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Molecular Therapy. Nucleic Acids Sep 2024Effective therapeutics are necessary for managing severe COVID-19 disease despite the availability of vaccines. Small interfering RNA (siRNA) can silence viral genes and...
Effective therapeutics are necessary for managing severe COVID-19 disease despite the availability of vaccines. Small interfering RNA (siRNA) can silence viral genes and restrict SARS-CoV-2 replication. Cell-penetrating peptides is a robust method for siRNA delivery, enhancing siRNA stability and targeting specific receptors. We developed a peptide HE25 that blocks SARS-CoV-2 replication by various mechanisms, including the binding of multiple receptors involved in the virus's internalization, such as ACE2, integrins and NRP1. HE25 not only acts as a vehicle to deliver the SARS-CoV-2 RNA-dependent RNA polymerase siRNA into cells but also facilitates their internalization through endocytosis. Once inside endosomes, the siRNA is released into the cytoplasm through the Histidine-proton sponge effect and the selective cleavage of HE25 by cathepsin B. These mechanisms effectively inhibited the replication of the ancestral SARS-CoV-2 and the Omicron variant BA.5 . When HE25 was administered , either by intravenous injection or inhalation, it accumulated in lungs, veins and arteries, endothelium, or bronchial structure depending on the route. Furthermore, the siRNA/HE25 complex caused gene silencing in lung cells . The SARS-CoV-2 siRNA/HE25 complex is a promising therapeutic for COVID-19, and a similar strategy can be employed to combat future emerging viral diseases.
PubMed: 38939051
DOI: 10.1016/j.omtn.2024.102227 -
Frontiers in Cellular and Infection... 2024and belong to the Bacteroidota phylum. Both species inhabit the oral cavity and can be associated with periodontal diseases. To survive, they must uptake heme from the...
INTRODUCTION
and belong to the Bacteroidota phylum. Both species inhabit the oral cavity and can be associated with periodontal diseases. To survive, they must uptake heme from the host as an iron and protoporphyrin IX source. Among the best-characterized heme acquisition systems identified in members of the Bacteroidota phylum is the Hmu system, with a leading role played by the hemophore-like HmuY (HmuY) protein.
METHODS
Theoretical analysis of selected HmuY proteins and spectrophotometric methods were employed to determine the heme-binding mode of the HmuY homolog (HmuY) and its ability to sequester heme. Growth phenotype and gene expression analysis of were employed to reveal the importance of the HmuY and Hmu system for this bacterium.
RESULTS
Unlike in , where HmuY uses two histidines for heme-iron coordination, other known HmuY homologs use two methionines in this process. HmuY is the first characterized representative of the HmuY family that binds heme using a histidine-methionine pair. It allows HmuY to sequester heme directly from serum albumin and HmuY, the HmuY homolog which uses two methionines for heme-iron coordination. In contrast to HmuY, which sequesters heme directly from methemoglobin, HmuY may bind heme only after the proteolytic digestion of hemoglobin.
CONCLUSIONS
We hypothesize that differences in components of the Hmu system and structure-based properties of HmuY proteins may evolved allowing different adaptations of species to the changing host environment. This may add to the superior virulence potential of over other members of the Bacteroidota phylum.
Topics: Heme; Porphyromonas gingivalis; Tannerella forsythia; Bacterial Proteins; Porphyromonas endodontalis; Humans; Gene Expression Regulation, Bacterial; Protein Binding; Iron
PubMed: 38938884
DOI: 10.3389/fcimb.2024.1421018 -
Frontiers in Neurology 2024Migraine, a prevalent neurological disorder, affects approximately 14.1% of the global population and disproportionately impacts females. This debilitating condition... (Review)
Review
Migraine, a prevalent neurological disorder, affects approximately 14.1% of the global population and disproportionately impacts females. This debilitating condition significantly compromises quality of life, productivity, and incurs high healthcare costs, presenting a challenge not only to individuals but to societal structures as a whole. Despite advances in our understanding of migraine pathophysiology, treatment options remain limited, necessitating ongoing research into effective therapies. This review delves into the complexity of migraine management, examining the roles of genetic predisposition, environmental influences, personalized treatment approaches, comorbidities, efficacy and safety of existing acute and preventive treatments. It further explores the continuum between migraine and tension-type headaches and discusses the intricacies of treating various migraine subtypes, including those with and without aura. We emphasize the recent paradigm shift toward trigeminovascular activation and the release of vasoactive substances, such as calcitonin gene-related peptide (CGRP), which offer novel therapeutic targets. We assess groundbreaking clinical trials, pharmacokinetic and pharmacodynamic perspectives, safety, tolerability, and the real-world application of CGRP monoclonal antibodies and gepants. In the face of persisting treatment barriers such as misdiagnosis, medication overuse headaches, and limited access to specialist care, we discuss innovative CGRP-targeted strategies, the high cost and scarcity of long-term efficacy data, and suggest comprehensive solutions tailored to Turkiye and developing countries. The review offers strategic recommendations including the formulation of primary care guidelines, establishment of specialized outpatient clinics, updating physicians on novel treatments, enhancing global accessibility to advanced therapies, and fostering patient education. Emphasizing the importance of lifestyle modifications and holistic approaches, the review underscores the potential of mass media and patient groups in disseminating critical health information and shaping the future of migraine management.
PubMed: 38938785
DOI: 10.3389/fneur.2024.1402569 -
Frontiers in Cardiovascular Medicine 2024This case report details the identification of a novel likely pathogenic splicing variant in the TTN gene, associated with dilated cardiomyopathy (DCM), in a 42-year-old...
This case report details the identification of a novel likely pathogenic splicing variant in the TTN gene, associated with dilated cardiomyopathy (DCM), in a 42-year-old male patient presenting with early-onset heart failure and reduced ejection fraction. DCM is a nonischemic heart condition characterized by left biventricular dilation and systolic dysfunction, with approximately one-third of cases being familial and often linked to genetic mutations. The TTN gene, encoding the largest human protein essential for muscle contraction and sarcomere structure, is implicated in about 25% of DCM cases through mutations, especially truncating variants. Our investigation revealed a previously unreported G > C mutation at the splice acceptor site in intron 356 of TTN, confirmed by Sanger sequencing and not found in population databases, suggesting a novel contribution to the understanding of DCM etiology. The case emphasizes the critical role of the TTN gene in cardiac function and the genetic complexity underlying DCM. A comprehensive literature review highlighted the prevalence and significance of splice variants in the TTN gene, particularly those affecting the titin A-band, which is known for its role in muscle contraction and stability. This variant's identification underscores the importance of genetic screening in patients with DCM, offering insights into the disease's familial transmission and potential therapeutic targets. Our findings contribute to the expanding knowledge of genetic factors in DCM, demonstrating the necessity of integrating genetic diagnostics in cardiovascular medicine. This case supports the growing evidence linking splicing mutations in specific regions of the TTN gene to DCM development and underscores the importance of genetic counseling and testing in managing heart disease.
PubMed: 38938651
DOI: 10.3389/fcvm.2024.1387063 -
Frontiers in Plant Science 2024Sea buckthorn ( ssp. ) is a deciduous shrub or small tree in the Elaeagnaceae family. It is dioecious, featuring distinct structures in female and male flowers. The...
Sea buckthorn ( ssp. ) is a deciduous shrub or small tree in the Elaeagnaceae family. It is dioecious, featuring distinct structures in female and male flowers. The MADS-box gene family plays a crucial role in flower development and differentiation of floral organs in plants. However, systematic information on the MADS-box family in sea buckthorn is currently lacking. This study presents a genome-wide survey and expression profile of the MADS-box family of sea buckthorn. We identified 92 MADS-box genes in the ssp. genome. These genes are distributed across 12 chromosomes and classified into Type I (42 genes) and Type II (50 genes). Based on the FPKM values in the transcriptome data, the expression profiles of HrMADS genes in male and female flowers of sea buckthorn showed that most Type II genes had higher expression levels than Type I genes. This suggesting that Type II may play a more significant role in sea buckthorn flower development. Using the phylogenetic relationship between sea buckthorn and , the ABCDE model genes of sea buckthorn were identified and some ABCDE model-related genes were selected for qRT-PCR analysis in sea buckthorn flowers and floral organs. Four B-type genes may be involved in the identity determination of floral organs in male flowers, and D-type genes may be involved in pistil development. It is hypothesized that ABCDE model genes may play an important role in the identity of sea buckthorn floral organs. This study analyzed the role of MADS-box gene family in the development of flower organs in sea buckthorn, which provides an important theoretical basis for understanding the regulatory mechanism of sex differentiation in sea buckthorn.
PubMed: 38938643
DOI: 10.3389/fpls.2024.1387613 -
Frontiers in Plant Science 2024The orchid genus R.Br. (Epidendroideae) comprises leafy autotrophic and leafless mycoheterotrophic species, with the latter confined to sect. . This study examined...
The orchid genus R.Br. (Epidendroideae) comprises leafy autotrophic and leafless mycoheterotrophic species, with the latter confined to sect. . This study examined plastome degeneration in in a phylogenomic and temporal context. Whole plastomes were reconstructed and annotated for 24 samples representing 14 species and two putatively new species, encompassing over 80% of species diversity in sect. . Phylogenomic analysis based on 68 plastid loci including a broad outgroup sampling across Orchidaceae found that sect. is the sister lineage to sect. , the only leafy autotrophic species in sect. , was found to be a sister to all leafless, mycoheterotrophic species, supporting a single evolutionary origin of mycoheterotrophy in the genus. Divergence-time estimations found that arose ca. 33.3 Ma near the lower boundary of the Oligocene and that crown diversification commenced in the late Miocene, ca. 11.3 Ma. Mycoheterotrophy in the genus was estimated to have evolved in the late Miocene, ca. 7.3 Ma, in sect. . The comparative assessment of plastome structure and gene degradation in revealed that plastid genes were pseudogenised or physically lost in all species, including in leafy autotrophic species of both sections. Levels of plastid gene degradation were found to vary among species as well as within species, providing evidence of relaxed selection for retention of the NADH dehydrogenase complex within the genus. exhibits an early stage of plastid genome degradation, as all species were found to have retained a full set of functional photosynthesis-related genes and housekeeping genes. This study provides important insights into plastid genome degradation along the transition from autotrophy to mycoheterotrophy in a phylogenomic and temporal context.
PubMed: 38938632
DOI: 10.3389/fpls.2024.1388537 -
PeerJ 2024is the only species distributed in the subtropical region within the spring ephemeral genus . Extensive human exploitation and habitat destruction have resulted in a...
BACKGROUND
is the only species distributed in the subtropical region within the spring ephemeral genus . Extensive human exploitation and habitat destruction have resulted in a rapid shrink of populations. This study utilizes microsatellite markers to analyze the genetic diversity and structure and to deduce historical population events of extant populations of .
METHODS
A total of 143 individuals from eight extant populations of , including two populations from Anhui Province and six populations from Zhejiang Province, were analyzed with using 21 pairs of microsatellite markers. Genetic diversity indices were calculated using Cervus, GENEPOP, GenALEX. Population structure was assessed using genetic distance (UPGMA), principal coordinate analysis (PCoA), Bayesian clustering method (STRUCTURE), and molecular variation analysis of variance (AMOVA). Population history events were inferred using DIYABC.
RESULTS
The studied populations of exhibited a low level of genetic diversity ( = 0.179, = 0.286), but a high degree of genetic differentiation ( = 0.521). The mean value of gene flow ( ) among populations was 1.082, indicating prevalent gene exchange pollen dispersal. Phylogeographic analyses suggested that the populations of were divided into two lineages, Zhejiang (ZJ) and Anhui (AH). These two lineages were separated by the Huangshan-Tianmu Mountain Range. AMOVA analysis revealed that 36.59% of total genetic variation occurred between the two groups. The ZJ lineage was further divided into the Hangzhou (ZJH) and Zhuji (ZJZ) lineages, separated by the Longmen Mountain and Fuchun River. DIYABC analyses suggested that the ZJ and AH lineages were separated at 5.592 ka, likely due to the impact of Holocene climate change and human activities. Subsequently, the ZJZ lineage diverged from the ZJH lineage around 2.112 ka. Given the limited distribution of and the significant genetic differentiation among its lineages, both and conservation strategies should be implemented to protect the germplasm resources of .
Topics: China; Microsatellite Repeats; Genetic Variation; Gene Flow; Cycadopsida; Bayes Theorem; Genetics, Population; Phylogeny
PubMed: 38938610
DOI: 10.7717/peerj.17554 -
PeerJ 2024White-rot fungi and bacteria communities are unique ecosystems with different types of symbiotic interactions occurring during wood decomposition, such as cooperation,...
Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam.
BACKGROUND
White-rot fungi and bacteria communities are unique ecosystems with different types of symbiotic interactions occurring during wood decomposition, such as cooperation, mutualism, nutritional competition, and antagonism. The role of chitin-active lytic polysaccharide monooxygenases (LPMOs) in these symbiotic interactions is the subject of this study.
METHOD
In this study, bioinformatics tools were used to analyze the sequence and structure of putative LPMOs mined by hidden Markov model (HMM) profiles from the bacterial metagenomic DNA database of collected humus samples around white-rot fungi in Cuc Phuong primary forest, Vietnam. Two genes encoding putative LPMOs were expressed in and purified for enzyme activity assay.
RESULT
Thirty-one full-length proteins annotated as putative LPMOs according to HMM profiles were confirmed by amino acid sequence comparison. The comparison results showed that although the amino acid sequences of the proteins were very different, they shared nine conserved amino acids, including two histidine and one phenylalanine that characterize the H1-Hx-Yz motif of the active site of bacterial LPMOs. Structural analysis of these proteins revealed that they are multidomain proteins with different functions. Prediction of the catalytic domain 3-D structure of these putative LPMOs using Alphafold2 showed that their spatial structures were very similar in shape, although their protein sequences were very different. The results of testing the activity of proteins GL0247266 and GL0183513 show that they are chitin-active LPMOs. Prediction of the 3-D structures of these two LPMOs using Alphafold2 showed that GL0247266 had five functional domains, while GL0183513 had four functional domains, two of which that were similar to the GbpA_2 and GbpA_3 domains of protein GbpA of bacteria. The GbpA_2 - GbpA_3 complex was also detected in 11 other proteins. Based on the structural characteristics of functional domains, it is possible to hypothesize the role of chitin-active GbpA-like LPMOs in the relationship between fungal and bacterial communities coexisting on decomposing trees in primary forests.
Topics: Vietnam; Mixed Function Oxygenases; Forests; Chitin; Metagenomics; Metagenome; Amino Acid Sequence
PubMed: 38938609
DOI: 10.7717/peerj.17553 -
PeerJ 2024Glutamine synthetase (GS), glutamate synthase (GOGAT), and nitrate reductase (NR) are key enzymes involved in nitrogen assimilation and metabolism in plants. However,...
BACKGROUND
Glutamine synthetase (GS), glutamate synthase (GOGAT), and nitrate reductase (NR) are key enzymes involved in nitrogen assimilation and metabolism in plants. However, the systematic analysis of these gene families lacked reports in soybean ( (L.) Merr.), one of the most important crops worldwide.
METHODS
In this study, we performed genome-wide identification and characterization of , , and genes in soybean under abiotic and nitrogen stress conditions.
RESULTS
We identified a total of 10 genes, six genes, and four genes in the soybean genome. Phylogenetic analysis revealed the presence of multiple isoforms for each gene family, indicating their functional diversification. The distribution of these genes on soybean chromosomes was uneven, with segmental duplication events contributing to their expansion. Within the nitrogen assimilation genes (NAGs) group, there was uniformity in the exon-intron structure and the presence of conserved motifs in NAGs. Furthermore, analysis of cis-elements in NAG promoters indicated complex regulation of their expression. RT-qPCR analysis of seven soybean NAGs under various abiotic stresses, including nitrogen deficiency, drought-nitrogen, and salinity, revealed distinct regulatory patterns. Most NAGs exhibited up-regulation under nitrogen stress, while diverse expression patterns were observed under salt and drought-nitrogen stress, indicating their crucial role in nitrogen assimilation and abiotic stress tolerance. These findings offer valuable insights into the genomic organization and expression profiles of , , and genes in soybean under nitrogen and abiotic stress conditions. The results have potential applications in the development of stress-resistant soybean varieties through genetic engineering and breeding.
Topics: Glycine max; Nitrogen; Gene Expression Regulation, Plant; Phylogeny; Glutamate-Ammonia Ligase; Stress, Physiological; Glutamate Synthase; Nitrate Reductase; Genome, Plant; Plant Proteins; Chromosomes, Plant; Droughts
PubMed: 38938604
DOI: 10.7717/peerj.17590 -
Frontiers in Immunology 2024The comorbidity rate of inflammatory bowel disease (IBD) and rheumatoid arthritis (RA) is high; nevertheless, the reasons behind this high rate remain unclear. Their...
BACKGROUND
The comorbidity rate of inflammatory bowel disease (IBD) and rheumatoid arthritis (RA) is high; nevertheless, the reasons behind this high rate remain unclear. Their similar genetic makeup probably contributes to this comorbidity.
METHODS
Based on data obtained from the genome-wide association study of IBD and RA, we first assessed an overall genetic association by performing the linkage disequilibrium score regression (LDSC) analysis. Further, a local correlation analysis was performed by estimating the heritability in summary statistics. Next, the causality between the two diseases was analyzed by two-sample Mendelian randomization (MR). A genetic overlap was analyzed by the conditional/conjoint false discovery rate (cond/conjFDR) method.LDSC with specific expression of gene analysis was performed to identify related tissues between the two diseases. Finally, GWAS multi-trait analysis (MTAG) was also carried out.
RESULTS
IBD and RA are correlated at the genomic level, both overall and locally. The MR results suggested that IBD induced RA. We identified 20 shared loci between IBD and RA on the basis of a conjFDR of <0.01. Additionally, we identified two tissues, namely spleen and small intestine terminal ileum, which were commonly associated with both IBD and RA.
CONCLUSION
Herein, we proved the presence of a polygenic overlap between the genetic makeup of IBD and RA and provided new insights into the genetic architecture and mechanisms underlying the high comorbidity between these two diseases.
Topics: Arthritis, Rheumatoid; Humans; Genome-Wide Association Study; Inflammatory Bowel Diseases; Genetic Predisposition to Disease; Linkage Disequilibrium; Polymorphism, Single Nucleotide; Mendelian Randomization Analysis; Comorbidity
PubMed: 38938570
DOI: 10.3389/fimmu.2024.1359857