Promoter choice is an essential consideration for transgene expression in gene therapy. The expression of multiple genes requires ribosomal entry or skip sites, or the use of multiple promoters. Promoters systems comprised of two separate, divergent promoters may significantly increase the size of genetic cassettes intended for use in gene therapy. However, an alternative approach is to use a single, compact bidirectional promoter. We identified strong and stable bidirectional activity of the RPBSA synthetic promoter comprised of a fragment of the human Rpl13a promoter, together with additional intron / exon structures. The Rpl13a-based promoter drove long-term bidirectional activity of fluorescent proteins. Similar results were obtained for the EF1-α and LMP2/TAP1 promoters. However, in a lentiviral vector, the divergent bidirectional systems failed to produce sufficient titres to translate into an expression system for dual chimeric antigen receptors (CAR) expression. Although bidirectional promoters show excellent applicability to drive short RNA in Sleeping Beauty transposon systems, their possible use in the lentiviral applications requiring longer and more complex RNA, such as dual CAR cassettes, is limited.

Phylostratigraphic analysis is a way to look anew on phylogenetic data in the evolutionary aspect. It allows counting the evolutionary age based on the analysis of genes, their orthologs and finding the last common ancestor. We performed phylostratigraphic analysis of Arabidopsis thaliana genes associated with several types of abiotic stresses (heat, cold, water-related, light, osmotic, salt, and oxidative) determined by the Gene Ontology annotation. Comparison of the distributions of ages of genes associated with stresses of different type has shown the heat stress to involve older genes while the light stress – younger genes. At the same time, all types of stress are characterized by a significantly higher proportion of old genes (common to all eukaryotes) compared to the whole set of A.thaliana genes. This can be explained by the involvement of basic molecular processes in plant cells into the stress response. Reconstruction and graphical analysis of the gene network of the heat stress educed several clusters associated with different response functions. Some of these clusters contain only ancient genes. The results obtained show that the phylostratigraphic analysis reveals the fundamental features of the organization of gene networks and their evolution.

The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pangenomes of several crops. The pan-genomes of crops constructed from various cultivars/accessions, landraces, and wild ancestral species represent a compendium of genes and structural variations and allow researchers to search for the novel genes and alleles that were inadvertently lost in domesticated crops during the historical process of crop domestication or in the process of extensive plant breeding. Fortunately, many valuable genes and alleles associated with desirable traits like disease resistance, abiotic stress tolerance, plant architecture, and nutrition qualities exist in landraces, ancestral species, and crop wild relatives. The novels genes from the wild ancestors and landraces can be introduced back to high-yielding varieties of modern crops by implementing classical plant breeding, genomic selection, and transgenic/gene editing approaches. Thus, pan-genomic represents a great leap in plant research and offers new avenues for targeted breeding for mitigating the impact of global climate change. Here we summarize the tools used for pangenome assembly and annotations, web-portals hosting plant pangenomes. Furthermore, we highlight a few discoveries made in crops using the pan-genomic approach and its future potential.

The work provides insights on the effect of fire on soil processes in Mediterranean-type ecosystems of Cyprus. Soil samples from mountainous sites that were subjected to a summer wildfire and adjacent control samples were collected. Incubations were used to estimate basal respiration and isolate soil CO2 release of heterotrophic microorganisms from autotrophic root respiration and heterotrophic respiration from litter decomposition. Physicochemical properties changes, bacteria community changes using DNA extraction and 16S rRNA gene analysis, and the effects of ash and fresh litter addition were studied to reveal the microbial composition and the post-fire soil function. Laboratory incubation showed that burned soils constantly showed higher microbial respiration rates compared with control unburned areas, even six months after fire. Adding ash to unburned samples increased microbial respiration, suggesting that increased nutrient availability positively corelates with increased release of CO2 from fire-affected soil. Elevated temperatures due to the wildfire exerted significant effects on the composition of soil bacterial community. Nevertheless, the wildfire did not affect the alpha-diversity of soil bacteria. New communities of microorganisms are still able to decompose fresh plant material after fire, but at a slower rate than natural pre-fire populations.

Abiotic stress is an adverse environmental factor that severely affects plant growth and development, and plants have developed complex regulatory mechanisms to adapt to these unfavourable conditions through long-term evolution. In recent years, many transcription factor families of genes have been identified to regulate the ability of plants to respond to abiotic stresses. Among them, AP2/ERF (APETALA2/ethylene responsive factor) family is a large class of plant-specific that regulate plant response to abiotic stresses and can also play a role in regulating plant growth and development. This paper reviews the structural features and classification of AP2/ERF transcription factors, that transcriptional regulation, reciprocal proteins, downstream genes and hormone-dependent signalling and hormone-independent signalling pathways are involved in the response to abiotic stress. The study of AP2/ERF transcription factors and interacting proteins, as well as the identification of their downstream target genes, can provide us with a more comprehensive understanding of the mechanism of plant action in response to abiotic stress, which can improve the tolerance ability of plants in abiotic stress, and provide more theoretical basis for rice to obtain more yields under abiotic stress.

In tobacco plants, symbiont endophytic fungi are widely distributed in all tissues where they play important roles. It is therefore important to determine the species distribution and characteristics of endophytic fungi in tobacco. Here, two parasitic fungi Leptosphaerulina chartarum and Curvularia trifolii were isolated and identified from normal tobacco tissue. We sequenced the mitogenomes of these two species and analysed their features, gene content, and evolutionary histories. The L. chartarum and C. trifolii mitochondrial genomes were 68,926 bp and 59,100 bp long circular molecules with average GC contents of 28.60% and 29.31%, respectively. The L. chartarum mitogenome contained 36 protein coding genes, 26 tRNA genes, and 2 rRNA genes (rrnL and rrnS), which were located on both strands. The C. trifolii mitogenome contained 26 protein coding genes, 29 tRNA genes, and 2 rRNA genes (rrnL and rrnS). The L. chartarum 26 tRNAs ranged from 70 bp to 84 bp in length, whereas the 29 tRNAs in C. trifolii ranged from 71 bp to 85 bp. L. chartarum and C. trifolii mtDNAs had an identical mitochondrial gene order and orientation and were phylogenetically identified as sisters. These data therefore provide an understanding of the gene content and evolutionary history of species within Pleosporales.

Several effective online and offline inference tools offer an interactive platform for inference, visualization, and analysis of gene regulatory networks. However, a tool currently needs to offer a scalable, lightweight, integrated online platform for carrying out inference, visualization, benchmarking, and extensive network analysis in an integrated manner. We introduce NetRA (Network Reconstruction and Analysis for Gene Regulatory Network), a comprehensive web tool for network analysis, visualization, and inference of large expression networks. Additionally, a platform for benchmarking and evaluation is provided. In order to deliver a highly scalable, lightweight, and rich user interface, the tool is created using the most recent technologies. We incorporate the original code of eleven (11) inference algorithms (not limited to) from Bioconductor in the current version. We also report a qualitative comparison of 11 candidate methods regarding prediction accuracy and network characteristics which will shed light on their performance against 4000 sizes synthetic DREAM network. We believe the tool will significantly aid biologists' downstream system biology research. NetRA tool can be extensible to different kinds of complex network analyses. Availability: On request ([email protected]).

Cervical cancer is associated with persistent infections by high-risk HPV types that may have nucleotide polymorphisms and, consequently, different oncogenic potentials. Therefore, the objective of this study was to evaluate the genetic variability and structural effects of E7 oncogene of HPV58 in cervical scraping samples from Brazilian women. The study was carried out with patients from hospitals in metropolitan area of Recife, PE, Brazil. The most frequent HPV type was HPV16, 18 and 58, respectively. Phylogenetic analysis showed that the isolates were classified as sublineages A2, C1 and D2. Two positively selected mutations were found in E7: 63G and 64T. The mutations G41R, G63D and T64A in E7 protein were predicted to reduce the stability of the protein structure. Regarding the interaction of the E7 variant of HPV58 with the signaling of the NF-kB pathway, we observed that the variant HPV58/UFPE-54S decreased the activity of the pathway when compared to the prototype and the other variants behaved similarly to the prototype and the prototype increased the activity of the pathway when compared to pcDNA. In this study, it was possible to identify mutations that may interfere in the molecular interaction between the viral oncoproteins and host proteins.

Identification of the differentially-expressed genes is important for clarification of the complex molecular mechanisms under drought conditions. In this experiment, transcriptome profiles of sensitive and tolerant tomato genotypes under drought stress were analyzed. Three up-regulated genes were selected, included CAB3 (Chlorophyll a-b binding protein3), SAMDC (S-adenosylmethionine decarboxylase proenzyme), and ACS9 (1-aminocyclopropane-1-carboxylate synthase 9). After bioinformatics analysis, tomato genotypes were subjected to drought stress and gene expression was determined using Real-Time-PCR. Physiological parameters of genotypes were also measured by spectrophotometer-based methods. According to the results, these three genes play a key role in stress tolerance. Expression of the CAB3 gene in both sensitive and tolerant genotypes was not significantly different compared to the control, but the SAMDC gene decreased in both genotypes and the ACS9 gene decreased in sensitive genotype and increased in tolerant genotype. The physiological analysis also showed that under stress conditions, the photosynthetic system of the plant was disrupted and the chlorophyll content was reduced, but, proline content and antioxidant enzymes activity increased, in which their quantity in the tolerant genotype was significantly higher than sensitive. Under drought stress, due to damage to the lipid membrane, Malondialdehyde content also increased, in which the sensitive genotype was more affected.

The major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates, and their proteins play a critical role in adaptive immunity for defense against a variety of pathogens. MHC diversity was lost in many species after experiencing a decline in size. To understand the variation and evolution of MHC genes in the Siberian ibex, Capra sibirica, which has undergone a population decline, we analyzed the variation of the second exon of MHC class II DRB genes in samples collected from five geographic localities in Xinjiang, China, that belong to three diverged mitochondrial clades. Consequently, we identified a total of 26 putative functional alleles (PFAs) with 260 bp in length from 43 individuals, and found one (for 27 individuals) to three (for 5 individuals) PFAs per individual, indicating the presence of one or two DRB loci per haploid genome. The Casi-DRB1*16 was the most frequently occurring PFA, Casi-DRB1*22 came after found in only seven individuals, 14 PFAs occurred once (7 PFAs twice), implying high frequency of rare PFAs. Interestingly, more than half of the (15) PFAs were specific to clade I, only one and three PFAs were specific to clades II and III, respectively. So, we assume that the polygamy and sextual segregation nature of this species likely contributed to the allelic diversity of DRB genes. Genetic diversity indices showed that PFAs of clade II were lower in nucleotide, amino acid, and supertype diversity compared to those of the other two clades. The way of allele sharing and FST values between three clades were to some extent in agreement with pattern observed in mitochondrial DNA divergence. In addition, recombination analyses revealed no evidence for significant signatures of recombination events. Alleles shared by clades III and the other two clades diverged 6 million years ago, and systematic neighbor grids showed cross-species polymorphisms. Together with the PAML and MEME analyses, the results indicated that the DRB gene in C. sibirica evolved under balancing and positive selection. However, by comparison, it can be clearly seen that different populations were under different selective pressures. Our results are valuable in understanding the diversity and evolution of the DRB gene in a mountain living C. sibirica and in making decisions on future long-term protection strategies.

Soybean is one of the world’s most economically significant crops and is widely utilized as an essential source of vegetable protein and edible oil. Cultivated soybean is domesticated from its annual counterpart, wild soybean, which is considered valuable germplasm for soybean breeding. However, wild soybean accessions generally produce seeds with impermeable coats, a trait known as hard seededness (HS), which is beneficial for long-term seed survival but is undesirable for the uniform water absorption and germination of seeds, thus limiting the utilization of wild soybeans in breeding. However, moderate HS can isolate the embryo from the surrounding environment and is thus beneficial for long-term seed storage and germplasm preservation. The HS trait is primarily associated with the structure and chemical composition of the seed coat. However, its development is also influenced by various environmental conditions, such as water and temperature. Genetic analysis has revealed that HS of soybean is a complex quantitative trait controlled by multiple genes or minor quantitative trait loci (QTL), with many QTLs and several causal genes currently identified. Investigating the physiological and molecular mechanisms underlying this trait is crucial for soybean breeding, production, and food processing. For this article, the literature was reviewed and condensed to create a well-rounded picture of the current understanding of internal and external factors, QTLs, causal genes, and the regulatory mechanisms related to the HS of soybean, with the aim of providing reference for future research and utilization of this trait.

Carotid intima-media thickness (CIMT) is a surrogate indicator for atherosclerosis and has been shown to predict cardiovascular risk in multiple large studies. Identifying and characterizing molecular markers for carotid atheroma plaque formation can be critical for early intervention and prevention of atherosclerosis. This study performed transcription factor (TF) network analysis of transcriptomic data focusing on two TF genes, ZNF385D, HAND2, whose polymorphisms reportedly associate with carotid atherosclerosis. Gene expression data were measured from pieces of carotid endarterectomy of hypertensive patients each paired with one sample of distant macroscopically intact tissue. TF networks were reconstructed for ZNF385D and HAND2 and their association with carotid atheroma progression examined using gene-set enrichment analysis with high statistical significance (p<6.95e-7) suggesting involvement of expression quantitative loci (eQTL). Examination of the regulation and correlation patterns suggests high clinical and interventional impacts of the two TF genes on impairing carotid atheroma plaque formation and preventing carotid atherosclerosis.

Lifestyle has been associated with breast cancer risk through different pathways, including oxidative stress. Antioxidant enzymes are endogenous defense mechanisms against oxidative stress damage, and this response might be modulated by the genetic variation in these enzyme-codifying genes. This study aimed to analyze the synergistic effect of an antioxidant Healthy Lifestyle Index (HeLiX) composed of principal components of Western dietary pattern, alcohol consumption, smoking and physical activity, and genetic polymorphisms in the first-line antioxidant response family genes SOD, GPX, and CAT on breast cancer risk. We included 176 SNPs, and only CAT rs554576 remained significant after correction for multiple comparisons. Breast cancer odds were reduced at the highest (T3) and medium (T2) tertiles of the HeLiX. When stratified by HeLiX, we observed a reduced risk of breast cancer with at least one T-allele, and the effect increased in a dose-dependent manner. Compared to the reference category (HeLiX T1 and AA genotype), women at the HeLiX T3 with AT and TT genotypes in postmenopausal women showed an OR = 0.15 (95% CI 0.07–0.32). For HeLiX T2 and AT genotype OR = 0.26 (95% CI 0.13–0.54); for TT genotype OR = 0.24 (95% CI 0.12–0.45). For premenopausal women, at the HeLiX T3 and AT genotype OR = 0.29 (95% CI 0.13–0.62); for the TT genotype OR = 0.21 (95% CI 0.08–0.51). We also observed an inverse association for HeLiX T2 and TT genotype (OR 0.39 95% CI 0.17–0.87). Our study shows a significant synergistic gene-environment interaction on an additive scale, contributing to understanding pathways involved in breast cancer etiology and prevention.

The excellent properties of nanomaterials have been confirmed in many fields, but the effects on plants are still unclear. In this study, we have found that bismuth vanadium promoted the growth of taproots and the development of lateral roots, increased the roots activity by regulating the expression of polyamine or hormone-related genes and reducing the accumulation of reactive oxygen species in Arabisdopsis thaliana. Meantime, BV had higher antimicrobial effect than that of graphene oxide (GO). These results showed us a new perspective possibility of nanomaterials assisting the development of plants and crops, which is expected to become one of the ways to solve the problem of controlling and promoting the development of plants and crops.

Inorganic polyphosphate (polyP) is an important factor of stress tolerance in microbial cells. In yeast, the major enzyme of polyP biosynthesis is Vtc4, a subunit of the vacuole transporter chaperone (VTC) complex. In this study, we demonstrated that Vtc4 knockout in Saccharomyces cerevisiae not only decreased polyP content but also caused shifts in the composition of the intracellular polyP pool and changed the stress tolerance profile. In the mutant S. cerevisiae, the level of short-chain acid-soluble polyPs was decreased nearly 10-fold, whereas that of longer acid-insoluble polyPs was decreased only 2-fold, suggesting the existence of other enzymes compensating the production of long-chain polyPs. The Δvtc4 mutant showed inhibition of Mg2+-dependent phosphate uptake and decreased resistance to alkaline stress but increased tolerance to oxidation and heavy metal ions, especially Mn2+. Quantitative PCR revealed the upregulation of the DDR2 gene implicated in multiple stress responses and downregulation of PHO84 encoding a phosphate and Mn2+ transporter, which could account for the effects on phosphate uptake and Mn2+-related stress response in the Δvtc4 mutant. Our study indicates that short-chain polyPs, plays an important role in the regulation of stress response in yeast.

Phosphate (Pi) deficiency reduces nodule formation and development in different legume species including common bean. Despite the significant progress in the understanding of the genetic responses underlying the adaptation of nodules to Pi deficiency, it is still unclear whether this nutritional deficiency interferes with the molecular dialog between legumes and rhizobia, if so, what part of the molecular dialog is impaired? In this study, we provide evidence demonstrating that Pi deficiency negatively affects critical early molecular and physiological responses required for a successful symbiosis between common bean and rhizobia. We demonstrated that the infection thread formation and the expression of PvNSP2, PvNIN, and PvFLOT2, genes controlling the nodulation process, were significantly reduced in Pi-deficient common bean seedlings. Further transcriptional analysis revealed that the expression of hormones-related genes is compromised in Pi-deficient seedlings inoculated with rhizobia. Additionally, we showed that regardless of the presence or absence of rhizobia, the expression of PvRIC1 and PvRIC2, two genes participating in the autoregulation of nodule number, was higher in Pi-deficient seedlings than in control seedlings. The data presented in this study shed light on the understanding of how Pi deficiency impacts the early steps of the symbiosis between common bean and rhizobia.

Atopic dermatitis (AD) has been extensively investigated for genetic associations utilizing both candidate gene approaches and genome-wide scans. Here, we comprehensively evaluated the available literature to determine the association of candidate genes in AD to gain additional insight in the etiopathogenesis of the disease. We systematically screened all studies that explored the association between polymorphisms and AD risks in cases of European and Asian ancestry and synthesized the available evidence through random-effects meta-analysis. We identified 97 studies that met our inclusion/exclusion criteria that examined 17 candidate loci in Europeans and 14 candidate genes in Asians. We confirmed the significant associations between FLG variants in both European and Asian populations and AD risk, while additional synthesis of available data revealed novel loci mapped to IL18 and TGFB1 genes in Europeans and IL12RB1 and MIF in Asians, that have not yet been identified by genome-wide association studies. Our findings provide comprehensive evidence for AD risk loci in cases of both European and Asian ancestries, validating previous associations as well as revealing novel loci that could imply previously unexplored biological pathways.

Hypoxia represents one of the key factors that stimulate the growth of leukemic cells in their niche. Leukemic cells in hypoxia are forced to reprogram their original transcriptome, miRNome, and metabolome. How the coupling of miRNAs/mRNAs helps to maintain or progress the leukemic status is still not fully described. MicroRNAs (miRNAs) regulate practically all biological processes within cells and play a crucial role in leukemia development/progression. Here we worked with the human cell line MEC-1 (human chronic lymphocytic leukemia (CLL)) where we deleted mature miR-155 by CRISPR/Cas9. MEC-1 cells in hypoxia showed a higher proliferation rate with a relatively low level of apoptosis. Interestingly, miR-155 deficiency decreased the proliferation rate in both, normoxia and hypoxia. Besides common hypoxia-related genes (HIF1α, EGLN1, VHL, HK1, and HK2), we also measured, genes for glucose transporters SLC2A1 (GLUT1) and SLC2A3 (GLUT3). Surprisingly, only SLC2A3 (GLUT3) showed significant overexpression in hypoxia conditions in miR-155 deficient MEC-1cells which points to the possible novel target of miR-155 in CLL. Increased glucose uptake and decreased lactate support our hypothesis that miR-155 deficiency and hypoxia transform cell metabolism. To conclude, miR-155 deficiency and hypoxia-impaired glucose metabolism stimulate GLUT3 in CLL cells.

The epigenetic mechanism of DNA methylation is essential for regulating gene expression and adaptation in plants, especially when exposed to various environmental stressors such as drought, heat, and nutrient availability. The impact of these stressors can lead to alterations in DNA methylation patterns and gene expression, which this study aims to investigate. Specifically, we are interested in understanding how DNA methylation plays a role in controlling the expression of stress-response genes, as well as genes involved in plant growth and development. To accomplish this, we are analyzing the changes in DNA methylation patterns and gene expression in response to different stressors like drought and heat. Our research findings suggest that DNA methylation is a vital regulator of plant adaptation to environmental stress, and we hope to gain further insight into these mechanisms by identifying genes that exhibit differential expression in response to stress and analyzing their DNA methylation status. This study offers valuable insights into the development of crops that can thrive under changing climate conditions.

The literature study delves into novel therapeutic strategies in transplantation medicine, highlighting unique approaches that could revolutionize current practices. It emphasizes novel patterns that have the potential to transform the current landscape. Commencing with a thorough examination of the historical environment, it traces crucial advances and changes in transplantation. The focus is on traditional techniques, emphasizing their limitations and challenges. An extensive examination of contemporary transplantation therapies offers valuable insights into the most recent progress in organ, cellular, and tissue transplantation. This analysis examines the immunological obstacles and outlines the current advancements and constraints. The exploration further navigates into novel models and concepts such as immunomodulation, developments in organ preservation techniques, gene editing, biomaterials, scaffold-based solutions, and the integration of precision medicine, artificial intelligence, and machine learning applications. Each section analyzes the potential for change and current progress in various areas, backed by relevant scientific sources up to 2023. The subsequent sections delve into innovative cellular therapies, biotechnological progress, current clinical trials, and case studies demonstrating effective applications. This examination delves into the ethical and regulatory considerations of innovative therapeutic procedures, emphasizing ethical implications, regulatory frameworks, and the importance of balancing innovation with patient welfare. The literature review concludes by offering a forward-looking perspective, emphasizing potential progress, anticipated challenges, and advocating for collaboration and interdisciplinary approaches to overcome limitations in the field of transplantation medicine.

Allergic reactions are the most frequent adverse effects of blood transfusion, and anaphylactic shock, although less frequent, is systemic and serious. The causes of allergic reactions to blood transfusions are largely unknown, but deficiencies in serum proteins such as haptoglobin (Hp) can lead to anaphylactic shock. A complete deletion of the haptoglobin gene (HPdel) was first identified in families with anomalous inheritance and then verified as a genetic variant that can cause anaphylactic shock because homozygotes of HPdel have an Hp deficiency. Thereby, they may produce antibodies against Hp from blood transfusions. HPdel is found in East and Southeast Asian populations, but not in other populations, with a frequency of approximately 0.9% to 4%. Diagnosis of Hp deficiency due to HPdel prior to transfusion is desirable because severe adverse reactions can be prevented by washing the red blood cells and/or platelets with saline or by administrating plasma products obtained from an Hp deficient donor pool. This review outlines the background of the identification of HPdel and several genetic and immunological methods developed for diagnosing Hp deficiency caused by HPdel.

Glioblastoma multiforme (GBM), the most prevalent primary malignant brain tumor in adults, exhibits a dismal 6.9% five-year survival rate post-diagnosis. Thymoquinone (TQ), the most abundant bioactive compound in Nigella Sativa, has been extensively researched for its anti-cancer properties across various human cancers. Yet, its specific anticancer mechanisms and pathways in glioblastoma remain to be elucidated. In this study, we assessed the impact of different TQ concentrations on the viability of A172 cells using WST-8 and Toluidine blue assays, followed by RNA sequencing (RNA-seq) to identify differentially expressed genes (DEGs). We confirmed their expression levels through quantitative RT-PCR and performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for these DEGs. RNA-seq revealed no significant gene expression changes at 2.5 µM and 5 µM TQ concentrations. However, at 25 µM and 50 µM, TQ significantly reduced cell viability in a dose-dependent manner. We identified 1548 DEGs at 25 µM TQ (684 upregulated, 864 downregulated) and 2797 DEGs at 50 µM TQ (1528 upregulated, 1269 downregulated), with 1202 DEGs common to both concentrations. TQ inhibited key pathways such as PI3K-Akt signaling, calcium signaling, focal adhesion, and ECM-receptor interaction in A172 cells. It downregulated several potential oncogenes (e.g., AEBP1, MIAT) and genes linked to GBM proliferation and migration (e.g., SOCS2, HCP5), while modulating Wnt signaling and upregulating tumor suppressor genes (e.g., SPRY4, BEX2). TQ also affected p53 downstream targets, maintaining p53 levels. This study elucidates the anticancer mechanisms of TQ in A172 GBM cells, underscoring its effects on multiple signaling pathways and positioning TQ as a promising candidate for innovative glioblastoma treatment strategies.

Phytoene desaturase (PDS) is a plant enzyme involved in carotenoid biosynthesis. The PDS gene has been used as a selective marker for genome editing in several plant species, including banana (Musa spp.). Its knockout promotes dwarfism and albinism, characteristics that are easily recognizable and highly favorable. In Musa spp., the A genome increases fruit production and quality, whereas the B genome is associated with tolerance to biotic and abiotic stresses. The objective of this study was to identify a molecular marker in the PDS gene to easily discriminate the A and B genomes of banana. A 2166 bp fragment for the ‘PDSMa’ marker was identified as polymorphic for the A genome (identification accuracy of 99.33%), whereas ~332 and ~225 bp fragments were detected for the ‘PDSMb’ primer with 100% accuracy using MedCalc software. To the best of our knowledge, this is the first study to use the PDS gene to determine doses of the A genome and identify the B genome in Musa spp., which will aid in evaluating the genomic constitution of banana hybrids and accessions at the seedling stage, and accelerating their classification in crop genetic improvement programs.

Anthracnose, caused by the fungus Colletotrichum lindemuthianum, poses a significant and widespread threat to the common bean crop. The use of plant genetic resistance has proven to be the most effective strategy for managing anthracnose disease. The Amendoim Cavalo (AC) Andean cultivar has resistance against multiple races of C. lindemuthianum, which is conferred by the Co-AC gene. Fine mapping of this resistance gene to common bean chromosome Pv01 enabled the identification of Phvul.001G244300, Phvul.001G244400, and Phvul.001G244500 candidate genes for further validation. In this study, we assessed the relative expression of Co-AC candidate genes, as well as other putative genes in vicinity of this locus and known resistance genes, in the AC cultivar following inoculation with the race 73 of C. lindemuthianum. Gene expression analysis revealed significantly higher expression levels of Phvul.001G244500. Notably, Phvul.001G244500 encodes a putative Basic Helix-Loop-Helix transcription factor, suggesting its involvement in the regulation of defense responses. Furthermore, we observed a significant modulation of the expression of defense related genes PR1a, PR1b, and PR2, in a time-course experiment. These findings contribute to the development of improved strategies for breeding anthracnose-resistant common bean cultivars, thereby mitigating the impact of this pathogen on crop yields and ensuring sustainable bean production.

The current systematic review examines whether there is an association between the genetic 5-HTTPLR pol-ymorphism and parenting and the mechanisms by which this association operates. The literature was searched in various databases such as PubMed, Scopus and ScienceDirect. In line with our inclusion criteria, nine articles were eligible out of 22. Most of the studies, analysed in this review, found an association between 5HTTLPR and parenting. Four studies found a direct association between 5-HTTLPR and parenting with conflicting findings: two studies found that mothers carrying the short variant were more sensitive to their infants, while two studies found that parents carrying the S allele were less sensitive. In addition, several studies found strong interaction between genetic and environmental factors, such as childhood stress and disruptive child behaviour, quality of early care experiences, poor parenting environment, and quality of environment. Only one study found an association between children’s 5HTTLPR and parenting. Parenting can be described as a highly complex construct influenced by multiple factors, including environmental, parenting and child charac-teristics. According to the studies, maternal 5-HTTLPR polymorphism is most likely associated with sensitive parenting.

The importance of genome organization at the supranucleosomal scale in the control of gene expression is increasingly recognized today. In mammals, Topologically Associating Domains (TADs) and the active / inactive chromosomal compartments are two of the main nuclear structures that contribute to this organization level. However, recent works reviewed here indicate that, at specific loci, chromatin interactions with nuclear bodies could also be crucial to regulate genome functions, in particular transcription. They moreover suggest that these nuclear bodies are membrane-less organelles dynamically self-assembled and disassembled through mechanisms of phase separation. We have recently developed a novel genome-wide experimental method, High-salt Recovered Sequences sequencing (HRS-seq), which allows the identification of chromatin regions associated with large ribonucleoprotein (RNP) complexes and nuclear bodies. We argue that the physical nature of such RNP complexes and nuclear bodies appears to be central in their ability to promote efficient interactions between distant genomic regions. The development of novel experimental approaches, including our HRS-seq method, is opening new avenues to understand how self-assembly of phase separated nuclear bodies possibly contributes to mammalian genome organization and gene expression.

Over recent decades, therapeutic proteins have had widespread success in treating a myriad of diseases. Glycosylation, a near universal feature of this class of drugs, is a critical quality attribute that significantly influences the physical properties, safety profile and biological activity of therapeutic proteins. Optimizing protein glycosylation, therefore, offers an important avenue to developing more efficacious therapies. In this review, we discuss specific examples of how variations in glycan structure and glycoengineering impacts the stability, safety, and clinical efficacy of protein-based drugs that are already in the market as well as those that are still in preclinical development. We also highlight the impact of glycosylation on next generation biologics such as T cell-based cancer therapy and gene therapy.

Vernonia amygdalina is an important nutritional and medicinal plant that is used to treat various diseases such as malaria and diabetes in Nigeria. In this study, we sequenced, assembled, and annotated the complete nucleotide sequence of the chloroplast genome of a V. amygdalina species isolated in Awka, Nigeria. The chloroplast genome is 153 149 bp in length and has a conserved structure that includes the LSC (84261 bp) region, the SSC (13152 bp) region, and the IR (27868 bp) regions. A total of 131 genes were identified, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Comparative analysis of the genome revealed species variations in the LSC region associated with the geographical location of the V. amygdalina plant. Phylogenetic analysis of the chloroplast genomes using FastTree showed that V. amygdalina clustered closest to the chloroplast of the Crepidiastrum genus. This study identifies the characteristics of the V. amygdalina chloroplast genome, which will improve our understanding of intraspecies diversity and the identification of potential molecular markers to determine geographical origin.

The research and development of non-viral gene therapy has been extensive over the past decade and has received a big push thanks to the successful approval of non-viral gene therapy products in recent times. Despite these developments, gene therapy applications in cancer have been limited. One of the main causes of this has been the imbalance in development of delivery vectors as compared to nucleic acid payloads. This paper reviews non-viral vectors that can be used to deliver nucleic acids for cancer treatment. It discusses various types of vectors and highlights their current applications. Additionally, it also discusses perspective on regulatory landscape to facilitate commercial translation of gene therapy.

Powdery mildew disease, caused by Sphaerotheca fusca, is a major disease affecting cucumbers cultivated in greenhouses. This study was conducted to find defense genes induced by DL-3-amino-butyric acid (BABA) and powdery mildew in cucumber. The 2000 and 5000 mg/L BABA treated cucumber exhibited disease severity of 25% and 5%, respectively, whereas the water treated cucumber leaves were severely infected, with a disease severity of 90%. BABA did not effect spore germination of the powdery mildew pathogen,. showing BABA is not antifungal agent against the pathogen. In quantitative real-time PCR analysis, BABA treated cucumber upregulated transcriptional level of the defense genes CsPAL, CsPR3,CsPR1, CsLOX1, CsLOX23, Cs LecRK6.1, CsWRKY20, and Cupi4 in cucumber to maximum levels at 48 h, whereas CsLecRK6.1 reached maximum expression after 24 h and futher salicylic acid (SA) levels were significantly increased in BABA-treated cucumber plants. In addition, the infected cucumber with powdery mildew enhanced the expression levels from1.6 to 47.3 fold of the defense genes PAL, PR3, PR1, Lox1, Lox 23, LecRK6.1, WRKY20, and Cupi4 compared to heathy cucumber. The results suggests the BABA induced defense response is associated with SA signal pathway-dependent systemic acquired resistance (SAR) in cucumber, which is involved in plant resistance mechanisms.

Whole-genome DNA sequencing of Lactobacillus D75 and D76 strains (Vitaflor, Russia) was performed using the PacBio RS II platform, followed by de novo assembly with SMRT Portal 2.3.0. The average nucleotide identity (ANI) test showed that both strains belong to the Lactobacillus helveticus, but not the L. acidophilus as previously assumed. 31 exopolysaccharide (EPS) production genes (nine of which form a single genetic cluster), 13 adhesion genes, 38 milk protein and 11 milk sugar utilization genes, 13 genes for and against specific antagonistic activity, aight antibiotic resistance genes, and also three CRISPR blocks and eight Cas I-B system genes were identified in the genomes of the both strains. The expression of some genes was confirmed. In fact, the presence of identified genes suggests that L. helveticus D75 and D76 are able to form biofilms on the outer mucin layer, inhibit the growth of pathogens and pathobionts, utilize milk substrates with the formation of digestible milk sugars and bioactive peptides, resist bacteriophages and show some genome-determined resistance to antibiotics, stimulate the host’s immune system. Pathogenicity genes have not been identified. The study results confirm the safety and high probiotic potential of the strains.

Background: Commensal Neisseria species are part of the oropharyngeal microbiome and important for health, but also serve as a reservoir for antimicrobial resistance. Little is known about the prevalence of these species in the general population, how this varies by age and how antimicrobial susceptibility varies between species. Methods: We assessed the prevalence and antimicrobial susceptibility of commensal Neisseria species in the parents (n=38) and children (n=50) of 35 families in Belgium.Results: Various commensal Neisseria (n=5) could be isolated from the participants. Most abundant were N. subflava and N. mucosa. N. subflava was detected in 77 of 88 (87.5%) individuals and N. mucosa in 64 of 88 (72.7%). N. mucosa was more prevalent in children (41/50 [82%]) than parents (23/38 [60.5%]; P<0.05), while N. bacilliformis was more prevalent in parents (7/36 [19.4%]) than children (2/50 [4%]; P<0.05). N. bacilliformis showed high ceftriaxone minimum inhibitory concentrations (MICs; median MIC 0.5mg/L; IQR 0.38-0.75) and these high MICs explained the higher ceftriaxone MICs of all Neisseria isolates from the parents than the children. The median azithromycin MIC of all Neisseria isolates per individual was positively correlated with the median family MIC (rho=0.24; P=0.033). The same association was found for the analysis limited to N. subflava (rho=0.36; P=0.004) and N. mucosa (rho=0.30; P=0.027). Interpretation: The most abundant commensal Neisseria species found in this population were N. subflava and N. mucosa, of which the prevalence of N. mucosa varied by age. The prevalence of N. bacilliformis also varied by age and showed concerningly high ceftriaxone MICs which warrant further investigation. We found evidence of clustering of azithromycin, but not ceftriaxone, MIC by family.

Suppressors of cytokine signaling (SOCS) genes are essential negative regulators that modulate cytokine signaling and play key roles in numerous biological processes, including immune responses. In this study, we cloned the complementary DNA (cDNA) sequences of two SOCS genes, designated as LvSOCS6 and LvSOCS7, from the white-leg shrimp, Litopenaeus vannamei. LvSOCS6 encoded a polypeptide of 463 amino acids (aa), spanning 1,392 base pairs (bp), while LvSOCS7 encodes a significantly larger polypeptide of 955 aa, encompassing 2,868 bp. Both LvSOCS proteins exhibited conserved domains associated with SOCS, including a centralized Src homology 2 (SH2) domain and a C-terminal SOCS box. Phylogenetic analysis revealed that the deduced aa sequences of LvSOCS6 and LvSOCS7 cluster within the invertebrate type I SOCS family, indicating their evolutionary relatedness. Tissue distribution analysis demonstrated ubiquitous expression of both LvSOCS genes across all examined tissues, with LvSOCS6 showing heightened expression in the gills and LvSOCS7 exhibiting a remarkable preference for the gills and stomach. Notably, mRNA expression patterns of LvSOCS genes following LPS and poly (I:C) stimulations exhibit significant upregulations, while PGN stimulation yields incongruous results across the experimented tissues. Interestingly, concurrent with the diminished expression of LvSOCS6 and LvSOCS7, there is a significant elevation in mRNA expression levels of LvSTAT, a vital component of the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway. These findings shed light on the potential involvement of the newly discovered type I SOCS genes in regulating the JAK/STAT pathway and assuming pivotal roles in orchestrating the innate immune responses in L. vannamei defense mechanisms.

Cardiovascular diseases (CVD) account for about 17.3 million annual deaths worldwide. 85% of these deaths occurred as a result of myocardial infarction (MI) and stroke. Chronic heart diseases, such as arterial hypertension (AH), coronary heart disease, various cerebrovascular diseases, dilated and hypertrophic cardiomyopathies are widespread, with a fairly high incidence of mortality and disability. Most of these diseases are characterized by cardiac arrhythmias, conduction and contractility disorders. Additionally, interruption of the electrical activity of the heart, the appearance of extensive ectopic foci and heart failure are all symptoms of a number of severe hereditary diseases. The molecular mechanisms leading to the development of CVD are associated with impaired permeability and excitability of cell membranes and mainly caused by dysfunction of cardiac Ca2+ channels. Acquired channelopathies are caused by metabolic disorders, increased tone of the sympathetic nervous system, age-related changes that lead to deterioration of coronary blood flow and hemodynamics. Currently known channelopathies, such as the long or short QT syndromes, Brugada and Lenegre syndromes, catecholaminergic polymorphic ventricular tachycardia, etc., are congenital and genetic disorders caused by mutations of genes "responsible" for the conductive properties of certain channel-forming proteins, including pore-forming subunits of Ca2+ channels. Over the past 50 years, more than 100 varieties of ion channels have been found in the cardiovascular system cells. The relationship between the activity of these channels and cardiac pathology, as well as the general cellular biological function, has been intensively studied on several cell types and experimental animal models in vivo и in situ. In this review, we discuss the origin of Ca2+ channelopathies and the role of Ca2+ channels of various types: L- R-, T-types voltage-gated calcium channels, RyR2, non-selective hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, transient receptor potential (TRPC, TRPM7, TRPA1) channels in the development of cardio-vascular pathology.

It was observed that a cluster of ordered genes (Hox1, Hox2, Hox3,…) in the genome are activated in the ontogenetic units (1, 2, 3,…) of an embryo along the Anterior/Posterior axis following the same order of the Hox genes. This Spatial Collinearity (SC) is very strange since it correlates events of very different spatial dimensions. It was later observed in vertebrates, that, in the above ordering, first is Hox1expressed in ontogenetic unit 1, followed later by Hox2 in unit 2, and even later Hox3 in unit 3….This temporal collinearity (TC) is an enigma and even to-day is explored in depth. In 1999 T. Kondo and D. Duboule, after posterior upstream extended DNA excisions , concluded that the Hox cluster behaves ‘as if’ TC disappears. Here the consideration of TC really disappearing is taken face value and its repercussions are analyzed. Furthermore, an experiment is proposed to test TC disappearance. An outcome of this experiment could be the reappearance (partial or total) of TC.

Objective: The aim of study is to find key genes and enriched pathways associated with lung cancer. Participants and Methods: Differentially expressed genes (DEGs) data of 54674 genes based on stage, tumor and status of lung cancer was taken from 66 patients of African American (AAs) origin. 2392 DEGs were found based on stage, 13502 DEGs were found based on tumor, 2927 DEGs were found based on status having p value (p<0.05). Results: Total 33 common DEGs were found from stage, tumor and status of lung cancer. Gene ontology (GO) and KEGG pathway enrichment analysis was performed and 49 significant pathways were obtained, out of which 10 pathways were found to be exclusively involved in lung cancer development. Protein-protein interaction (PPI) network analysis found 69 nodes and 324 edges and identified 10 hub genes based on their highest degrees. Module analysis of PPI found that ‘Viral carcinogenesis’, ‘pathways in cancer’, ‘notch signaling pathway’, ‘AMPK signaling pathways’ had a close association with lung cancer. Conclusion: These identified DEGs regulate other genes which play important role in growth of lung cancer. The key genes and enriched pathways identified can thus help in better identification and prediction of lung cancer.

Expanding previous efforts to survey the visual opsin repertoires of the Hemiptera, this study confirms that homologs of the UV- and LW-opsin subfamilies are conserved in all Hemiptera, while the B-opsin subfamily is missing from the Heteroptera and subgroups of the Sternorrhyncha and Auchenorrhyncha, i.e. aphids (Aphidoidea) and planthoppers (Fulgoroidea), respectively. Unlike in the Heteroptera, which are characterized by multiple expansions of the LW-opsin subfamily, the lack of B-opsin correlates with the presence of tandem-duplicated UV-opsins in aphids and planthoppers. Available data on organismal wavelength sensitivities and retinal gene expression patterns lead to the conclusion that, in both groups, one UV-opsin paralog shifted from ancestral UV peak sensitivity to derived blue sensitivity, thereby compensating for the lost B-opsin. Two parallel bona fide tuning site substitutions compare to 18 non-corresponding amino acid replacements in the blue-shifted UV-opsin paralogs of aphids and planthoppers. Most notably, while the aphid blue-shifted UV-opsin clade is characterized by a replacement substitution at one of the best-documented UV/blue tuning sites (Rhodopsin site 90), the planthopper blue-shifted UV-opsin paralogs retained the ancestral lysine at this position. The combined findings identify aphid and planthopper UV-opsins as a new valuable data sample for studying adaptive opsin evolution.

Ophiura sarsii is a common brittle star species across Arctic and subarctic regions of Atlantic and Pacific oceans. In the Barents Sea O. sarsii is among the dominant echinoderms. We studied genetic diversity of O. sarsii by sequencing the 548 bp fragment of mitochondrial COI gene. O.sarsii demonstrated high genetic diversity in the Barents Sea. Both major Atlantic mtDNA lineages were present in the Barents Sea and were evenly distributed between the northern waters around Svalbard archipelago and the southern part near Murmansk coast of Kola Peninsula. Both regions, as well as other parts of the O.sarsii range, were characterized by high haplotype diversity with a significant number of private haplotypes, being mostly satellites to the two dominant haplotypes, each belonging to a different mtDNA clade. Demographic analyses indicated that the demographic and spatial expansion of Ophiura sarsii in the Barents Sea most plausibly has started during the Bølling–Allerød interstadial, during the deglaciation of the western margin of the Barents Sea.

Croton L. (Euphorbiaceae) is a very specious genus and consists of about 1,250 species, mainly distributed in tropical Asia and China. The first complete plastome sequence from the genus, Croton tiglium, is reported in this study (NCBI acc. No. MH394334). The plastome is 150,021 bp in length. The lengths of LSC and SSC are 111,654 bp and 18,167 bp, respectively. However, the length of the IR region is only 10,100 bp and includes only four rrn and four trn genes, and a small part of the ycf1 gene. We propose two-step IR contractions to explain this unique IR region of the C. tiglium plastome. First, the IR contracted from rps19-rpl2 to ycf2-trnL-CAA on the LSC/IRb boundary. Second, the IR contracted from ycf2-trnL-CAA to rrn16-trnV-GAC on the LSC/IRa boundary. In addition, duplicated copies of psaI genes were discovered in the C. tiglium plastome. Both copies were located side by side between accD and ycf4 genes, but one copy was pseudogenized because of a five-basepair (TAGCT) insertion in the middle of the gene following frameshift mutation. The plastome contains 112 genes, of which 78 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Sixteen genes contain one intron and two genes have two introns. The infA gene is lost. Twelve large repeats were detected in the plastome. All large repeats are located in the LSC region. Also, 272 simple sequence repeats (SSRs) were identified. The penta-SSRs accounted for 45% of total SSRs, followed by mono- (32%), di- (12%), tetra (6%) and tri-SSRs (5%). Most of them were distributed in the large single copy (LSC) region (85%). In addition, 76% of the SSRs were located in the intergenic spacer (IGS). Phylogenetic analysis suggested that C. tiglium is a sister group of Jatropha curcas with 100% bootstrap support. Seven Euphorbiaceae species formed one clade with 100% bootstrap support.

Passion fruit is a valued tropical fruit crop that faces environment-related growth strains. TCP genes are important for both growth modulation and stress prevention in plants. Herein, we systematically analyzed the TCP gene family in passion fruit, recognizing 30 members. Genes exhibiting closer phylogenetic relationships exhibited similar protein and gene structures. Gene members of the TCP family showed developmental stage or tissue-specific expression profiles during the passion fruit life cycle. Transcriptome data also demonstrated that many PeTCPs showed induced expression in response to hormonal treatments and cold, heat, and salt stress. Based on transcriptomics data, eight candidate genes were chosen for preferential gene expression confirmation under cold stress conditions. Additionally, four TCP genes exhibited in silico binding with cold stress-related miRNA319s. This study will aid in the establishment of novel germplasm, as well as the further investigation of the roles of PeTCPs and their cold stress resistance characteristics.

Pratylenchus loosi is an important root-lesion nematode that cause damage to tea plantations in Iran and all over the world. The present study reports on the characterization and evolution of three ß-1,4-engoglucanase genes Pl-eng-2, Pl-eng-3 and Pl-eng-4. The gene structure of Pl-eng-2 was fully determined with the predicted signal peptide and devoid of the linker domain and carbohydrate-binding domain, while Pl-eng-3 and Pl-eng-4 were only partially sequenced. The transcription of Pl-eng-2 was localized in the secretory esophageal glands of all life stages, but it was upregulated in male and females stages. Exon/intron structures of Pl-eng-2, Pl-eng-3 and Pl-eng-4 confirmed that they resulted from gene duplication followed by sequence and gene structure diversification with loss of linker domain and carbohydrate-binding domain during evolution. Phylogenetic analysis further confirmed that nematode endoglucanases resulted from horizontal gene transfer of a bacterial gene as Pl-eng-3 showed sister relationships with CelB cellulase of Bacillus subtilis. Silencing Pl-eng-2 by in vitro RNA interference, produced a 60% decrease of the transcript level. The reproductive ability of silenced P. loosi showed a 35% reduction of eggs and larval stages compared to untreated nematodes suggesting that this gene is involved in the early steps of invasion.

In the last two decades many detailed full transcriptomic studies on complex biological samples have been published and included in large gene expression repositories. These studies primarily provide bulk expression signal for each sample, including multiple cell-types mixed within the global signal. The cellular heterogeneity in these mixtures does not allow the activity of specific genes in specific cell types to be identified. Therefore, inferring relative cellular composition is a very powerful tool to achieve a more accurate molecular profiling of complex biological samples. In recent decades, computational techniques have been developed to solve this problem by applying cell deconvolution methods, designed to decompose cell mixtures into their cellular components and calculate the relative proportions of these elements. Some of them, only calculate the cell proportions (supervised methods), while other deconvolution algorithms can also identify the gene signatures specific for each cell type (unsupervised methods). In these work, five deconvolution methods (CIBERSORT, FARDEEP, DECONICA, LINSEED and ABIS) were implemented and used to analyze blood and immune cells, and also cancer cells, in complex mixture samples (using three bulk expression datasets). Our study provides three analytical tools (corrplots, cell-signature plots and bar-mixture plots) that allow a thorough comparative analysis of the cell mixture data. The work indicates that CIBERSORT is a robust method optimized for the identification of immune cell-types, but not as efficient in the identification of cancer cells. We also observed that LINSEED is a very powerful unsupervised method that provides precise and specific gene signatures for each of the five main immune cell-types analyzed: neutrophils and monocytes (in the myeloid lineage), B-cells, NK cells and T-cells (in the lymphoid lineage).

The world faces two seemingly unrelated challenges—a shortfall in the STEM workforce and increasing antibiotic resistance among bacterial pathogens. We address these two challenges with Tiny Earth, an undergraduate research course that excites students about science and creates a pipeline for antibiotic discovery.

Heat shock transcription factors (HSFs) participate in regulating many environmental stress responses and biological processes in plants. Maize (Zea mays L.) is a major cash crop that is grown worldwide. However, the growth and yield of maize are affected by several adverse environmental inputs. Therefore, investigating the factors that regulate maize growth and development and resistance to abiotic stress is an essential task for developing stress-resilient maize varieties. Thus, a comprehensive genome-wide identification analysis was performed to identify HSFs in the maize genome. The current study identified 25 ZmHSFs, randomly distributed throughout the maize genome. Phylogenetic analysis revealed that ZmHSFs are divided into three classes and 13 sub-classes. Gene structure and protein motif analysis supported the results obtained through the phylogenetic analysis. Domain analysis showed the DNA-binding domain to be the most conserved region of ZmHSFs. Segmental duplication is shown to be responsible for the expansion of ZmHSFs. Most of the ZmHSFs are localized inside the nucleus, and the ZmHSFs which belong to the same group show similar physio-chemical properties. The 3D structures revealed comparable conserved ZmHSFs protein structures. RNA-seq analysis revealed a major role of class A HSFs including, ZmHSFA-1a and ZmHSFA-2a in all the maize growth stages, i.e., seed, vegetative, and reproductive development. Furthermore, ZmHSFs displayed an obvious spatiotemporal expression. Under abiotic stress conditions (heat, drought, cold, UV, and salinity), members of class A and B ZmHSFs are induced. Gene ontology (GO) annotation analysis indicated a major role of ZmHSFs in resistance to environmental stress and regulation of primary metabolism. Further, the protein-protein interaction analysis showed that ZmHSFs interact with several molecular chaperons and major stress-responsive proteins. To summarize, this study provides novel insights for functional studies on the ZmHSFs in maize breeding programs.

Background and Objectives: Light therapy (LT) is used as an adjunctive treatment for sleep problems. This study evaluates the impact of LT on sleep quality and sleep-related parameters in patients with sleep disorders. Materials and Methods: We performed a pilot randomized, open-label clinical trial. Fourteen patients aged 20–60 years with sleep disorders for more than three months were randomized into the control and LT groups (1:1 ratio). The LT group was instructed to use a device that provides bright LT (6000 K, 380 lux, wavelength 480 nm) for at least 25 minutes before 09:00 am for two weeks. A self-reported questionnaire was used to evaluate circadian preference, mood, and sleep-related parameters. We analyzed serum cortisol levels and clock genes expression. Results: The Epworth Sleepiness Scale (ESS), insomnia severity index, and Pittsburgh Sleep Quality index were significantly improved within the LT group only after the two-week period. When comparing the two groups, only the change in ESS significant was significant (mean difference; control: -0.14 vs LT: -1.43, p=0.021) after adjusting for baseline characteristics. There were no significant differences in serum cortisol or clock genes expression. Conclusions: LT can improve daytime sleepiness in patients with sleep disorders; however, further well-designed studies are warranted to confirm its efficacy.

Non-coding RNAs, specifically microRNAs (miRNAs), exhibit altered expression and contribute significantly to the pathological processes observed in numerous diseases, encompassing various types of human cancers. Recent discoveries regarding miRNAs underscore their crucial roles in tumor pathogenesis and their responses to diverse therapeutic interventions. miRNAs are a subset of non-coding RNAs that regulate the expression of a multitude of genes post-transcriptionally and thus are potential diagnostic, prognostic, and predictive biomarkers and have also emerged as potential therapeutics. Because miRNAs are involved in the post-transcriptional regulation of their target mRNAs via repressing gene expression, defects in the miRNA biogenesis pathway and miRNA expression perturb the expression of a multitude of oncogenic or tumor-suppressive target genes that are involved in the pathogenesis of various cancers. As such, numerous miRNAs have been identified to be downregulated or upregulated in many types of cancers functioning as either oncomiRs or oncosuppressor miRs. Moreover, dysregulation of miRNA biogenesis pathways can also change miRNA expression and function in cancer. Profiling deregulated miRNAs in many cancer types has been shown to correlate with disease diagnosis, indicate optimal treatment options, and predict response to a specific therapy. Specific miRNA signatures can track all stages of disease including many cancer types and hold potential as biomarkers and therapeutic targets as well as therapeutics as miRNA mimics and inhibitors (antagomirs). As such, identifying specific miRNAs and mRNAs they regulate in many types of cancer along with downstream pathways can be used as potential therapeutic targets. Because a single miRNA can regulate a pool of targets involved in similar cellular processes and pathways, thereby amplifying the cellular response, this potentially makes miRNAs powerful therapeutics to restore cell functions that are altered as part of a disease phenotype. However, because a single miRNA regulates multiple gene expressions their cellular effects are numerous leading to potential off-target effects. Besides their intended targeting issues, there is a need to reduce the immunogenic reactions and determine the minimal dosing to achieve the desired effect while minimizing side effects. As such, a careful risk evaluation of miRNA therapeutics is needed to minimize off-target effects and to avoid overdosing of miRNA drugs. Furthermore, a limited understanding and validation of the specific roles of miRNAs limits their clinical application. In addition, there are many challenges concerning the delivery, sensitivity, specificity, toxicity, and applicability of the potential utility of miRNAs as therapeutic targets or therapeutics. Thus, future work will warrant if miRNAs can be used as cancer biomarkers as well as therapeutics for clinical application.

Mechanical damage of plant tissues leads to the activation of methanol production and its release in the atmosphere. The gaseous methanol or vapors emitted by the damaged plant induce resistance in neighboring intact plants to bacterial pathogens but create favorable conditions for the viral infection spread. Among Nicotiana benthamiana methanol-inducible genes (MIGs) most are associated with plant defense and intercellular transport. Here we characterize NbMIG21 that encodes a 209-aa protein (NbMIG21p) which does not share any homology with annotated proteins. NbMIG21p was demonstrated to contain nucleolus localization signals (NoLS). Co-localization studies with fibrillarin and coilin, nucleolus and Cajal bodies marker proteins, revealed that NbMIG21p is distributed between these subnuclear structures. Our results show that recombinant NbMIG21 possess DNA-binding properties . Similar to gaseous methanol effect an increased NbMIG21 expression leads to the downregulation of the nuclear import of NLS-containing proteins as was demonstrated on the model GFP-NLS protein. Moreover, upregulated NbMIG21 facilitates tobacco mosaic virus (TMV) intercellular transport. We identified NbMIG21 promoter (PrMIG21) and showed that it is methanol-sensitive thus induction of NbMIG21 expression occurs at the level of transcription. Our findings suggest that methanol-activated NbMIG21 might participate in creating favorable conditions for the viral reproduction and spread.

Excess weight, which is seen as the background cause of most diseases, is gradually becoming the most important problem in the world. The cafeteria diet is robust diet that mimics the western diet and provides rapid weight gain associated with the obesity, diabetes, and cancer. The relationship between obesity and cancer is well known. For this reason, it is of great importance to reveal the first molecular and metabolic alterations that occur before entering the obesity process with any factor to understand the pathology of many diseases and to treat them in the early period. The beneficial effects of probiotics are attributed to their metabolite content with antioxidant properties or the postbiotic metabolites produced by them. In this study, the effects of different dietary practices on the hepatic antioxidant system of rats in developmental period were investigated by real-time PCR, enzyme activity measurements, and quantitative measurements of metabolites. After all, it was observed that CAF caused serious impairments by affecting the hepatic antioxidant system at gene and protein levels, and these impairments were relatively reversed with SCD Probiotics supplementation. In addition, regardless of the CAF diet, the regulatory effect of SCD Probiotics supplementation on the hepatic antioxidant system is remarkable.

Suppressors of cytokine signaling (SOCS) influence cytokine and growth factor signaling by negatively regulating the JAK-STAT pathway. This maintains homeostasis during host immune response. However, functional characterization of SOCS family members in invertebrates is limited. In this study, we discovered the Type-I subfamily of the SOCS genes in the mealworm beetle, T. molitor. The full-length ORFs of TmSOCS5, TmSOCS6, and TmSOCS7 consisted of 1,389, 897 and 1,458 nucleotides, encoding polypeptides of 462, 297 and 485 amino acids, respectively, The C-terminal region of TmSOCS was highly conserved in the SH2 and SOCS box domains. Phylogenetic analysis revealed that the three SOCS genes clustered within the same sub-family and the highest amino acid identity was with the Tribolium castaneum SOCS genes (TcSOCS). While the expression of TmSOCS5 and TmSOCS6 was low in larval, pupal, and adult stages of the insect, TmSOCS7 showed higher expression. The expression of TmSOCS5 and TmSOCS6 was higher in larval hemocytes and adult ovary. The microbes expressed the three TmSOCS genes to varying degrees. C. albicans elicited the strongest response in the host with highest 15-fold expression in TmSOCS7 3 h post-inoculation. Collectively, these data suggest that the Type I TmSOCS could play a role in eliciting host immunity.

Streptomyces sp. HNS054, which was previously isolated from a marine sponge, demonstrates vigorous growth and facile genetic modification. This study explores its potential as a marine ac-tinomycete chassis through complete genome sequencing and genetic engineering. With a 7.5 Mb genome containing 6678 predicted genes, 21 secondary metabolic biosynthetic gene clusters (BGCs), and 8 common site-specific recombination (SSR) system attB loci, HNS054 shows a close phylogenetic relation to S. griseoincarnatus strain RB7AG. Utilizing multiplexed site-specific ge-nome engineering (MSGE) and the CRISPR/Cas9 method, engineered strains derived from HNS054 (with three copies of the target BGCs) produce higher amounts of aborycin and ac-tinorhodin than S. coelicolor M1346 (containing three copies of the same BGCs). HNS054 stands out for its remarkable characteristics, including salt tolerance, rapid growth, and compatibility with synthetic biology tools, and positions it as a promising candidate for developing marine ac-tinomycete hosts to enhance secondary metabolite production.

As a major infectious disease in chickens, Newcastle disease causes considerable economic losses in the poultry industry, especially in developing countries where there is limited access to effective vaccination. Therefore, enhancing resistance to the virus in commercial chickens through breeding is a promising way to promote poultry production. In this study, we investigated gene expression changes at 2 and 6 dpi after infection at day21 with a lentogenic Newcastle disease virus in a commercial egg-laying chicken hybrid using RNA sequencing analysis. By comparing NDV challenged and nonchallenged groups, 526 differentially expressed genes (DEGs) (FDR &lt; 0.05) were identified at 2 dpi, and only 36 at 6 dpi. For the DEGs at 2 dpi, IPA analysis predicted inhibition of multiple signaling pathways in response to NDV that regulate immune cell development and activity, neurogenesis and angiogenesis. Upregulation of Interferon Induced Protein with Tetratricopeptide Repeats 5 (IFIT5) in response to NDV was consistent between the current and most previous studies. Sprouty RTK Signaling Antagonist 1 (SPRY1), a DEG in the current study is located in a significant QTL associated with virus load at 6 dpi in the same population. These identified pathways and DEGs provide potential targets to further study breeding strategy to enhance NDV resistance in chickens.

Repetitive elements, often referred to as selfish genes, pose significant challenges to genome assembly and read mapping in bioinformatics. These elements can replicate within the genome without providing functional benefits to the host organism, leading to complexities in accurate genome analysis. This study presents a simulation-based approach to illustrate the impact of repetitive elements on read mapping accuracy. By comparing genome sequences with and without repetitive elements, we demonstrate how these selfish genes create ambiguities and errors in read alignment. The findings underscore the importance of developing advanced bioinformatics tools aligned with artificial intelligence to mitigate the effects of repetitive sequences and improve the reliability of genomic analyses.

Understanding gene expression changes in chicks after vaccination against Newcastle Disease (ND) can reveal vaccine biomarkers. There is limited data on chicks’ early immune response after ND vaccination. Two trials aimed into this knowledge gap. In experiment one, forty-two 13 days-old specific pathogen free (SPF) chicks were used. Harderian glands (Hg) and tracheas (Tc) from five birds per group were sampled at 12, 24, and 48 hours post-vaccination (hpv) to evaluate the gene transcription levels by RNA sequencing (RNA-seq) and RT-qPCR. Results of RNA-seq were compared by glmFTest, while results of RT-qPCR were compared by t-test. With RNA-seq, significant up-regulation of interferon related genes along with JAK-STAT signaling pathways regulation was observed in the Hg at 24- hpv. None of the DEGs identified by RNA-seq were positive for RT-qPCR. Experiment 2 used one-hundred and twelve SPF and commercial chickens at 1 day-old and 14 days-old. Only the commercial birds had maternal antibodies for NDV. By RNA-seq, twenty core DEGs associated with innate immunity and viral genome replication inhibition were identified. Genes previously unlinked to NDV response, such as USP41, were identified. This research present genes with potential as immunity biomarkers for vaccines, yet further investigation is needed to correlate the core gene expression with viral shedding post-vaccination.

Cleidocranial dysplasia (CCD) is an autosomal dominant skeletal dysplasia characterized by persistent open skull sutures whit bulging calvaria, hypoplasia or aplasia of clavicles permitting abnormal opposition of the shoulders, wide public symphysis, short middle phalanx of the fifth fingers and vertebral, craniofacial and dental anomalies. It is a rare disease, with a prevalence of 1-9/1,000,000, high penetrance, and variable expression. The responsible gene of CCD is the runt-related transcription factor 2 gene (RUNX2). We characterize the clinical, genetic and bioinformatic results of four CCD cases. Two Mexican familial with 6 affected members, 9 asymptomatic individuals, and two sporadic cases with CCD, as well as 100 healthy controls. Genomic DNA analyses of the RUNX2 gene was performed for Sanger sequencing. Bioinformatics tools, used to predict the function, stability, and structural changes of the mutated RUNX2 proteins. Three novel heterozygous mutations (c.651_652del; c.538_539delinsCA; c.662T>A) and a previously reported mutation (c.674G>A) were detected. In silico analysis showed that all mutations had functional, stability, and structural alterations in RUNX2 protein. Our results show novel mutations that enrich the pool of RUNX2 gene mutations with CCD. In addition, one patient presented clinical data not previously reported that could represent an expanded phenotype of sever expression.

Sweetpotato is an important miscellaneous grain crop in China, which is threatened by a variety of diseases and insect pests in the process of cultivation and production. sweetpotato stem rot is one of the common sweetpotato diseases, which seriously affects the yield and quality of sweetpotato. However, there are few studies on the mechanism of resistance to stem rot in sweetpotato. In this study, transcriptome sequencing analysis was carried out on the samples at different stages (T1, T2, T3) of stem rot pathogen infecting Xushu 48, and 44839 (T1-VS-T2), 81436 (T1-VS-T2) and 61932 (T2-VS-T3) differentially expressed genes (DEGs) were obtained. The DEGs were mainly concentrated in Alanine, aspartate and glutamate metabolism (ko00250), Carbon fixation in photosynthetic organisms (ko00710) and Amino sugar and nucleotide sugar metabolism (ko00520) and some candidate genes related to plant pathogen infection, such as receptor-like protein kinase (RLK5, RLK7), LRR receptor-like serine/threonine-protein kinase (SERK1), bHLH137, ERF9, MYB73 and NAC053, were screened. The results of this study provide genetic resources for the research on stem rot resistance of sweetpotato and provide theoretical basis for sweetpotato resistance breeding.

Coordination of activities between nuclei and organelles in plant cells involves information exchange, in which phytohormones may play an essential role. Therefore, dissection of the mechanisms of hormone-related integration between phytohormones and mitochondria is an important and challenging task. Here, we found that inputs from multiple hormones may cause changes in transcript accumulation of mitochondrial-encoded genes and nuclear genes encoding mitochondrial (mt) proteins. In particular, treatments with exogenous hormones induced changes in GUS expression in the reporter line possessing a 5'-deletion fragment of the RPOTmp promoter. These changes corresponded in part to up- or downregulation of RPOTmp in wild-type plants, which affected the transcription of mt-encoded genes, implying that promoter fragments of the RPOTmp gene are functionally involved in responses to IAA (indole-3-acetic acid), ACC (1-aminocyclopropane-1-carboxylic acid), and ABA (abscisic acid). Hormone-dependent modulations in the expression of mt-encoded genes can also be mediated through mitochondrial transcription termination factors 15, 17, and 18 of the mTERF family and genes for tetratricopeptide repeat proteins that are coexpressed with mTERF genes, in addition to SWIB5 encoding a mitochondrial SWI/SNF (nucleosome remodelling) complex B protein. These genes specifically responded to hormone treatment, displaying both negative and positive regulation in a context-dependent manner. According to bioinformatic resources, their promoter regions possess putative cis-acting elements involved in responses to phytohormones. Alternatively, hormone-related transcriptional activity of these genes may be modulated indirectly, which is especially relevant for brassinosteroids (BS). In general, the results of the study indicate that hormones are essential mediators that are able to cause alterations in the transcript accumulation of mt-related nuclear genes, which in turn trigger the expression of mt genes.

Monitoring water supply requires, among other quality indicators, the identification of the cyanobacte-ria community taking into account their potential impact in terms of water quality. In this work, cya-nobacteria strains were isolated from Cheffia reservoir and identified based on morphological features, 16S rRNA gene, phylogenetic analysis, and toxin production by PCR screening of the genes involved in the biosynthesis of cyanotoxins (mcyA, mcyE, sxtA, sxtG, sxtI, cyrJ, and anaC). Thirteen strains repre-senting six different genera: Aphanothece, Microcystis, Geitlerinema, Lyngbya, Microcoleus, and Pseudanabaena were obtained. The results demonstrated the importance of morphological features in determining the genus or the species when incongruence between the morphological and phylogenetic analysis occurs and only the utility of the 16S rRNA gene on determining higher taxonomic levels. The phylogenetic analysis confirmed the polyphyly of cyanobacteria for the Microcystis and Oscillatoriales genera. Unexpectedly, Aphanothece sp. CR 11 had the genetic potential to produce microcystins. Our study gives new insight instead of picocyanobacteria toxic genotype in this ecosystem. Thus, conven-tional water treatment methods in this ecosystem have to be adapted.

Water deficit greatly affects global crop growth and productivity, particularly in water-limited environments like upland rice cultivation, leading to reduced grain yield. Plants activate various defense mechanisms during water deficit, involving numerous genes and complex metabolic pathways. Exploring orthologous genes, linked to enhanced drought tolerance, can aid functional validation in target species using genomic data from model organisms. Here, we studied the OsCPK5 gene in upland rice, an AtCPK6 ortholog from A. thaliana, by overexpressing it in the BRSMG Curinga cultivar. Transformants were assessed under two conditions: water deficit applied 79 days after seeding, lasting 14 days, followed by 7 days of irrigation at 80% field capacity. Physiological data and samples were collected at R3, R6, and R8 stages. GM plants consistently exhibited higher OsCPK5 gene expression across stages, peaking during grain filling. During this phase, GM plants displayed reduced stomatal conductance, photosynthetic rate, and increased water use efficiency compared to non-GM plants under drought. GM plants also exhibited higher filled grain percentage in both irrigation conditions. Their drought susceptibility index was 0.9 times lower than NGM plants, and they maintained a higher chlorophyll a/b index, indicating sustained photosynthesis. NGM plants under water deficit exhibited more leaf senescence, while OsCPK5-overexpressing plants retained green leaves. Overall, OsCPK5 overexpression induced diverse drought tolerance mechanisms, hinting at potential for future development of more drought-tolerant rice cultivars.

Heart is composed of muscle cells called cardiomyocytes, including a specialized population, named pacemaker cells, that form the Cardiac Conduction System (CCS), responsible for generating the action potential dictating heart contractions. Failure of the CCS system leads to cardiac arrhythmias requiring complicated therapies and often surgical implantation of electrical pacemakers. However, recent research focusses on development of novel therapies using biological pacemakers aiming to substitute electrical devices. While most signalling pathways and transcription factors involved in the development of the pacemaker cells are known, the upstream regulatory networks need to be predicted through computer-based databases, mathematical modelling as well as functional testing of the regulatory elements in vivo, indicating the need for further research. Here we summarise the current knowledge about the vertebrate myocardial CCS system and development of the pacemaker cells and emphasise areas of future research to clarify the regulation of muscle pacemaker cells and ease development of biological therapies.

The possibility of treating more patients for a longer time, has exploded the concept of anticipation in the systemic treatment of metastatic prostate cancer (mPC). The genetic analysis of Damage DNA Repair (DDR) mutations in pathogenetic variants (PV) and the development of poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitors led to the first valid precision medicine option tailored for mPC. PARP inhibitors are repeating the same evolutionary path experienced for androgen receptor signaling inhibitors (ARSI), starting from the late stage of second line mCRPC in a limited population and time frame. Inevitably also PARP inhibitors will be absorbed by the concept of anticipation and intensification of care. The anticipation of PARP inhibitors in the first line mCRPC therapy is already underway and further one in mHSPC will soon be verified. According to the crosstalk between androgen receptors (AR) and DNA repair, the new message that is emerging is that the combination of PARP inhibitors with ARSI, disconnects PARP from the genetic analysis. Most of the recent trials analyzing PARP inhibitors plus abiraterone or enzalutamide, enrolled first line mCRPC irrespectively to gene PV. The conclusion of the PROPEL trial was that the advantage was independent to PV status, however the highest advantage was reported in BRCA1/2 mutated subgroup. The conclusion of the MAGNITUDE trial was different, with a significant advantage only in the DDR mutated subgroup and the DDR non-mutated was closed for further enrollment. The combination of PARP inhibitors with ARSI represents a significant strategy in the concept of anticipation and intensification of care in mPC. However, it should not nullify the advantages of precision medicine linked to the genetic analysis of DDR.

Gastrodia pubilabiata is a nonphotosynthetic and mycoheterotrophic orchid belonging to subfamily Epidendroideae. Compared to other typical angiosperm species, the plastome of G. pubilabiata is dramatically reduced in size to be only 30,698 base pairs (bp). This reduction has led to the loss of most photosynthesis-related genes and some housekeeping genes in the plastome, which now only contains 19 protein coding genes, three tRNAs, and three rRNAs. This study decoded the entire mitogenome of G. pubilabiata, which consisted of 44 contigs with a total length of 867,349 bp. Its mitogenome contained 38 protein coding genes, nine tRNAs, and three rRNAs. To determine possible gene transfer events between the plastome and the mitogenome, individual BLASTN searches were conducted, using all available orchid plastome sequences and flowering plant mitogenome sequences. Plastid rRNA fragments were found at a high frequency in the mitogenome. Seven plastid protein coding gene frangments (ndhC, ndhJ, ndhK, psaA, psbF, rpoB, and rps4) were also identified in the mitogenome of G. pubilabiata. Phylogenetic trees using these seven plastid protein coding gene fragments suggested that horizontal gene transfer (HGT) from plastome to mitogenome occurred before losses of photosynthesis related genes, leading to the lineage of G. pubilabiata. Compared to species phylogeny of the lineage of orchid, it was estimated that HGT might have occurred approximately 30 million years ago.

Prostate cancer (PCa) Lung metastases are rarely resected, therefore PCa lung metastases are insufficiently molecularly characterized. We recently identified carcinoembryonic antigen cell adhesion molecule 6 (CEACAM6) as a potential driver of pulmonary metastatic spread. Here, we show the biological significance of CEACAM6 in PCa cell proliferation, apoptosis and migration. CEACAM6 was silenced by siRNA in PC3 cells. Functional assessment of apoptosis, cell viability, proliferation and migration were performed in siRNA-CEACAM6 PC3 cells. Non-treated and scrambled (scr) RNA PC3 cells were used as control. Following a specific knockdown of CEACAM6 in PC3 cells, the expression of CEACAM6 protein was significantly decreased in comparison to controls. Cell viability and cell counts decreased in CEACAM6 silent PC3 cells. In contrast, caspase-3 activity was highly elevated in siRNA-CEACAM6 PC3. Furthermore, by performing a cell scratch assay, the migration ratio in siRNA-CEACAM6 PC3 cells were significantly diminished compared with the control group after 48 hours of post transfection incubation. CEACAM6 as a cell adhesion molecule has been implicated in promoting metastatic disease in several solid tumours such as colorectal or gastric cancer. We could show that silencing of CEACAM6 has a significant functional effect on PCa cells. CEACAM6 might play an important role in fostering metastatic spread to the lung of PCa patients via enhancing proliferation and suppressing apoptosis. CEACAM6 might therefore pose an attractive therapeutic target to prevent metastatic disease.

Regular physical activity is considered one of the most valid tools able to reduce the risk of on-set of many diseases in humans. However, it is known that intense physical activity is able to induce high levels of genomic damage, while a moderate exercise was found to induce a favora-ble adaptive response by the organism. We evaluated, in a sample of amateur athletes practicing different disciplines, the level of genomic damage by means of the buccal micronuclei assay, comparing obtained data with those of subjects who practiced sport occasionally or that do not practiced any sport. The aim was to evaluate whether physical activity affects background levels of genomic damage and whether the different sports disciplines, as well as some genes poly-morphisms, differentially affect these levels. A total of 206 subjects, 125 athletes and 81 controls, were recruited. Athletes showed significantly lower values of micronuclei, nuclear buds and bi-nucleated cells with respect to controls. Sprinters and martial arts athletes showed significantly higher frequencies of micronuclei than other categories of athletes. Finally, neither sex nor gene polymorphisms seem to influence the levels of genomic damage, confirming that the observed genomic damage is probably due to the type of the sport activity.

Charcot–Marie–Tooth disease (CMT) and associated neuropathies constitute the most predominant genetically transmitted neuromuscular conditions; however, effective pharmacological treatments remain elusive. The extensive genetic heterogeneity of CMT, which impacts the peripheral nerves and results in a lifelong disability, presents a significant barrier to the development of comprehensive treatments. An estimated 100 loci within the human genome are linked to various forms of CMT and its related inherited neuropathies. This review delves into prospective therapeutic strategies used for the most frequently encountered CMT variants, namely CMT1A, CMT1B, CMTX1, and CMT2A. Compounds such as PXT3003, which are currently under clinical and preclinical investigation, and a broad array of therapeutic agents and their corresponding mechanisms have been discussed in this review. Furthermore, the progress in established gene therapy techniques, including gene replacement via viral vectors, exon skipping using antisense oligonucleotides, splicing modification, and gene knockdown, has been appraised. Each of these gene therapies has the potential for substantial advancements in future research.

Diabetes is a chronic condition that worsens living conditions and causes significant problems, particularly in the vascular system. Many different treatment options are used to prevent these negative effects of diabetes. The most important of these is changing living conditions and exercising regularly.This study aimed todetermining the impacts of a 6-week anaerobic exercise protocol on the blood glucose levels and Glut4 gene expression in the muscle tissues of streptozocin (STZ)-induced diabetic rats. A total of 45 rats were separate control, sedentary, and exercise groups (n=15 each). The STZ used to induce diabetes in rats was applied once with a single intraperitoneal injection. No diabetes was created in the control group, and no exercise was performed, whereas in the sedentary group, diabetes was induced, and no exercise was applied. It was determined that the Glut4 gene expression in the muscle tissue of the exercise group was importantly increased when compared with the sedentary diabetes group.Glut4 gene is an important gene involved in blood glucose regulation and anaerobic exercise significantly increased the expression level of this gene in our study.

Caseous lymphadenitis (CL) is a chronic contagious disease that affects small ruminants and is characterized by the formation of pyogranulomas in lymph nodes and other organs. However, the pathogenesis of this disease and the response of the host genome to infection are not yet fully understood. This study aimed to investigate the whole blood transcriptome and evaluate differential gene expression during the later stages of CL in naturally infected ewes. The study included diseased, serologically positive (EP), exposed, serologically negative (EN) ewes from the same infected flock and healthy ewes (CN) from a different flock. RNA sequencing was performed using the Illumina NextSeq system, and differential gene expression was estimated using DESeq2 and Edge R approaches. The analysis identified 191 annotated differentially expressed genes (DEGs) in the EP group (102 upregulated and 89 downregulated) and 256 DEGs in the EN group (106 upregulated and 150 downregulated). Infection influenced numerous immunoregulatory interactions between lymphoid and nonlymphoid cells in both EP and EN ewes. Immune DEGs were preferentially assigned to antigen presentation through the MHC complex, T-lymphocyte mediated immunity, and extracellular matrix interactions. Furthermore, the EP group showed altered regulation of cytokine and chemokine signalling and activation and recombination of B-cell receptors. Conversely, NF-kappa B signalling, apoptosis, and stress response were the main processes influenced in the EN group. In addition, statistically significant enrichment of the essential immune pathways of Binding and Uptake of Ligands by Scavenger Receptors in EP and p53 signalling in the EN group was found. In conclusion, this study provides new insights into the disease course and host‒pathogen interaction in naturally CL-infected sheep by investigating the blood transcriptome.

Standardized gene nomenclature supports unambiguous communication and identification of the scientific literature associated with genes. To support the increasing number of annotated genomes that are now available for comparative studies, gene nomenclature authorities coordinate the assignment of approved gene names that can be readily propagated across species. Theofanopoulou et al. (Theofanopoulou et al. 2021) propose a new nomenclature for the genes encoding oxytocin and arginine vasopressin and their receptors. Rather than changing to a different nomenclature system, we propose minor updates to the current approved nomenclature of these vertebrate genes to better reflect their evolutionary history. We call on authors, journal editors and reviewers to help support communication and indexing of gene-related publications by working with existing gene nomenclature committees and ensuring that standardized gene nomenclature is routinely used.

Background. Mitochondrial dysfunction has been identified as a pathophysiological hallmark of disease onset and progression in patients with Parkinsonian disorders. Besides the overall emergence of gene therapies in treating these patients, this highly relevant molecular concept has not yet been defined as a target for gene therapeutic approaches. Methods. This narrative review will discuss the experimental evidence suggesting mitochondrial dysfunction as a viable treatment target in patients with monogenic and idiopathic Parkinson’s disease. In addition, we will focus on general treatment strategies and crucial challenges which need to be overcome. Results. Our current understanding of mitochondrial biology in parkinsonian disorders opens up the avenue for viable treatment strategies in Parkinsonian disorders. Insights can be obtained from primary mitochondrial diseases. However, substantial knowledge gaps and unique challenges of mitochondria-targeted gene therapies need to be addressed to provide innovative treatments in the future. Conclusions. Mitochondria-targeted gene therapies are a potential strategy to improve an important primary disease mechanism in Parkinsonian disorders. However, further studies are needed to address the unique design challenges for mitochondria-targeted gene therapies.

Cognitive networks have evolved to cope with uncertain environments in order to make reliable decisions. Such decision making circuits need to respond to the external world in efficient and flexible ways, and one potentially general mechanism of achieving this is grounded in critical states. Mounting evidence has shown that brains operate close to such critical boundaries consistent with self-organized criticality (SOC). Is this also taking place in small-scale living systems, such as cells? Here we explore a recent model of engineered gene networks that have been shown to exploit the feedback between order and control parameters (as defined by expression levels of two coupled genes) to achieve a SOC state. We suggest that such SOC motif could be exploited to generate adaptive behavioral patterns and might help design fast responses in synthetic cellular and multicellular organisms.

For developmental processes we know most of the gene networks controlling specific cell responses. We still have to determine how these networks cooperate and how signals become integrated. The JNK pathway is one of the key elements modulating cellular responses during development. Yet, we still know little on how the core components of the pathway interact with additional regulators or how this network modulates cellular responses in the whole organism in homeostasis or during tissue morphogenesis. We have performed a promoter analysis searching for potential regulatory sequences of puc and identified different specific enhancers directing gene expression in different tissues and at different developmental times. Remarkably, some of these domains respond to the JNK activity, but not all. Altogether, these analyses show that puc expression regulation is very complex and that JNK activities participate in non-previously known processes during the development of Drosophila.

This review was carried out to identify different beta-lactamase resistance genes reported in published literature from Nigeria and to determine the proportion estimates of the important beta-lactamase resistance genes in Nigeria. Sixty-three (63) articles were included in this review based on the eligibility criteria. All the beta-lactamases reported were detected from the Gram-negative bacteria, most especially from Enterobacteriaceae (n=53). Thirty-six different beta-lactamase genes have been reported from Nigeria. These genes belong to the narrow-spectrum, AmpC, extended-spectrum, and carbapenemase beta-lactamase resistance genes. Eight (8) genes (bla_DHA, bla_CTXM-1, bla_CTXM-14, bla_GES-1, bla_VEB-1, bla_OXA-1, bla_OXA-2, and bla_TEM-1) were shared between animals and humans, 5 genes (bla_SHV-1, bla_SHV-2, bla_SHV-11, bla_SHV-12, and bla_NDM-1) were common to both humans and environment while none of the genes was unique to both animals and environment. Four genes including bla_CMY, bla_TEM-1, bla_AmpC, and internationally pandemic bla_CTXM-15 gene were unique to animals, humans, and the environment. No carbapenemase gene was reported from animals yet. The pooled proportion estimate of ESBL genes in Nigeria was 31% (95% CI: 26-36%, P<0.0001), while the estimate of bla_CTXM-15 gene in Nigeria was 46% (95% CI: 36-57%, P<0.0001). The proportion estimate of AmpC genes was 32% (95% CI: 11-52%, P<0.001), while the estimate for carbapenemases was 8% (95% CI: 5-12%, P<0.001). This study has provided information on the beta-lactamases distribution in Nigeria. This is necessary for a better understanding of molecular epidemiology of clinically important beta-lactamases especially the extended-spectrum beta-lactamases and carbapenemases in Nigeria.

The Brassica family contains several economically important crops, including rapeseed (Brassica napus, 2n = 38, AACC), the second largest source of seed oil and protein meal worldwide. However, research in rapeseed is hampered because it is complicated and time-consuming for researchers to access different types of expression data. We therefore developed the Brassica Expression Database (BrassicaEDB, https://biodb.swu.edu.cn/brassica/) for the research community. We conducted RNA sequencing (RNA-Seq) of 103 tissues from rapeseed cultivar ZhongShuang11 (ZS11) at seven developmental stages (seed germination, seedling, bolting, initial flowering, full-bloom, podding, and maturation). We determined the expression patterns of 101,040 genes via FPKM analysis and displayed the results using the eFP browser. We also analyzed transcriptome data for rapeseed from 70 BioProjects in the SRA database and obtained three types of expression level data (FPKM, TPM, and read counts). We used this information to develop the BrassicaEDB, including eFP, Treatment, Coexpression, and SRA Project modules based on gene expression profiles and Gene Feature, qPCR Primer, and BLAST modules based on gene sequences. The BrassicaEDB provides comprehensive gene expression profile information and a user-friendly visualization interface for Brassica crop researchers. Using this database, researchers can quickly retrieve the expression level data for target genes in different tissues and in response to different treatments to elucidate gene functions and explore the biology of rapeseed at the transcriptome level.

1) Background: CFH and HTRA1 genes are traditional markers of increased risk of AMD across populations. Recent findings suggest that additional genes, for instance, in the dystrophin-associated protein complex might be promising markers for AMD. 2) Methods: Here, we performed a case-control study to assess the effect of SGCD single nucleotide polymorphisms (SNPs), a member of this protein family, on AMD diagnosis and phenotype. We performed a case-control study of 134 cases with 134 unpaired controls. Cases were 60 years or older (CARMS grade 4-5, as assessed by experienced ophthalmologists following the AAO guidelines), without other retinal disease or history of vitreous-retinal surgery. Controls were outpatients aged 60 years or older, with no drusen or RPE changes on fundus exam and negative family history of AMD. We examined SNPs in the SGCD gene: rs931798, rs140617, rs140616, and rs970476 by sequencing and RT-PCR. Genotyping quality check and univariate analyses were performed with PLINK v.1.9. Furthermore, logistic regression models were done in SAS v.9.4 and haplotype configurations in R v.3.3.1. 3) Results: After adjusting for clinical covariates, the G/A genotype of the SGCD gene (rs931798) significantly increases the odds of being diagnosed with AMD in 81% (1.81, 95%CI 1.06-3.14, p=0.031), especially the geographic atrophy phenotype (1.82, 95%CI 1.03-3.21, p=0.038) compared to the G/G homozygous. Moreover, the GATT haplotype in this gene (rs931798, rs140617, rs140616, and rs970476) is associated with lower odds of AMD (Adjusted OR 0.13, 95%CI 0.02-0.91, p=0.041). 4) Conclusions: SGCD is a promising gene for AMD research. Further corroboration in other populations is warranted.

Clustered regularly interspaced short palindromic repeats (CRISPR) based gene-editing has begun to transform the treatment landscape of genetic diseases. The history of the discovery of CRISPR/CRISPR-associated (Cas) proteins/single guide RNA (sgRNA)-based gene-editing since the first report of repetitive sequences of unknown significance in 1987 is fascinating, instructive, and inspiring for future advances. The recent approval of CRISPR-Cas9-based gene therapy to treat patients with severe sickle cell anemia and transfusion-dependent beta thalassemia has renewed hope for treating other hematologic diseases, including patients with germline predisposition to hematologic malignancies, who would benefit greatly from the development of CRISPR-based gene therapies. The purpose of this manuscript is three-fold: first, a chronological description of the history of CRISPR-Cas9-sgRNA-based gene editing; second, a brief description of the current state of clinical research in hematologic diseases, including selected applications in treating hematologic diseases with CRISPR-based gene therapy; and third, the current progress in gene therapies in inherited hematologic diseases and bone marrow failure syndromes, to hopefully stimulate efforts towards developing these therapies for patients with inherited bone marrow failure syndromes and other inherited conditions with germline predisposition to hematologic malignancies.

Rice blast and brown planthopper (BPH) are two of the most destructive diseases and pests in rice (Oryza sativa L.) production in China. The development of multi-resistant varieties is widely recognized as the most efficient and environmentally friendly approach to controlling crop diseases and pests. Functional molecular markers (FMMs) have been developed from functional variants in the genic region associated with trait variation, greatly enhancing the efficiency of identifying and pyramiding valuable genes in crop breeding. In this study, two FMMs and a multiplex PCR amplification system were developed for two major broad-spectrum BPH resistance genes, Bph6 and Bph9. By assistance of FMMs in multi-resistant rice restorer line development pipeline, two lines (Huahui7713 and Huahui3006) with blast and BPH resistance were developed by pyramiding three resistance genes Pigm, Bph6 and Bph9. Huahui7713 and Huahui3006 as male lines, two new hybrid rice varieties (WeiLiangYou7713 and Xuanliangyou3006) were certificated and commercial released in China. WeiLiangYou7713 and Xuanliangyou3006 showed improved blast and BPH resistance, and no penalty on yield and grain-quality. Annual promotion area of WeiLiangYou7713 has exceeded 53.3 thousand hectares, indicating its widespread adoption and success in the market. Huahui7713 and Huahui3006 could have great potential for utilization in blast and BPH resistance rice breeding.

Pediculus humanus capitis, the head louse, is an obligate blood-sucking ectoparasite that occurs in six divergent mitochondrial haplogroups (A, D, B, F, C and E), each exhibiting a particular geographic distribution. A few years ago, several studies reported the presence of different pathogenic agents in head lice specimens from different clades collected worldwide. These findings suggest that head louse could be a vector for dangerous diseases and therefore a serious public health problem. Herein, we aimed to study the mitochondrial genetic diversity, the PHUM540560 gene polymorphisms profile of head lice collected in Guinea, as well as to screen for the pathogens present in these lice. In 2018, a total of 155 head lice were collected from 49 individuals at the Medicals Centers of rural (Maférinyah village) and urban (Kindia city) areas, in Guinea. All head lice were subjected to genetic analysis and screened for the presence of several pathogens using molecular tools. The results showed that all head lice belonged to the haplogroups C/E using the duplex qPCR which detects both clades. Standard PCR and sequencing revealed that all specimens belonged to the haplogroup E, including 8 haplotypes, whither 6 new identified for the first time in this study. The study of the PHUM540560 gene polymorphisms in our Guinean head lice revealed that 7/40 (17.5%) of our tested samples exhibit three different polymorphism profiles compared to the clade A-head lice PHUM540560 gene profile, while the remaining specimens 33/40 (82,5%) showed the same PHUM540560 gene polymorphism profile as the previously reported clade A-body lice. Molecular investigations of the targeted pathogens revealed only the presence of Acinetobacter species in 9% of our samples using real time PCR. Sequencing results identified highlighted the presence of several Acinetobacter species, including Acinetobacter baumannii (14.3%), Acinetobacter nosocomialis (14.3%), Acinetobacter variabilis (14.3%), Acinetobacter haemolyticus (7.2%), Acinetobacter towneri (7.2%). Furthermore, a candidate new species of Acinetobacter sp. (7.2%) was detected. Positive specimens were collected from 24,5% individuals in Maférinyah. We also investigated in our study the carbapenem’s-resistant profile of A. baumannii, none of our specimens were positive for the following resistance genes blaOXA-21, blaOXA-24 and blaOXA-58. To the best of our knowledge, our study is the first to report the existence of the Guinean haplogroup E, the PHUM540560 gene polymorphism profile as well as the presence of Acinetobacter species in head lice collected from Guinea.

Many dioecious plants have sex chromosomes that are cytologically heteromorphic, but about half of species lack cytological differences between males and females and are thus homomorphic. Very little is known about the size and content of the non-recombining sex-determining region (SDR) in these species. Here, we assess the size and content of the SDR of the diploid dioecious herb Mercurialis annua, which has homomorphic sex chromosomes and shows signatures of mild Y-chromosome degeneration. We used RNAseq to identify new Y-linked markers for M. annua. Twelve of 24 transcripts with male-specific and male-biased expression could only be PCR-amplified from males and are thus Y-linked. We found a further six Y-linked sequences that were present in males but not females using genome capture data from multiple populations. We used the Y-linked sequences to identify and sequence 17 sex-linked bacterial artificial chromosomes (BACs), which form 11 groups of non-overlapping sequence, covering a total sequence length of about 1.5 Mb. Content analysis of this region suggests it is enriched for repeats, has a low gene density and contains few candidate sex-determining genes. The BACs map to a subset of the sex-linked region of the genetic map, which is estimated to be at least 14.5 Mb. This is substantially larger than estimates for other dioecious plants with homomorphic sex chromosomes, especially given the small genome size of M. annua. Our data provide a rare, high-resolution view of the homomorphic Y chromosome of a dioecious plant.

The IgM and IgT classes were previously identified and characterized in the Antarctic teleost Trematomus bernacchii, a species belonging to the Perciform suborder Notothenoidei. Herein we characterized the gene encoding the polymeric immunoglobulin receptor (pIgR) in the same species and compared it to pIgR of multiple teleost species belonging to five perciform sub-orders, including 11 Antarctic and one non-Antarctic (Cottoperca gobio) notothenioid species, the latter living in less cold periantarctic sea. Antarctic pIgR genes displayed particularly long in-trons marked by sites of transposable elements and transcription factors. Furthermore, analysis of T. bernacchii pIgR cDNA unveiled multiple amino acid substitutions unique to Antarctic species, all introducing adaptive features, including N-glycosylation sequons. Interestingly, C. gobio shared most features with the other perciforms rather than with the cold adapted relatives. T. bernacchii pIgR transcripts were predominantly expressed in mucosal tissues, as indicated by q-PCR and in situ hybridization analysis. These results suggest that in cold adapted species pIgR preserved its fundamental role in mucosal immune defense, although remarkable gene structure modifications occurred.

Plant-parasitic nematodes cause expressive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. The chemical methods that have been deployed to control nematodes were largely banned from use due to their poor specificity and high toxicity. Hence, there is an urgent need for the development of cleaner and more specific control methods. Recent advances in nematode genomics, including in phytoparasitic species, provide an unprecedented opportunity to identify genes and functions specific to these pests. Using phylogenomics, we compared 61 nematode genomes, including 16 for plant-parasitic species and identified more than 24,000 protein families specific to these parasites. In the genome of Meloidogyne incognita, one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein databases. Among these phytoparasites-specific proteins, ca. 1,000 shared the same properties as known secreted effectors involved in essential parasitic functions. Of those, 68 were novel and showed strong expression during the endophytic phase of the nematode life cycle, based on both RNA-seq and RT-qPCR analyses. Besides effector candidates, transcription-related and neuro-perception functions were enriched in phytoparasites-specific proteins, revealing interesting targets for nematode control methods. This phylogenomics analysis, constitutes an unprecedented resource for the further understanding of the genetic basis of nematode adaptation to phytoparasitism and for the development of more efficient control methods.

The indigenous communities across the globe especially in the rural areas consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many of the traditional food plants are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. TFPs are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in times of pandemics and other situations like COVID-19. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realising the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of traditional food plants for their improvements, further cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in few TFPs. This suggests that there is ample scope of integrated use of modern omics and editing tools/techniques for improvement of TFPs and their use for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.

Background: Biomarkers are essential for identification of individuals at high risk of mild cognitive impairment (MCI) for potential prevention of dementia. We investigated DNA methylation in the ApoE gene and plasmatic apolipoprotein E (ApoE) levels as MCI biomarkers in Colombian subjects with MCI and controls. Methods: 100 participants were included (71% women, average age, 70 yrs., range 43-91). MCI was diagnosed by neuropsychological testing, medical and social history, activities of daily living, cognitive symptoms and neuroimaging. Multivariate logistic regression models adjusted by age and gender were performed to examine the risk association of MCI with plasma ApoE and APOE methylation Results: MCI was diagnosed in 41 subjects (average age, 66.5±9.6 yrs.) and compared with 59 controls. Elevated plasma ApoE and APOE methylation of CpGs 165, 190, and 198 were risk factors for MCI (P<0.05). Higher CpG-227 methylation correlated with lower risk for MCI (P=0.002). Only CpG-227 was significantly correlated with plasmatic ApoE levels (correlation coefficient=-0.665; P=0.008). Conclusion: Differential APOE methylation and increased plasma ApoE levels were correlated with MCI. These epigenetic patterns can be used as potential biomarkers to identify early stages of MCI.

Multiple myeloma (MM) is a genetically complex disease that results from a multistep transformation of normal to malignant plasma cells in the bone marrow. However, the molecular mechanisms responsible for the initiation and heterogeneous evolution of MM remain largely unknown. A fundamental step needed to understand the oncogenesis of MM and its response to therapy is the identification of driver mutations. The introduction of gene expression profiling (GEP) in MM was an important step in elucidating the molecular heterogeneity of MM and its clinical relevance. Since some mutations in myeloma occur in non-coding regions, studies based on the analysis of mRNA provide more comprehensive information on the oncogenic pathways and mechanisms relevant to MM biology. In this review, we discuss the role of gene expression profiling in understanding the biology of multiple myeloma together with the clinical manifestation of the disease, as well as its impact on treatment decisions and future directions.

As the prevalence of antimicrobial resistance genes is increasing in microbes, we are facing the return of the preantibiotic era. Consecutively, the number of studies concerning antibiotic resistance and its spread in the environment is rapidly growing. Next generation sequencing technologies are widespread used in many areas of biological research and antibiotic resistance is no exception. For the rapid annotation of whole genome sequencing and metagenomic results considering antibiotic resistance, several tools and data resources were developed. These databases, however can differ fundamentally in the number and type of genes and resistance determinants they comprise. Furthermore, the annotation structure and metadata stored in these resources can also contribute to their differences. Several previous reviews were published on the tools and databases of resistance gene annotation, however, to our knowledge, no previous review focused solely and in depth on the differences in the databases. In this review, we compare the most well-known and widely used antibiotic resistance gene databases based on their structure and content. We believe that this knowledge is fundamental for selecting the most appropriate database for a research question and for the development of new tools and resources of resistance gene annotation.

Leucine-rich repeat receptor-like kinases (LRR-RLKs) have been reported to play important roles in plant growth, development and stress responses. However, no comprehensive analysis of this family has been performed in Gossypium, which are important economic crop and suffer various stresses in growth and development. Here we conducted a comprehensive analysis of LRR-RLK family in four Gossypium species (G. arboreum, G. barbadense, G. hirsutum and G. raimondii). A total of 1641 LRR-RLK genes were identified in the four Gossypium species involved in our study. Maximum-likelihood phylogenetic tree revealed that all the LRR-RLK genes were divided into 21 subgroups. Exon-intron organization structure of LRR-RLK genes kept relative conserved in subfamilies and between Arabidopsis and Gossypium. Subfamilies XI and XII were found dramatically expanded in Gossypium. Tandem duplication acted as an important mechanism in expansion of Gossypium LRR-RLK gene family. Function analysis suggested that plant hormone signaling and plant-pathogen interaction pathway were enriched in Gossypium LRR-RLK genes. Promoters analysis and expression profiles analysis revealed that Gossypium LRR-RLK genes were extensively regulated by TFs, phytohormone and various environmental stimuli, and play key roles in stress defense and diverse development processes. Our study provided valuable information for further function study of Gossypium LRR-RLK genes.

Background: The Hengduan Mountains are one of the most species–rich mountainous areas in the world. The origin and evolution of such a remarkable biodiversity are likely to be associated with geological or climatic dynamics, as well as taxon-specific biotic processes (e.g., hybridization, polyploidization, etc.). Here, we investigate the mechanisms fostering the diversification of the endemic Himalopsyche martynovi complex, a poorly known group of aquatic insects. Methods: We used multiple allelic datasets generated from 691 AHE loci to reconstruct species and RaxML phylogenetic trees. We selected the most reliable phylogenetic tree to perform network and gene flow analyses. Results: Phylogenetic reconstructions and network analysis identified three clades, including H. epikur, H. martynovi sensu stricto and H. cf. martynovi. Himalopsyche martynovi sensu stricto and H. cf. martynovi present an intermediate morphology between H. epikur and H. viteceki, the closest known relative to the H. martynovi–complex. The gene flow analysis revealed extensive gene flow among these lineages. Conclusion: Our results suggest that H. viteceki and H. epikur are likely to have contributed to the evolution of H. martynovi sensu stricto and H. cf. martynovi via gene flow, and thus, our study provides insights in the diversification process of a lesser–known ecological group, and hints at the potential role of gene flow in the emergence of biological novelty in the Hengduan Mountains.

Cholesterol siRNA conjugates attract attention because they allow the delivery of siRNA into cells without the use of transfection agents. In this study, we compared the efficacy and duration of silencing induced by cholesterol conjugates of selectively and totally modified siRNAs and their heteroduplexes of the same sequence and explored the impact of linker length between the 3' end of the sense strand of siRNA and cholesterol on the silencing activity of “light” and “heavy” modified siRNAs. All 3'-cholesterol conjugates were equally active under transfection, but the conjugate with a C3 linker was less active than those with longer linkers (C8 and C15) in a carrier-free mode. At the same time, they are significantly inferior in activity to the 5'-cholesterol conjugate. Shortening the sense strand carrying cholesterol by 2 nucleotides from the 3'-end did not have a significant effect on the activity of the conjugate. Replacing the antisense strand or both strands with fully modified ones has a significant effect on silencing as well as improving the duration in transfection-mediated and carrier-free modes. A significant 78% suppression of MDR1 gene expression in KB-8-5 xenograft tumors developed in mice promises an advantage from the use of fully modified siRNA cholesterol conjugates in combination chemotherapy.

Flax seed is one of the richest plant sources of linolenic acid (LIN) and also contains unsaturated linoleic acid (LIO) and oleic acid (OLE). Stearoyl-ACP desaturases (SAD) and fatty acid desaturases (FAD) play a key role in the synthesis of flax fatty acids (FA). We sequenced flax seed transcriptomes at the 3, 7, 14, 21, and 28 day after flowering (DAF) for ten flax varieties with different oil FA compositions grown under three temperature/watering conditions. Expression levels of 25 genes of SAD, FAD2, and FAD3 families were evaluated. FAD3b, FAD3a, FAD2b-2, SAD3-1, SAD2-1, SAD2-2, SAD3-2, FAD2a-1, and FAD2a-2 had the highest expression levels, which changed significantly during seed development. These genes probably play a key role in the FA synthesis in flax seeds. High temperature and insufficient watering shifted the maximum expression levels of the FAD and SAD genes to earlier development stages, while the opposite trend was observed for low temperature and excessive watering. Differences in FAD and SAD expression profiles under different growth conditions could contribute to the FA composition of linseed oil. Stop codons in the FAD3a gene, resulting in reduced LIN content, decreased the level of the FAD3a transcript. Some difference in reaching the maximum expression level during seed development was observed between 1) SAD3-1, SAD3-2, and FAD2b-2 and 2) SAD2-1, SAD2-2, FAD2a-1, FAD2a-2, FAD3a, and FAD3b. These groups possibly contribute somewhat differently to the synthesis of FA at different development stages.

Sulfate transporters (SULTRs) are responsible for the uptake of the sulfate (SO42−) ions in the rhizosphere by the roots and their distribution in plant organs. In this study, SULTR family members in the genome of the two oilseed crops, Camelina sativa, and Brassica napus, were identified and characterized based on their sequence structure, duplication events, phylogenetic relationships, phosphorylation sites, and expression levels. Herein, 36 and 45 putative SULTR genes were recognized from the genome of C. sativa, and B. napus, respectively. SULTR proteins were predicted as basophilic proteins with low hydrophilicity in both studied species. According to phylogenetic relationships, we divided SULTRs into five groups, in which SULTRs 3 showed highest variation. Besides, several duplication events were observed between SULTRs. The first duplication event was predicted approximately five million years ago between three SULTRs 3.1 in C. sativa. Two subunits were indicated in the 3D structure of SULTRs that the active binding sites differed between C. sativa and B. napus. According to available RNA-seq data, SULTRs showed diverse expression in tissues and response to stimuli. SULTRs 3 showed an expression in all tissues. SULTRs 3.1 were more upregulated in response to abiotic stresses in C. sativa, while SULTRs 3.3, and SULTRs 2.1 showed an upregulation in B. napus. Furthermore, SULTRs 3 and SULTRs 4.1 showed an upregulation in response to biotic stresses in B. napus. Based on the distribution of cis-regulatory elements in the promoter region, we speculated that SULTRs might be controlled by phytohormones such as ABA, and MeJA. Therefore, it seems that SULTR genes in C. sativa have been more influenced by evolutionary processes and have acquired more diversity.

Panax ginseng C.A.Mey. is an adaptogenic plant traditionally used to enhance mental and physical capacities in cases of weakness, exhaustion, tiredness, loss of concentration, and during recovery. According to ancient records, Red Ginseng root preparations enhance longevity with long-term intake. Recent pharmacokinetic studies of ginsenosides in humans and our in vitro study in neuronal cells suggest that ginsenosides are effective when their level in blood is shallow - at concentrations from 10-6 to 10-18 M. In the present study, we compared the effects of Red Ginseng root preparation HRG80TM(HRG) at concentrations from 0.01 to 10,000 ng/ml with effects of White Ginseng (WG) and purified ginsenosides Rb1, Rg3, Rg5 and Rk1 on gene expression of isolated hippocampal neurons. The aim of this study was to predict the effects of differently expressed genes on cellular and physiological functions in organismal disorders and diseases. Gene expression profiling was performed by transcriptome-wide mRNA microarray analyses in murine HT22 cells after treatment with ginseng preparations. Ingenuity pathway downstream/upstream analysis (IPA) was performed with datasets of significantly up-or downregulated genes, and expected effects on cellular function and disease were identified by IPA software. Ginsenosides Rb1, Rg3, Rg5, and Rk1 have substantially various effects on gene expression profiles (signatures) and are different from signatures of HRG and WG. Furthermore, the signature of HRG is changed significantly with dilution from 10000 to 0.01 ng/ml. Network pharmacological analyses of gene expression profiles showed that HRG exhibits predictable positive effects in neuroinflammation, senescence, apoptosis, and immune response, suggesting beneficial soft-acting effects in cancer, gastrointestinal, and endocrine systems diseases and disorders in a wide range of low concentrations in blood.

The pro-protein convertase FURIN (PCSK3) is implicated in a wide range of normal and pathological biological processes such as infectious disease, cancer and cardiovascular disease. Previously, we performed a systemic inhibition of FURIN in a mouse model of atherosclerosis and demonstrated significant plaque reduction and alterations in macrophage function. To understand the cellular mechanisms affected by FURIN inhibition in myeloid cells, we optimized a CRISPR-mediated gene deletion protocol for successfully deriving hemizygous (HZ) and nullizygous (NZ) FURIN knockout clones in U937 monocytic cells using lipotransfection based procedures and a dual guide RNA delivery strategy. We observed differences in monocyte and macrophage functions involving phagocytosis, lipid accumulation, cell migration, inflammatory gene expression, cytokine release patterns, secreted proteomics (cytokines) and whole-genome transcriptomics between wild-type, HZ and NZ FURIN clones. These studies provide a mechanistic basis on the possible roles of myeloid cell FURIN in cardiovascular disorders.

Neonatal diffuse cutaneous mastocytosis (NDCM) is defined as the infiltration of the epidermis by a clonal proliferation of mast cells, observed at birth, without initial signs of systemic involvement. The typical driver mutation is located in the KIT gene. We report a rare case of a boy, born at term, presenting already at birth with generalized subcutaneous nodules, on the face, scalp, trunk, back, hands, and feet. The spleen, liver and inflammatory markers were normal at birth. Tryptase was significantly elevated. Bone marrow biopsy showed no mast cell involvement at age 2 months. A punch biopsy at age 2 months revealed CD117-positive cells diffusely infiltrating the skin, with subsequent DNA NGS sequencing for the formalin fixed paraffin embedded tissue (FFPE) identifying the pathogenic NM_000222.3:c.1504_1509dup; p.(Ala502_Tyr503dup) variant in the KIT gene previously associated with cutaneous mastocytosis. At 2 years follow-up, he had splenomegaly and multiple cervical, and inguinal adenopathy while the skin nodules persisted especially on the scalp with accompanying pruritus. He received oral and local sodium cromoglycate, oral antihistamines, antibiotic cream for skin infection, and iron supplementation, however compliance to treatment was relatively low. The prognosis is difficult to predict, as he developed systemic involvement, failure to thrive and mild psychomotor delay. A case aggregation of NDCM reported in the literature was performed to provide a comprehensive overview of this rare pathology, to better understand the prognosis. NDCM is a life-threatening disease with severe complications. Almost half had severe complications, such as mast hepatosplenomegaly, adenopathy, bacterial infections, mast cell leukaemia, and systemic involvement.

The chitin synthase B gene is a key enzyme in the chitin synthesis of insect peritrophic matrix (PM), affecting insects' feeding behavior. The chitin synthase B gene has been cloned from the transcription library of Heortia vitessoides Moore. RT-qPCR showed that HvChsb was highly expressed in the larval stage of H. vitessoides, especially on the first day of the prepupal stage, and in the midgut of larvae and the abdomen of adults. After starvation treatment, HvChsb was found to be significantly inhibited with time. After 48 h of starvation, the feeding experiment showed that HvChsb increased with the prolongation of the refeeding time. The experimental data showed that feeding affected the expression of HvChsb. HvChsb was effectively silenced by RNA interference, so its function was lost, significantly decreasing the survival rate of H. vitessoides. The survival rate from larval-to-pupal stages was only 43.33%, accompanied by abnormal phenotypes. It can be seen that HvChsb plays a key role in the average growth and development of H. vitessoides.

Numerous in vitro studies on isolated cells have been conducted to uncover the molecular mechanisms of action of Panax ginseng Meyer root extracts and purified ginsenosides. However, the concentrations of ginsenosides and the extracts used in these studies were much higher than detected in pharmacokinetic studies in humans and animals orally administered with ginseng preparations at therapeutic doses. Our study aimed to assess: (a) the effects of ginsenoside Rg5, the major "rare" ginsenoside of Red Ginseng, on gene expression in the murine neuronal cell line HT22 in a wide range of concentrations, from 10-4 to 10-18 M, and (b) the effects of differentially expressed genes on cellular and physiological functions in organismal disorders and diseases. Gene expression profiling was performed by transcriptome-wide mRNA microarray analyses in HT22 cells after treatment with ginsenoside Rg5. Ginsenoside Rg5 exhibits soft-acting effects on gene expression of neuronal cells in a wide range of physiological concentrations and strong reversal impact at high (toxic) concentration: significant up- or downregulation of expression of about 300 genes at concentrations from 10-6 M to 10-18 M, and dramatically increased both the number of differentially expressed target genes (up to 1670) and the extent of their expression (fold changes compared to unexposed cells) at a toxic concentration of 10-4 M. Network pharmacology analyses of genes expression profiles using Ingenuity pathway analysis (IPA) software showed that at low physiological concentrations, ginsenoside Rg5 has the potential to activate the biosynthesis of cholesterol and to exhibit predictable effects in senescence, neuroinflammation, apoptosis, and immune response, suggesting soft-acting, beneficial effects on organismal death, movement disorders, and cancer.

Indonesia is one of the most biodiverse countries in the world and a promising resource for novel natural compound producers. Actinomycetes produce about two-thirds of all clinically used antibiotics. Thus, exploiting Indonesia’s microbial diversity for actinomycetes may lead to the discovery of novel antibiotics. A total of 422 actinomycete strains were isolated from three different unique areas in Indonesia and tested for their antimicrobial activity. Nine potent bioactive strains were prioritized for further drug screening approaches. The nine strains were cultivated in different solid and liquid media and a combination of genome mining analysis and mass spectrometry (MS)-based molecular networking was employed to identify potential novel compounds. By correlating secondary metabolite gene cluster data with MS-based molecular networking results, we identified several gene cluster-encoded biosynthetic products from the nine strains, including naphthyridinomycin, amicetin, echinomycin, tirandamycin, antimycin, and desferrioxamine B. Besides, eight putative ion clusters and numerous gene clusters were detected that could not be associated with any known compound, indicating that the strains can produce novel secondary metabolites. Our results demonstrate that sampling of actinomycetes from unique and biodiversity-rich habitats, such as Indonesia, along with a combination of gene cluster networking and molecular networking approaches, accelerates natural product identification.

RNA-guided genomic transcriptional regulation tools, namely Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) and CRISPR-mediated gene activation (CRISPRa), are a powerful technology for the field of functional genomics. Deriving from the CRISPR/Cas9 system, both systems comprise a catalytically dead Cas9 (dCas9) and a single guide RNA (sgRNA). This type of dCas9 is incapable of cleaving DNA but retains its ability to specifically bind to DNA. The binding of the dCas9/sgRNA complex to a target gene results in transcriptional interference. The CRISPR/dCas9 system has been explored as a tool for transcriptional modulation and genome imaging. Despite its potential applications and benefits, the challenges and limitations faced by the CRISPR/dCas9 system include the off-target effects, PAM sequence requirement, efficient delivery methods, and the CRISPR/dCas9-interfered crops being labeled as genetically modified organisms in several countries. This review highlights the progression of CRISPR/dCas9 technology as well as its applications and potential challenges in crop improvement.

During the response of plants to adverse stresses, aquaporin (AQP) plays a prominent role in membrane water transport based on received upstream signals. In addition, they have various physical parts for dealing with environmental stresses. Due to the importance of the AQP gene family, studies have been conducted investigating the function and regulatory system of these genes. However, many of their molecular aspects are still unknown. This study aims to carry out a genomic-wide investigation of the AQP gene family in durum wheat using bioinformatics tools and to investigate the expression patterns of some members in response to salt stress. Our results showed that there are 80 TtAQP genes in durum wheat, which are classified into four main groups based on phylogenetic analysis. Many duplications were observed between the members of the TtAQP gene family, and high diversity in response to post-translational modifications was observed between TtAQP family members. The expression pattern of TtAQP genes disclosed that these genes are primarily upregulated in response to salt stress. Besides, qPCR data revealed that TtAQPs are more induced in delayed responses to salinity stress. Overall, our findings illustrate that TtAQP members are diverse in terms of their structure, regulatory systems and expression levels.

Viroids are known the smallest plant pathogens, and although their genome sequences do not encode proteins, they can cause disease in economically important crops. In order to control viroid diseases and mitigate their damage, genetic resources used for breeding of the viroid-resistant crop have been searched, but the practical resistant trait has not been found in almost all viroid-crop combinations, as well as the tolerant trait. Due to the difficulty in exploiting naturally occurring resistance or tolerance, various effective strategies have been devised to control viroid diseases using non-transforming or transforming techniques. Meanwhile, extensive findings related to viroid resistance and tolerance may lead to confer resistance or tolerance to viroid infection by combining with the recently emerged new technologies (e.g., spray-induced gene silencing and genome-editing technologies), which are believed to be more environmentally viable and acceptable to the general public than previously reported approaches. In particular, some genome-modified crops produced by the latter technology are already on the market. In this review, we comprehensively summarize the current status about investigation of naturally occurring genetic traits for viroid resistance and tolerance, accumulating knowledge about host factors involved in viroid pathogenicity, and various basic technologies developed to try to possible viroid disease control strategies. Furthermore, we discuss prospects and challenges for the achievement of more effective, practical, and sustainable disease control of viroid.

Chromophobe renal cell carcinoma (chRCC) and oncocytoma (RO) are renal tumor types originating from alpha intercalated cells of the collecting ducts of the kidney. Both tumor types have similar gross histological morphology and increased mitochondria, which leads to difficulties differentiating between these tumors, especially with core biopsy samples. This study aims to apply a machine learning approach to develop a molecular classifier based on transcriptomics data. Here we generated a meta-data set containing 62 chRCC and 45 RO gene expression arrays. Arrays were subjected to quality control steps, and genes were selected based on differential expression and ROC analysis. The final gene list was evaluated with UMAP based dimension reduction followed by density-based clustering with 95.5% accuracy. Molecular profiling by KEGG pathway analysis identified enrichment of fatty acid oxidation pathway in RO. We finally identified and validated the 30-gene signature, with an accuracy of 94.4% to distinguish chRCC from RO on UMAP analysis. Our results show that chRCC and RO have a distinct gene signature that can differentiate these tumors and complement histology for routine diagnosis of these two tumors.

(1) Background: Investigating the characteristics of photosynthetic physiological changes of leaves in Mangifera indica L. cv. 'GuIfei' under enhanced UV-B radiation, natural light exposed trees were regarded as control, and 96 kJ·m-2·d-1enhanced UV-B radiation was artificially simulated in the field; (2) Methods: The changes of fruit maturity and fruit quality, leaf net photosynthetic rate (Pn), photosynthetic pigments contents, photochemical reaction, activities of photosynthetic enzymes and their genes expressions were determined; (3) Results: Compared with CK, the percentage of mature fruits of the treatment was significantly increased, and fruit quality was better. The net photosynthetic rate (Pn), the contents of photosynthetic pigment, Hill reaction activity and photochemical quenching coefficient (qP) of the treatment leaves showed a significantly higher trend than CK. The activities of Rubisco and RCA, and the expression of Rubisco genes rbcL and rbcS were significantly increased; (4) Conclusions: 96 kJ·m-2·d-1 enhanced UV-B radiation treatment improved Rubisco activity through increasing the expression of Rubisco genes rbcL and rbcS, thereby enhancing the CO2-fixing capacity and dark reaction capacity of leaves. Based on this, it raised the net photosynthetic rate of leaves, which promoted the early maturity of 'Guifei' mango by the fast accumulating photosynthetic products.

Age-related macular degeneration (AMD) is an eye disease and the most common cause of vision loss in the Western World. In its advanced stage, AMD occurs in two clinically distinguished forms: dry and wet, but only wet AMD is treatable. However, the treatment based on repeated injections with vascular endothelial growth factor A (VEGFA) antagonists may at best stop the disease progression and prevent or delay vision loss but without an improvement of visual dysfunction. Moreover, it is a serious mental and financial burden for patients and may be linked with some complications. The recent first success of intravitreal gene therapy with ADVM-022, which transformed retinal cells to continuous production of aflibercept, a VEGF antagonist, after a single injection, has opened a revolutionary perspective in wet AMD treatment. Promising results obtained so far in other ongoing clinical trials support this perspective. In this narrative/hypothesis review, we present basic information on wet AMD pathogenesis and treatment, the idea of gene therapy in retinal diseases, update evidence on completed and ongoing clinical trials with gene therapy for wet AMD, and perspectives on the road to the clinic of “one and done” therapy for wet AMD to replace a lifetime of injections. Gene editing targeting the VEGFA gene is also presented as another gene therapy strategy to improve wet AMD management.