Repurposing of the enhancer-promoter communication underlies the compensation of Mesp2 by Mesp1

Organisms are inherently equipped with buffering systems against genetic perturbations. Genetic compensation, the compensatory response by upregulating another gene or genes, is one such buffering mechanism. Recently, a well-conserved compensatory mechanism was proposed: transcriptional adaptation of homologs under the nonsense-mediated mRNA decay pathways. However, this model cannot explain the onset of all compensatory events. We report a novel genetic compensation mechanism operating over the Mesp gene locus. Mesp1 and Mesp2 are paralogs located adjacently in the genome. Mesp2 loss is partially rescued by Mesp1 upregulation in the presomitic mesoderm (PSM). Using a cultured PSM induction system, we reproduced the compensatory response in vitro and found that the Mesp2-enhancer is required to promote Mesp1. We revealed that the Mesp2-enhancer directly interacts with the Mesp1 promoter, thereby upregulating Mesp1 expression upon the loss of Mesp2. Of note, this interaction is established by genomic arrangement upon PSM development independently of Mesp2 disruption. We propose that the repurposing of this established enhancer-promoter communication is the mechanism underlying this compensatory response for the upregulation of the adjacent gene.

Nanoparticle mediated gene therapy: a trailblazer armament to fight CNS disorders

Central nervous system (CNS) disorders account for boundless socioeconomic burdens with devastating effects among the population, especially the elderly. The major symptoms of these disorders are neurodegeneration, neuroinflammation, and cognitive dysfunction caused by inherited genetic mutations or by genetic and epigenetic changes due to injury, environmental factors, and disease-related events. Currently available clinical treatment for CNS diseases, i.e., Alzheimer’s disease, Parkinson’s disease, stroke, and brain tumor have significant side effects and are largely unable to halt the clinical progression. So, gene therapy displays a new paradigm in the treatment of these disorders with some modalities, varying from suppression of endogenous genes to expression of exogenous genes. Both viral and non-viral vectors are commonly used for gene therapy. Viral vectors are quite effective but associated with immunogenicity and carcinogenicity like severe side effects, and poor target cell specificity. Thus, non-viral vectors, mainly nanotherapeutics like nanoparticles (NPs), opt-out to be a realistic approach in gene therapy in achieving higher efficacy. NPs demonstrate a new avenue in pharmacotherapy for the delivery of drugs or genes to their selective cells or tissue thus providing concentrated and constant drug delivery to targeted tissues, minimizing systemic toxicity and side effects. The current review will emphasize the role of NPs in mediating gene therapy for CNS disorders treatment. Moreover, the challenges and perspectives of NPs in gene therapy will be summarized.

Telomere Shortening and Its Association with Cell Dysfunction in Lung Diseases

Telomeres are localized at the end of chromosomes to provide genome stability; however, the telomere length tends to be shortened with each cell division inducing a progressive telomere shortening (TS). In addition to age, other factors, such as exposure to pollutants, diet, stress, and disruptions in the shelterin protein complex or genes associated with telomerase induce TS. This phenomenon favors cellular senescence and genotoxic stress, which increases the risk of the development and progression of lung diseases such as idiopathic pulmonary fibrosis, chronic obstructive pulmonary disease, SARS-CoV-2 infection, and lung cancer. In an infectious environment, immune cells that exhibit TS are associated with severe lymphopenia and death, whereas in a noninfectious context, naïve T cells that exhibit TS are related to cancer progression and enhanced inflammatory processes. In this review, we discuss how TS modifies the function of the immune system cells, making them inefficient in maintaining homeostasis in the lung. Finally, we discuss the advances in drug and gene therapy for lung diseases where TS could be used as a target for future treatments.

B Chromosomes’ Sequences in Yellow-Necked Mice Apodemus flavicollis—Exploring the Transcription

B chromosomes (Bs) are highly polymorphic additional chromosomes in the genomes of many species. Due to the dispensability of Bs and the lack of noticeable phenotypic effects in their carriers, they were considered genetically inert for a long time. Recent studies on Bs in Apodemus flavicollis revealed their genetic composition, potential origin, and spatial organization in the interphase nucleus. Surprisingly, the genetic content of Bs in this species is preserved in all studied samples, even in geographically distinct populations, indicating its biological importance. Using RT-PCR we studied the transcription activity of three genes (Rraga, Haus6, and Cenpe) previously identified on Bs in A. flavicollis. We analysed mRNA isolated from spleen tissues of 34 animals harboring different numbers of Bs (0–3). The products of transcriptional activity of the analysed sequences differ in individuals with and without Bs. We recorded B-genes and/or genes from the standard genome in the presence of Bs, showing sex-dependent higher levels of transcriptional activity. Furthermore, the transcriptional activity of Cenpe varied with the age of the animals differently in the group with and without Bs. With aging, the amount of product was only found to significantly decrease in B carriers. The potential biological significance of all these differences is discussed in the paper.

Screening for Odorant Receptor Genes Expressed in Aedes Aegypti Involved in Blood-Feeding and Oviposition Behaviors

Background: Aedes aegypti is one of the most important vector worldwide, and its survival and reproductive processes depend heavily on the olfactory system. In this study, the expression levels of all odorant receptor (OR) genes of Ae. aegypti were explored in different physiological periods to identify olfactory genes that may be associated with mosquito blood sucking and searching for oviposition sites.Methods: Four groups, consisting of Ae. aegypti males (M), pre-blood-feeding females (F), post-blood-feeding females (B) and post-oviposition females (O), were established. A total of 114 pairs of primer targeting all OR genes were designed based on the whole genome of Ae. aegypti. The expression of OR genes was evaluated by real-time fluorescence quantitative PCR for relative quantification and the comparison of differences between groups.Results: A total of 53 differentially expressed OR genes were identified between males and females in Ae. aegypti antennae. And 8, 5 and 13 differentially expressed OR genes were identified before versus after blood feeding, before versus after oviposition and post-blood-feeding versus post-oviposition, respectively. Meanwhile, 16 OR genes were significantly differentially expressed in multiple physiological periods of mosquitoes.Conclusions: A large number of ORs with significant intergroup differences and high expression levels were screened in this study, including OR75, OR88, OR110 and OR115 and so on. Some of these genes are reported for the first time, providing possible targets for the development of mosquito control pathways based on the olfactory system.

Molecular Cloning and Functional Characterization of a Sterol 3-O-Glucosyltransferase Involved in Biosynthesis of Steroidal Saponins in Trigonella foenum-graecum

Fenugreek (Trigonella foenum-graecum), a pharmacologically important herb, is widely known for its antidiabetic, hypolipidemic, and anticancer effects. The medicinal properties of this herb are accredited to the presence of bioactive steroidal saponins with one or more sugar moieties linked to the C-3 OH position of disogenin or its C25-epimer yamogenin. Despite intensive studies regarding pharmacology and phytochemical profiles of this plant, enzymes and/or genes involved in synthesizing the glycosidic part of fenugreek steroidal saponins are still missing so far. This study reports the molecular cloning and functional characterization of a key sterol-specific glucosyltransferase, designated as TfS3GT2 here, from fenugreek plant. The recombinant TfS3GT2 was purified via expression in Escherichia coli, and biochemical characterization of the recombinant enzyme suggested its role in transferring a glucose group onto the C-3 hydroxyl group of diosgenin or yamogenin. The functional role of TfS3GT2 in the steroidal saponin biosynthesis was also demonstrated by suppressing the gene in the transgenic fenugreek hairy roots via the RNA interference (RNAi) approach. Down-regulation of TfS3GT2 in fenugreek generally led to reduced levels of diosgenin or yamogenin-derived steroidal saponins. Thus, Tf3SGT2 was identified as a steroid-specific UDP-glucose 3-O-glucosyltransferase that appears to be involved in steroidal saponin biosynthesis in T. foenum-graecum.

Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird

Procellariiform seabirds rely on their sense of smell for foraging and homing. Both genomes and transcriptomes yield important clues about how olfactory receptor (OR) subgenomes are shaped by natural and sexual selection, yet no transcriptomes have been made of any olfactory epithelium of any bird species thus far. Here we assembled a high-quality genome and nasal epithelium transcriptome of the Leach’s storm-petrel (Oceanodroma leucorhoa) to extensively characterize their OR repertoire. Using a depth-of-coverage-assisted counting method, we estimated over 160 intact OR genes (∼500 including OR fragments). This method reveals the highest number of intact OR genes and the lowest proportion of pseudogenes compared to other waterbirds studied, and suggests that rates of OR gene duplication vary between major clades of birds, with particularly high rates in passerines. OR expression patterns reveal two OR genes (OR6-6 and OR5-11) highly expressed in adults, and four OR genes (OR14-14, OR14-12, OR10-2, and OR14-9) differentially expressed between age classes of storm-petrels. All four genes differentially expressed between age classes were more highly expressed in chicks compared to adults, suggesting that ORs genes may exhibit ontogenetic specializations. Three highly differentially expressed OR genes also had high copy number ratios, suggesting that expression variation may be linked to copy number in the genome. We provide better estimates of OR gene number by using a copy number-assisted counting method, and document ontogenetic changes in OR gene expression that may be linked to olfactory specialization. These results provide valuable insight into the expression, development, and macroevolution of olfaction in seabirds.

Acute Infectious Gastroenteritis: The Causative Agents, Omics-Based Detection of Antigens and Novel Biomarkers

Acute infectious gastroenteritis (AGE) is among the leading causes of mortality in children less than 5 years of age worldwide. There are many causative agents that lead to this infection, with rotavirus being the commonest pathogen in the past decade. However, this trend is now being progressively replaced by another agent, which is the norovirus. Apart from the viruses, bacteria such as Salmonella and Escherichia coli and parasites such as Entamoeba histolytica also contribute to AGE. These agents can be recognised by their respective biological markers, which are mainly the specific antigens or genes to determine the causative pathogen. In conjunction to that, omics technologies are currently providing crucial insights into the diagnosis of acute infectious gastroenteritis at the molecular level. Recent advancement in omics technologies could be an important tool to further elucidate the potential causative agents for AGE. This review will explore the current available biomarkers and antigens available for the diagnosis and management of the different causative agents of AGE. Despite the high-priced multi-omics approaches, the idea for utilization of these technologies is to allow more robust discovery of novel antigens and biomarkers related to management AGE, which eventually can be developed using easier and cheaper detection methods for future clinical setting. Thus, prediction of prognosis, virulence and drug susceptibility for active infections can be obtained. Case management, risk prediction for hospital-acquired infections, outbreak detection, and antimicrobial accountability are aimed for further improvement by integrating these capabilities into a new clinical workflow.

Identification of multi-antibiotic resistant bacteria isolated from Vietnamese climbing perch (Anabas testudineus) on fish farms in Ho Chi Minh City, Vietnam

Climbing perch (Anabas testudineus) is considered a cultured species with high economic value and is widely distributed in several Asian countries, including Vietnam. In climbing perch aquaculture, antibiotic and antibacterial agents have been overused, leading to the emergence of antibiotic-resistant bacteria or genes in the aquatic environment as well as in the seafood products. These antibiotic-resistant bacteria and/or genes can then be spread to human through the food chain, generating detrimental consequences for public health and environment. In this study, 14 bacterial strains were isolated from Vietnamese climbing perch collected from various fish farms in Ho Chi Minh City which possess abnormal symptoms on the outside and in their organs. These bacterial strains were then subjected to several biochemical tests to characterize their colony morphologies. Besides, gene sequencing was performed and as compared to the 16S rRNA, 4 bacterial strains were identified with a high percentage in similarity, including Pseudomonas aeruginosa (99.7%), Aeromonas caviae (99.93%), Kosakonia sacchari (100%), and Edwardsiella ictaluri (99.44%). Additionally, these bacteria showed high levels of antibiotic resistance against beta-lactam, tetracycline, and others. Taken together, these results showed that the four identified bacterial strains isolated from Vietnamese climbing perch circulated in fish farms in Ho Chi Minh City. Their current status of multi-antibiotic resistance indicates further alternative sources of antimicrobial agents, for example, natural compounds, to overcome antibiotic resistance. It is then crucial to identify fish diseases, the associated pathogens, and the new alternatives for antibiotics to protect aquatic ecosystems and water resources.

Non-Coding RNA Networks in Pulmonary Hypertension

Non-coding RNAs (ncRNAs) are involved in various cellular processes. There are several ncRNA classes, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). The detailed roles of these molecules in pulmonary hypertension (PH) remain unclear. We systematically collected and reviewed reports describing the functions of ncRNAs (miRNAs, lncRNAs, and circRNAs) in PH through database retrieval and manual literature reading. The characteristics of identified articles, especially the experimental methods, were carefully reviewed. Furthermore, regulatory networks were constructed using ncRNAs and their interacting RNAs or genes. These data were extracted from studies on pulmonary arterial smooth muscle cells, pulmonary artery endothelial cells, and pulmonary artery fibroblasts. We included 14 lncRNAs, 1 circRNA, 74 miRNAs, and 110 mRNAs in the constructed networks. Using these networks, herein, we describe the current knowledge on the role of ncRNAs in PH. Moreover, these networks actively provide an improved understanding of the roles of ncRNAs in PH. The results of this study are crucial for the clinical application of ncRNAs.