically stable system for biosynthetic production of an extended AdoMet analogue, which enables mild metabolic labeling of a DNMT-specific methylome in live mammalian cells.
PubMed: 38943667
DOI: 10.1021/jacs.4c06529 -
Molekuliarnaia Biologiia 2024Streptococcus pyogenes Cas9 (SpCas9) is the most popular tool in gene editing; however, off-target mutagenesis is one of the biggest impediments in its application. In...
Streptococcus pyogenes Cas9 (SpCas9) is the most popular tool in gene editing; however, off-target mutagenesis is one of the biggest impediments in its application. In our previous study, we proposed the HH theory, which states that sgRNA/DNA hybrid (hybrid) extrusion-induced enhancement of hydrophobic interactions between the hybrid and REC3/HNH is a key factor in cleavage initiation. Based on the HH theory, we analyzed the interactions between the REC3 domain and hybrid and obtained 8 mutant sites. We designed 8 SpCas9 variants (V1-V8), used digital droplet PCR to assess SpCas9-induced DNA indels in human cells, and developed high-fidelity variants. Thus, the HH theory may be employed to further optimize SpCas9-mediated genome editing systems, and the resultant V3, V6, V7, and V8 SpCas9 variants may be valuable for applications requiring high-precision genome editing.
Topics: Humans; Gene Editing; CRISPR-Associated Protein 9; CRISPR-Cas Systems; Streptococcus pyogenes; HEK293 Cells; INDEL Mutation; RNA, Guide, CRISPR-Cas Systems; DNA
PubMed: 38943587
DOI: No ID Found -
Molekuliarnaia Biologiia 2024Regulation of retrotransposon activity in somatic tissues is a complex mechanism that has still not been studied in detail. It is strongly believed that siRNA...
Regulation of retrotransposon activity in somatic tissues is a complex mechanism that has still not been studied in detail. It is strongly believed that siRNA interference is main mechanism of retrotransposon activity regulation outside the gonads, but recently was demonstrated that piRNA interference participates in retrotransposon repression during somatic tissue development. In this work, using RT-PCR, we demonstrated that during ontogenesis piRNA interference determinates retrotransposon expression level on imago stage and retrotransposons demonstrate tissue-specific expression. The major factor of retrotransposon tissue-specific expression is presence of transcription factor binding sites in their regulatory regions.
Topics: Animals; Drosophila melanogaster; Retroelements; RNA, Small Interfering; Gene Expression Regulation, Developmental; Transcription Factors; Drosophila Proteins; Organ Specificity; Binding Sites; RNA Interference
PubMed: 38943583
DOI: No ID Found -
Molekuliarnaia Biologiia 2024Breast cancer is the most common type of cancer among women. The study of the mechanisms of metastasis, the main cause of death from breast cancer, as well as the search...
Breast cancer is the most common type of cancer among women. The study of the mechanisms of metastasis, the main cause of death from breast cancer, as well as the search for new markers for early diagnosis and prognosis of breast cancer, is an extremely topical issue. New perspectives in the diagnosis and treatment of breast cancer are opened by the mechanisms of gene regulation involving non-coding RNAs, in particular, long non-coding RNAs (lncRNAs). In this work, we analyzed the methylation levels of seven lncRNA genes (MEG3, SEMA3B-AS1, HAND2-AS1, KCNK15-AS1, ZNF667-AS1, MAGI2-AS3, and PLUT) by quantitative methyl-specific PCR on a set of 79 paired (tumor/normal) samples of breast cancer. Hypermethylation of all seven lncRNA genes was revealed, and hypermethylation of HAND2-AS1, KCNK15-AS1, MAGI2-AS3, and PLUT was detected in breast cancer for the first time. It was found that the level of meth ylation of the studied lncRNA genes correlated statistically significantly with the stage of the tumor process, the size of the tumor, and the presence of metastases in the lymph nodes. Thus, methylation of the seven studied lncRNA genes is associated with the development and progression of breast cancer, and these genes can be useful as potential markers in the diagnosis and prognosis of breast cancer.
Topics: Humans; RNA, Long Noncoding; Female; Breast Neoplasms; DNA Methylation; Gene Expression Regulation, Neoplastic; Middle Aged; Biomarkers, Tumor; Disease Progression; Adult; Aged
PubMed: 38943582
DOI: No ID Found -
Molekuliarnaia Biologiia 2024The mobile genetic elements IS630/Tc 1/mariner (ITm) are widespread DNA transposons that make a significant contribution to the evolution of eukaryotic genomes. With the...
The mobile genetic elements IS630/Tc 1/mariner (ITm) are widespread DNA transposons that make a significant contribution to the evolution of eukaryotic genomes. With the start of large-scale application of next-generation sequencing (NGS) technologies and the emergence of many new whole genome sequences of organisms in nucleotide sequence collections, the ITm elements have been identified in most taxa of the eukaryotic tree of life. Although ITm diversity has been studied in detail, new elements are still found, thus expanding the respective DNA transposon group and calling for review of its classification. Bivalve L31 elements were for the first time analyzed in detail to describe their structures, diversity, distribution, and phylogenetic position among the ITm elements. The L31 transposons were found to form an independent superfamily of an ancient origin within the ITm group. Rather high diversity was observed within the L31 clade; i.e., five phylogenetic clusters were identified. In mollusks, the L31 transposons have been detected only in the subclass Autobranchia and predominate in diversity and number in the infraclass Pteriomorphia. A protein encoded by open reading frame 2 (ORF2) was shown to be an integral structural component of almost all full-length L31 elements. The results provide for a better understanding of the evolution of particular ITm transposons. Further study of the L31 transposons in other taxa (cnidarians) and functional investigation of the ORF2 protein product will help to better understand the evolution of DNa transposons, the mechanisms of their horizontal transfer, and their contribution to eukaryotic biodiversity.
Topics: Animals; DNA Transposable Elements; Bivalvia; Phylogeny; Evolution, Molecular; Open Reading Frames
PubMed: 38943580
DOI: No ID Found -
Molekuliarnaia Biologiia 2024It has been 10 years since CRISPR/Cas technology was applied to edit the genomes of various organisms. Its ability to produce a double-strand break in a DNA region... (Review)
Review
It has been 10 years since CRISPR/Cas technology was applied to edit the genomes of various organisms. Its ability to produce a double-strand break in a DNA region specified by the researcher started a revolution in bioengineering. Later, the Base Editing (BE) method was developed. BE is performed via the formation of single-strand breaks by the mutant form of Cas nuclease (nickase), fused with deaminases and other enzymes. It can be used to promote A ↔ G and C ↔ T transitions, and a C → G transversion. Just over 3 years ago, a new Prime Editing (PE) variant of CRISPR/Cas was invented. Unlike BE, in PE the nickase is fused with reverse transcriptase, capable of building a new DNA chain using the pegRNA template. The pegRNA consists of an elongated guide RNA with an extra sequence at the 3'-end. Prime editing makes it possible to insert the desired mutations into this extra sequence and to carry out any substitutions and indels of bases without the use of special donor DNA. To date, a number of PE variants have been proposed; they are briefly considered in this review with an emphasis on prime editing of plant genomes. Some attention is also paid to pegRNA design programs, as well as evaluation of the efficiency of the editing. Such a variety of PE techniques is due to the opportunities of high-precision introduction of desired changes with a rather low frequency of off-target mutations in the genomes of various organisms. The relatively low efficiency of prime editing inspires researchers to offer new approaches. There is hope that further development of the technology will improve PE enough to take its rightful place among the genome targeting methods that are suitable for any organisms, and will have a positive impact on the agricultural sector, industrial biotechnologies, and medicine.
Topics: Gene Editing; CRISPR-Cas Systems; Genome, Plant; RNA, Guide, CRISPR-Cas Systems; Humans
PubMed: 38943578
DOI: No ID Found -
Molekuliarnaia Biologiia 2024Photochemical reactions in cell DNA are induced in various organisms by solar UV radiation and may lead to a series of biological responses to DNA damage, including... (Review)
Review
Photochemical reactions in cell DNA are induced in various organisms by solar UV radiation and may lead to a series of biological responses to DNA damage, including apoptosis, mutagenesis, and carcinogenesis. The chemical nature and the amount of DNA lesions depend on the wavelength of UV radiation. UV type B (UVB, 290-320 nm) causes two main lesions, cyclobutane pyrimidine dimers (CPDs) and, with a lower yield, pyrimidine (6-4) pyrimidone photoproducts (6-4PPs). Their formation is a result of direct UVB photon absorption by DNA bases. UV type A (UVA, 320-400 nm) induces only cyclobutane dimers, which most likely arise via triplet-triplet energy transfer (TTET) from cell chromophores to DNA thymine bases. UVA is much more effective than UVB in inducing sensitized oxidative DNA lesions, such as single-strand breaks and oxidized bases. Of the latter, 8-oxo-dihydroguanine (8-oxodG) is the most frequent, being produced in several oxidation processes. Many recent studies reported novel, more detailed information about the molecular mechanisms of the photochemical reactions that underlie the formation of various DNA lesions. The information is mostly summarized and analyzed in the review. Special attention is paid to the oxidation reactions that are initiated by reactive oxygen species (ROS) and radicals generated by potential endogenous photosensitizers, such as pterins, riboflavin, protoporphyrin IX, NADH, and melanin. The review discusses the role that specific DNA photoproducts play in genotoxic processes induced in living systems by UV radiation of various wavelengths, including human skin carcinogenesis.
Topics: Ultraviolet Rays; Humans; DNA Damage; Pyrimidine Dimers; Reactive Oxygen Species; DNA; Animals; Apoptosis; Oxidation-Reduction; 8-Hydroxy-2'-Deoxyguanosine
PubMed: 38943577
DOI: No ID Found