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Oral premalignant disorders (OPMDs) are a group of potentially malignant conditions that pose a significant health burden globally. MicroRNAs (miRNAs), small non-coding RNA molecules, have emerged as crucial regulators of gene expression and have been implicated in various biological processes, including carcinogenesis. This review synthesizes existing knowledge to provide a comprehensive understanding of the molecular mechanisms underlying OPMDs and to highlight the potential of miRNAs as promising biomarkers and therapeutic targets. Additionally, this review seeks to explore the potential of miRNA-based diagnostic biomarkers for early detection of OPMDs in the current literature on miRNAs in OPMDs, examining their involvement in disease pathogenesis, diagnostic potential, and therapeutic implications. Dysregulated miRNAs can target genes involved in critical cellular processes, such as cell cycle regulation, apoptosis, and DNA repair, leading to disease progression. Notably, miR-21, miR-31, miR-135b, and miR-486-5p have shown promise as potential biomarkers for early detection of oral premalignant lesions. Furthermore, the paper discusses the therapeutic implications of miRNAs in OPMDs. Preclinical studies have demonstrated the efficacy of miRNA-targeted therapies, such as miRNA mimics and inhibitors, in suppressing the growth of oral premalignant lesions. Early-phase clinical trials have shown promising results, indicating the potential for personalized treatment approaches. The findings underscore the importance of understanding the molecular mechanisms underlying these disorders and provide insights for the development of improved diagnostic and therapeutic strategies. However, they pose certain limitations given their intrinsic variability in expression profiles, the need for optimized isolation and detection methods, and potential hurdles in transitioning from preclinical success to clinical applications. Thus, future clinical studies are warranted to fully exploit the potential of miRNAs in the management of OPMDs., (© 2024. The Author(s), under exclusive licence to The Society of The Nippon Dental University.)

Background: Exosomes are the smallest extracellular vesicles (30-150 nm) secreted by all cell types, including synovial fluid. However, because biological fluids are complex, heterogeneous, and contain contaminants, their isolation is difficult and time-consuming. Furthermore, the pathophysiology of osteoarthritis (OA) involves exosomes carrying complex components that cause macrophages to release chemokines and proinflammatory cytokines. This narrative review aims to provide in-depth insights into exosome biology, isolation techniques, role in OA pathophysiology, and potential role in future OA therapeutics., Methods: A literature search was conducted using PubMed, Scopus, and Web of Science databases for studies involving exosomes in the osteoarthritis using keywords "Exosomes" and "Osteoarthritis". Relevant articles in the last 15 years involving both human and animal models were included. Studies involving exosomes in other inflammatory diseases were excluded., Results: Despite some progress, conventional techniques for isolating exosomes remain laborious and difficult, requiring intricate and time-consuming procedures across various body fluids and sample origins. Moreover, exosomes are involved in various physiological processes associated with OA, like cartilage calcification, degradation of osteoarthritic joints, and inflammation., Conclusion: The process of achieving standardization, integration, and high throughput of exosome isolation equipment is challenging and time-consuming. The integration of various methodologies can be employed to effectively address specific issues by leveraging their complementary benefits. Exosomes have the potential to effectively repair damaged cartilage OA, reduce inflammation, and maintain a balance between the formation and breakdown of cartilage matrix, therefore showing promise as a therapeutic option for OA., Competing Interests: Conflict of interestThe author(s) declared no potential conflicts of interest with respect to research, authorship, and/or publication of this article., (© Indian Orthopaedics Association 2024. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Background: Meniscal injuries frequently require surgical intervention to restore knee joint function and stability. Intraoperative platelet-rich plasma (PRP) injection has emerged as a potential adjunctive therapy to enhance tissue healing post-meniscal repair. This systematic review and meta-analysis aimed to evaluate the efficacy of PRP in terms of pain relief, functional recovery, and overall success rates in patients undergoing meniscal repair procedures ., Methods: A comprehensive search strategy was employed to identify relevant studies across Scopus, PubMed, Embase, and the Cochrane Library databases. The inclusion criteria encompassed human studies, including randomized controlled trials (RCTs), cohorts, and case-control studies, focusing on intraoperative platelet-rich plasma (PRP) use post-meniscal repair and reporting outcomes related to pain, functionality, and cure rates. Exclusion criteria comprised animal studies, non-English publications, studies lacking relevant outcome measures, and those with insufficient data. Two reviewers independently screened titles and abstracts, resolving disagreements through consensus or consultation with a third reviewer, followed by a full-text assessment for potentially eligible studies. Data extraction was conducted independently by two reviewers using a standardized form. The reliability of observational studies was evaluated using the Newcastle-Ottawa Scale. Subgroup analyses and pooled effect estimates for main outcomes were computed using RevMan 5.3, a meta-analysis tool., Results: The demographic analysis revealed that the PRP group had an average age of 41.39 years, while the control group had an average age of 42.1 years. In terms of gender distribution, the PRP group consisted of 61 men and 29 women, while the control group had 62 men and 34 women. Pain ratings showed a preference for PRP with a mean difference of 4.83 ( p  = 0.13). However, there was no significant difference in Lysholm scores (mean difference: - 0.44, p = 0.91) or IKDC scores (mean difference: 2.80, p  = 0.14) between the PRP and control groups. Similarly, ROM measures did not show a statistically significant difference, with a mean difference of 2.80 ( p  = 0.18). Additionally, there was no significant distinction in failure rates between the PRP and control groups, as indicated by a weighted mean difference of 0.71 ( p  = 0.52). These findings suggest that while PRP may offer some benefits in pain relief, its impact on functional recovery, range of motion, and failure rates following meniscal repair procedures is inconclusive., Conclusion: The current evidence regarding the effect of intraoperative platelet-rich plasma (PRP) injection on patients undergoing meniscal repair remains inconclusive. While some studies suggest potential benefits in terms of pain relief and functional recovery, others show no significant differences compared to control groups. The impact of PRP therapy on overall success rates, including rates of re-tear and revision surgery, is also uncertain. Further well-designed randomized controlled trials with larger sample sizes are needed to provide more robust evidence and guide clinical practice in orthopedic surgery., (© Indian Orthopaedics Association 2024. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Inflammatory arthritis commonly initiates in the soft tissues lining the joint. This lining swells, as do the cells in it and inside the joint fluid, producing chemicals that induce inflammation signs such as heat, redness, and swelling. MicroRNA (miRNA), a subset of non-coding small RNA molecules, post-transcriptionally controls gene expression by targeting their messenger RNA. MiRNAs modulate approximately 1/3 of the human genome with their multiple targets. Recently, they have been extensively studied as key modulators of the innate and adaptive immune systems in diseases such as allergic disorders, types of cancer, and cardiovascular diseases. However, research on the different inflammatory joint diseases, such as rheumatoid arthritis, gout, Lyme disease, ankylosing spondylitis, and psoriatic arthritis, remains in its infancy. This review presents a deeper understanding of miRNA biogenesis and the functions of miRNAs in modulating the immune and inflammatory responses in the above-mentioned inflammatory joint diseases. According to the literature, it has been demonstrated that the development of inflammatory joint disorders is closely related to different miRNAs and their specific regulatory mechanisms. Furthermore, they may present as possible prognostic and diagnostic biomarkers for all diseases and may help in developing a therapeutic response. However, further studies are needed to determine whether manipulating miRNAs can influence the development and progression of inflammatory joint disorders.

MicroRNAs (miRNAs) are short, 19-23 nucleotide non-coding RNA molecules that regulate gene expression by silencing or degrading the target mRNA gene. Since their discovery in the nineties of the last century, they have emerged as key inflammatory regulators. Inflammation induces the synthesis of various miRNAs that modulate the expression of multiple molecules involved in orchestrating the inflammatory response. This review aims to provide an insight into the role of miRNAs as potential biomarkers, mediators, and potential therapeutic targets of dental pulp inflammation. A literature search was conducted using the keywords; biogenesis of microRNA, human dental pulp cells, pulpitis, and inflammation in PubMed and Scopus index databases for all the published articles dealing with the role of miRNAs in pulp inflammation in the last 10 years. According to the literature, there is a clear correlation between miRNAs and several physiological events, as well as their role as mediators of innate immune response and inflammation in dental pulp cells. Our narrative review stipulates that numerous miRNAs play a key role in modulating inflammation, delaying or enhancing cell repair, cell differentiation, and survival in dental pulp diseases. However, further studies are required for the validation of miRNAs as reliable biomarkers in dental pulp pathology and their targeted therapy., (© 2022. The Author(s), under exclusive licence to The Society of The Nippon Dental University.)

Breast cancer (BC) is the most common cancer type among women with a distinct clinical presentation, but the survival rate remains moderate despite advances in multimodal therapy. Consequently, a deeper understanding of the molecular etiology is required for the development of more effective treatments for BC. The relationship between inflammation and tumorigenesis is well established, and the activation of the pro-inflammatory transcription factor nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) is frequently identified in BC. Constitutive NF-κB activation is linked to cell survival, metastasis, proliferation, and hormonal, chemo-, and radiotherapy resistance. Moreover, the crosstalk between NF-κB and other transcription factors is well documented. It is reported that vitamin C plays a key role in preventing and treating a number of pathological conditions, including cancer, when administered at remarkably high doses. Indeed, vitamin C can regulate the activation of NF-κB by inhibiting specific NF-κB-dependent genes and multiple stimuli. In this review, we examine the various NF-κB impacts on BC development. We also provide some insight into how the NF-κB network may be targeted as a potential vulnerability by using natural pro-oxidant therapies such as vitamin C.

MicroRNAs (miRNAs) are the small noncoding RNA molecules which regulate target gene expression posttranscriptionally. They are known to regulate key cellular processes like inflammation, cell differentiation, cell proliferation, and cell apoptosis across various ocular diseases. Due to their easier access, recent focus has been laid on the investigation of miRNA expression and their involvement in several conjunctival diseases. The aim of this narrative review is to provide understanding of the miRNAs and describe the current role of miRNAs as the mediators of the various conjunctival diseases. A literature search was made using PubMed, Scopus, and Web of Science databases for studies involving miRNAs in the conjunctival pathological conditions. Original articles in the last 10 years involving both human and animal models were included. Literature search retrieved 27 studies matching our criteria. Pertaining to the numerous literatures, there is a strong correlation between miRNA and the various pathological conditions that occur in the conjunctiva. miRNAs are involved in various physiological processes such as cell differentiation, proliferation, apoptosis, development, and inflammation by regulating various signaling pathways, genes, proteins, and mediators. Pterygium was the most studied conjunctival disease for miRNA involvement, whereas miRNA research in allergic conjunctivitis is still in its early stages. Our review provides deep insights into the various miRNAs playing an important role in the various conjunctival diseases. miRNAs do have the potential to serve as noninvasive biomarkers with diagnostic, prognostic, and therapeutic implications. However, multitudinous studies are required to validate miRNAs as the reliable biomarkers in conjunctival pathologies and its targeted therapy.

Despite the advances in treatment using chemotherapy or targeted therapies, due to static survival rates, non-small cell lung cancer (NSCLC) is the major cause of cancer-related deaths worldwide. Epigenetic-based therapies have been developed for NSCLC by targeting DNA methyltransferases (DNMTs) and histone-modifying enzymes. However, treatment using single epigenetic agents on solid tumours has been inadequate; whereas, treatment with a combination of DNMTs inhibitors with chemotherapy and immunotherapy has shown great promise. Dietary sources of phytochemicals could also inhibit DNMTs and cancer stem cells, representing a novel and promising way to prevent and treat cancer. Herein, we will discuss the different DNMTs, DNA methylation profiling in NSCLC as well as current demethylating agents in ongoing clinical trials. Therefore, providing a concise overview of future developments in the field of epigenetic therapy in NSCLC., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Vernal Keratoconjunctivitis (VKC) is a chronic conjunctival inflammatory condition that typically affects children. Extracellular microRNAs (miRNAs) are small noncoding RNA molecules, the expression of which is reported to regulate cellular processes implicated in several eye diseases. The aim of this preliminary study is to identify the miRNA expression profile in the tears of children with VKC vis-à-vis controls, and to statistically evaluate these miRNAs as potential diagnostic biomarkers of VKC. The study involved a VKC group and a control group. Tear specimens were collected using Schirmer's strips. RNA was isolated using miRNeasy Micro kit and quantification was performed using an Agilent Bioanalyzer RNA 6000 Nano kit and Small RNA kit. miRNA profiling was performed using the Agilent microarray technique. A total of 51 miRNAs (48 upregulated and three downregulated) were differentially expressed in the tears of children with VKC and controls. The three most significantly upregulated miRNAs were hsa-miR-1229-5p, hsa-miR-6821-5p, and hsa-miR-6800-5p, and the three most significantly downregulated miRNAs were hsa-miR-7975, hsa-miR-7977, and hsa-miR-1260a. All the upregulated miRNAs are potential diagnostic biomarkers of VKC pending validation due to their larger discriminatory area under the curve (AUC) values. miRNA target prediction analysis revealed multiple overlapping genes that are known to play a role in conjunctival inflammation. We identified a set of differentially expressed miRNAs in the tears of children with VKC that may play a role in VKC pathogenesis. This study serves as the platform study for future miRNA studies that will provide a deeper understanding of the pathophysiology of VKC., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Syed, Shahidan, Shatriah and Zunaina.)

Environmental damage is without a doubt one of the most serious issues confronting society today. As dental professionals, we must recognize that some of the procedures and techniques we have been using may pose environmental risks. The usage and discharge of heavy metals from dental set-ups pollute the environment and pose a serious threat to the ecosystem. Due to the exclusive properties of nanosized particles, nanotechnology is a booming field that is being extensively studied for the remediation of pollutants. Given that the nanoparticles have a high surface area to volume ratio and significantly greater reactivity, they have been greatly considered for environmental remediation. This review aims at identifying the heavy metal sources and their environmental impact in dentistry and provides insights into the usage of nanoparticles in environmental remediation. Although the literature on various functions of inorganic nanoparticles in environmental remediation was reviewed, the research is still confined to laboratory set-ups and there is a need for more studies on the usage of nanoparticles in environmental remediation., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2022 Lakshmi Thangavelu et al.)

How stable and temperature-dependent variations in DNA methylation and nucleosome occupancy influence alternative splicing (AS) remains poorly understood in plants. To answer this, we generated transcriptome, whole-genome bisulfite, and MNase sequencing data for an epigenetic Recombinant Inbred Line (epiRIL) of A. thaliana at normal and cold temperature. For comparative analysis, the same data sets for the parental ecotype Columbia (Col-0) were also generated, whereas for DNA methylation, previously published high confidence methylation profiles of Col-0 were used. Significant epigenetic differences in an identical genetic background were observed between Col-0 and epiRIL lines under normal and cold temperatures. Our transcriptome data revealed that differential DNA methylation and nucleosome occupancy modulate expression levels of many genes and AS in response to cold. Collectively, DNA methylation and nucleosome levels exhibit characteristic patterns around intron-exon boundaries at normal and cold conditions, and any perturbation in them, in an identical genetic background is sufficient to modulate AS in Arabidopsis., (Crown Copyright © 2021. Published by Elsevier Inc. All rights reserved.)

Alternative splicing (AS) is a major gene regulatory mechanism in plants. Recent evidence supports co-transcriptional splicing in plants, hence the chromatin state can impact AS. However, how dynamic changes in the chromatin state such as nucleosome occupancy influence the cold-induced AS remains poorly understood. Here, we generated transcriptome (RNA-Seq) and nucleosome positioning (MNase-Seq) data for Arabidopsis thaliana to understand how nucleosome positioning modulates cold-induced AS. Our results show that characteristic nucleosome occupancy levels are strongly associated with the type and abundance of various AS events under normal and cold temperature conditions in Arabidopsis. Intriguingly, exitrons, alternatively spliced internal regions of protein-coding exons, exhibit distinctive nucleosome positioning pattern compared to other alternatively spliced regions. Likewise, nucleosome patterns differ between exitrons and retained introns, pointing to their distinct regulation. Collectively, our data show that characteristic changes in nucleosome positioning modulate AS in plants in response to cold., (© 2020 The Authors New Phytologist © 2020 New Phytologist Trust.)

Next-generation sequencing (NGS) technologies - Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/post-transcriptional level. Global analysis of mature mRNAs, transcripts from nuclear run-on assays, and nascent chromatin-bound mRNAs using short as well as full-length and single-molecule DRS reads have uncovered potential roles of different forms of RNA polymerase II during the transcription process, and the extent of co-transcriptional pre-mRNA splicing and polyadenylation. These tools have also allowed mapping of transcriptome-wide start sites in cap-containing RNAs, poly(A) site choice, poly(A) tail length, and RNA base modifications. The emerging theme from recent studies is that reprogramming of gene expression in response to developmental cues and stresses at the co-/post-transcriptional level likely plays a crucial role in eliciting appropriate responses for optimal growth and plant survival under adverse conditions. Although the mechanisms by which developmental cues and different stresses regulate co-/post-transcriptional splicing are largely unknown, a few recent studies indicate that the external cues target spliceosomal and splicing regulatory proteins to modulate alternative splicing. In this review, we provide an overview of recent discoveries on the dynamics and complexities of plant transcriptomes, mechanistic insights into splicing regulation, and discuss critical gaps in co-/post-transcriptional research that need to be addressed using diverse genomic and biochemical approaches., (© 2020 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.)

Antigen delivery framework utilising polymer-based nanomaterial is broadly used in biomedicine because of their high efficacy, antigenicity and biocompatibility. In this study, hepatitis B surface antigen fabricated chitosan-polyethylene glycol nanocomposite (HBsAg-CS-PEG NC) was prepared by in situ ionic gelation method which brought about highly stable nanoformulation that was characterised by electron microscopy, atomic force microscopy (AFM) Fourier transform infrared spectroscopy (FTIR). Particles morphology by electron microscopy studies reveals spherical, electron-dense, nanostructure with 100-120 nm. AFM studies show a uniform distribution of particles with distinct roughness. Specific interaction of polymers with the vaccine or surface modification and functionalization were confirmed by FTIR analysis. Synthesised nanocomposite exhibited high antigen loading and entrapment efficiency. Release profile study carried out under in vitro condition indicates that a gradual increase in release at increasing time intervals which confirms noteworthy stability and release pattern. Enhanced immunogenicity of the nanocomposite was determined by induction of rosette formation and rate of phagocytosis using T cell rosette formation assay (TCRF assay) and mouse leukemic monocyte macrophage phagocytosis assay. Notable enhancement on rosette formation and phagocytosis percentage was recorded in nanocomposite treatment as dose-dependent manner. Biocompatibility or non-target effect was done by evaluating acute or subacute toxicity against Wistar rat model and hemocompatibility. Hemocompatibility was measured by determination of hemolysis, antioxidative enzymes, erythrocytes aggregation and serum protein profiling. No sign of toxicity and mortality was observed in all the tested parameters of nanocomposite treated animal model. Hemocompatibility studies indicate that nanocomposite treatment was not shown hemolysis, changes in antioxidative enzymes and serum protein profiling which all confirms the best biocompatibility of the synthesised nanocomposite. Phytotoxic effect of the nanocomposite studied with Vigna mungo, Vigna radiata) and Brassica nigra seeds indicate that the nanocomposite treatment was not affecting seedlings emergence or germination index. All these findings unmistakably uncover that the nanocomposite fabricated HBsAg vaccine nanoformulation utilised as a successful immunising agent which constructed from its high immunogenic property and best biocompatibility against appropriate test model framework and investigated another sight in inoculation immunology part., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Alternative splicing (AS) of pre-mRNAs contributes to transcriptome diversity and enables plants to generate different protein isoforms from a single gene and/or fine-tune gene expression during different development stages and environmental changes. Although AS is pervasive, the genetic basis for differential isoform usage in plants is still emerging. In this study, we performed genome-wide analysis in 666 geographically distributed diverse ecotypes of Arabidopsis thaliana to identify genomic regions [splicing quantitative trait loci (sQTLs)] that may regulate differential AS. These ecotypes belong to different microclimatic conditions and are part of the relict and non-relict populations. Although sQTLs were spread across the genome, we observed enrichment for trans -sQTL ( trans -sQTLs hotspots) on chromosome one. Furthermore, we identified several sQTL (911) that co-localized with trait-linked single nucleotide polymorphisms (SNP) identified in the Arabidopsis genome-wide association studies (AraGWAS). Many sQTLs were enriched among circadian clock, flowering, and stress-responsive genes, suggesting a role for differential isoform usage in regulating these important processes in diverse ecotypes of Arabidopsis. In conclusion, the current study provides a deep insight into SNPs affecting isoform ratios/genes and facilitates a better mechanistic understanding of trait-associated SNPs in GWAS studies. To the best of our knowledge, this is the first report of sQTL analysis in a large set of Arabidopsis ecotypes and can be used as a reference to perform sQTL analysis in the Brassicaceae family. Since whole genome and transcriptome datasets are available for these diverse ecotypes, it could serve as a powerful resource for the biological interpretation of trait-associated loci, splice isoform ratios, and their phenotypic consequences to help produce more resilient and high yield crop varieties., (Copyright © 2019 Khokhar, Hassan, Reddy, Chaudhary, Jabre, Byrne and Syed.)

Plants, unlike animals, exhibit a very high degree of plasticity in their growth and development and employ diverse strategies to cope with the variations during diurnal cycles and stressful conditions. Plants and animals, despite their remarkable morphological and physiological differences, share many basic cellular processes and regulatory mechanisms. Alternative splicing (AS) is one such gene regulatory mechanism that modulates gene expression in multiple ways. It is now well established that AS is prevalent in all multicellular eukaryotes including plants and humans. Emerging evidence indicates that in plants, as in animals, transcription and splicing are coupled. Here, we reviewed recent evidence in support of co-transcriptional splicing in plants and highlighted similarities and differences between plants and humans. An unsettled question in the field of AS is the extent to which splice isoforms contribute to protein diversity. To take a critical look at this question, we presented a comprehensive summary of the current status of research in this area in both plants and humans, discussed limitations with the currently used approaches and suggested improvements to current methods and alternative approaches. We end with a discussion on the potential role of epigenetic modifications and chromatin state in splicing memory in plants primed with stresses.

Alternative splicing (AS) generates multiple transcripts from the same gene, however, AS contribution to proteome complexity remains elusive in plants. AS is prevalent under stress conditions in plants, but it is counterintuitive why plants would invest in protein synthesis under declining energy supply. We propose that plants employ AS not only to potentially increasing proteomic complexity, but also to buffer against the stress-responsive transcriptome to reduce the metabolic cost of translating all AS transcripts. To maximise efficiency under stress, plants may make fewer proteins with disordered domains via AS to diversify substrate specificity and maintain sufficient regulatory capacity. Furthermore, we suggest that chromatin state-dependent AS engenders short/long-term stress memory to mediate reproducible transcriptional response in the future., (Crown Copyright © 2019. Published by Elsevier Ltd. All rights reserved.)

Plants display exquisite control over gene expression to elicit appropriate responses under normal and stress conditions. Alternative splicing (AS) of pre-mRNAs, a process that generates two or more transcripts from multi-exon genes, adds another layer of regulation to fine-tune condition-specific gene expression in animals and plants. However, exactly how plants control splice isoform ratios and the timing of this regulation in response to environmental signals remains elusive. In mammals, recent evidence indicate that epigenetic and epitranscriptome changes, such as DNA methylation, chromatin modifications and RNA methylation, regulate RNA polymerase II processivity, co-transcriptional splicing, and stability and translation efficiency of splice isoforms. In plants, the role of epigenetic modifications in regulating transcription rate and mRNA abundance under stress is beginning to emerge. However, the mechanisms by which epigenetic and epitranscriptomic modifications regulate AS and translation efficiency require further research. Dynamic changes in the chromatin landscape in response to stress may provide a scaffold around which gene expression, AS and translation are orchestrated. Finally, we discuss CRISPR/Cas-based strategies for engineering chromatin architecture to manipulate AS patterns (or splice isoforms levels) to obtain insight into the epigenetic regulation of AS., (© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Oral mucosal lesions (OMLs) present with a variety of manifestations, emanating largely from tobacco chewing, smoking, and consumption of alcohol. Evolution of the lesions may be facilitated by poor oral hygiene and restorative dental materials, as well as by trauma, infections, and immune-mediated diseases. Two hundred consecutive patients seen at a pre-eminent dermatologic clinic formed the study group. They were interviewed about clinical manifestations, duration of the lesion, patient's age and sex, and incriminating factors. After informed consent had been gained, a thorough clinical examination was performed to define the precise morphology, site, and distribution of lesions. Confirmation of the clinical diagnosis by histopathology and other relevant techniques was confirmed.

Oral lichen planus (OLP), a well-known entity, is often neglected; however, its assessment is considered essential for evolving future strategies for treatment. Thirty-three patients with OLP from 200 consecutive patients with oral mucosal lesions were studied according to demography. Tobacco chewing, smoking, and alcohol intake were recorded. Examination of the oral cavity, using a head light and tongue depressor, was undertaken to define the morphology of the lesion(s). Colored photographs were an essential part of the process. OLP, a frequently encountered manifestation of oral mucosal lesions, was responsible for 16.50% of the total number of lesions. There was a preponderance of lesions in women aged 40 to 59 years, in contrast to men in the same age group. The duration of the lesions was variable, and tobacco chewing/smoking and amalgam fillings might have exacerbated them. Morphology ranged from a reticular, erythematous pattern to an erosive one. The diagnosis is largely clinical, but it can be confirmed by histopathology.

Oral mucosal lesions are a common occurrence in dermatology. In part III of this series, the authors discuss the epidemiology and etiopathology of these lesions, including clinical classifications, modifying factors, and incriminating agents.

A 52-year-old air conditioner mechanic presented with progressively itchy grayish white eruptions affecting the skin and mucous membranes, including his palms and soles for the past 2 months. The inner aspects of the palms and weight-bearing areas of the soles were the initial sites of presentation, resulting in a diffuse thickness of the palms and soles, which inhibited his everyday activity. The eruptions were asymptomatic but conspicuous. There was marked presence of multiple erythematous to grayish white (violaceous) flat-topped polygonal papules of varying sizes, with a few coalescing to form plaques. The papules varied in size from 5 mm to 4 cm and had prominent adherent scales on top when examined after smearing with mineral oil. Koebnerization was seen over the shin. The lesions were found on the wrists, forearms, ankles, legs, and thighs. There was a yellow to brown thick symmetric hyperkeratosis of the palms and soles, including the medial and lateral aspect of the fingers and toes, sparing the dorsal surfaces of the hands and feet (Figure 1). In addition, the medial arch and weight-bearing region of both soles were involved. The nails showed subungual hyperkeratosis, nail plate discoloration, and paronychia of the toes and fingers. Hyperkeratosis and scaly plaques were also identified in the web spaces (Figure 2). The buccal mucosa showed symmetrical white plaques with a lacy white pattern.

Circadian clocks are a great evolutionary innovation and provide competitive advantage during the day/night cycle and under changing environmental conditions. The circadian clock mediates expression of a large proportion of genes in plants, achieving a harmonious relationship between energy metabolism, photosynthesis, and biotic and abiotic stress responses. Here it is shown that multiple paralogues of clock genes are present in soybean (Glycine max) and mediate flooding and drought responses. Differential expression of many clock and SUB1 genes was found under flooding and drought conditions. Furthermore, natural variation in the amplitude and phase shifts in PRR7 and TOC1 genes was also discovered under drought and flooding conditions, respectively. PRR3 exhibited flooding- and drought-specific splicing patterns and may work in concert with PRR7 and TOC1 to achieve energy homeostasis under flooding and drought conditions. Higher expression of TOC1 also coincides with elevated levels of abscisic acid (ABA) and variation in glucose levels in the morning and afternoon, indicating that this response to abiotic stress is mediated by ABA, endogenous sugar levels, and the circadian clock to fine-tune photosynthesis and energy utilization under stress conditions. It is proposed that the presence of multiple clock gene paralogues with variation in DNA sequence, phase, and period could be used to screen exotic germplasm to find sources for drought and flooding tolerance. Furthermore, fine tuning of multiple clock gene paralogues (via a genetic engineering approach) should also facilitate the development of flooding- and drought-tolerant soybean varieties., (© The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

In order to succinctly interpret the clinical undertones of oral lichen planus and lichenoid tissue reaction/interface dermatitis, the well-recognized oral mucosal lesions, it is mandatory to comprehend oral cavity biology in the right perspective, the clinical connotations of which have been highlighted in perspective to facilitate diagnosis. In addition, a focus is formed on systemic association. Additionally, the imperative of salient histopathology in the diagnosis is emphasized for instant reference.

It is important to evaluate the background of oral cavity biology to define morphologic abrasions in oral mucosa following a host of local and/ or systemic disorders. The oral cavity is not only the beginning of the digestive system, but it also plays a significant role in communication; the voice (although the voice is produced in the throat), tongue, lips, and jaw are its essential components to produce the range of sounds. The vestibule and the oral cavity are its major parts, and are usually moist. The lips and the teeth are in approximation, marking its start up. The anatomy of the oral cavity in brief has been reviewed in right prospective for disease related changed morphology, thus facilitating interpretation.

Many sources of drought and flooding tolerance have been identified in soybean, however underlying molecular and physiological mechanisms are poorly understood. Therefore, it is important to illuminate different plant responses to these abiotic stresses and understand the mechanisms that confer tolerance. Towards this goal we used four contrasting soybean (Glycine max) genotypes (PI 567690--drought tolerant, Pana--drought susceptible, PI 408105A--flooding tolerant, S99-2281--flooding susceptible) grown under greenhouse conditions and compared genotypic responses to drought and flooding at the physiological, biochemical, and cellular level. We also quantified these variations and tried to infer their role in drought and flooding tolerance in soybean. Our results revealed that different mechanisms contribute to reduction in net photosynthesis under drought and flooding stress. Under drought stress, ABA and stomatal conductance are responsible for reduced photosynthetic rate; while under flooding stress, accumulation of starch granules played a major role. Drought tolerant genotypes PI 567690 and PI 408105A had higher plastoglobule numbers than the susceptible Pana and S99-2281. Drought stress increased the number and size of plastoglobules in most of the genotypes pointing to a possible role in stress tolerance. Interestingly, there were seven fibrillin proteins localized within the plastoglobules that were up-regulated in the drought and flooding tolerant genotypes PI 567690 and PI 408105A, respectively, but down-regulated in the drought susceptible genotype Pana. These results suggest a potential role of Fibrillin proteins, FBN1a, 1b and 7a in soybean response to drought and flooding stress., (Copyright © 2014 Elsevier Masson SAS. All rights reserved.)

Background: The objective of study was to determine pulmonary artery variations and other associated cardiac defects in patients with Tetralogy of Fallot. This cross-sectional, descriptive study was carried out at The Children's Hospital and the Institute of Child Health, Lahore, from January 2006 to December 2012. All patients with Tetralogy of Fallot, who underwent cardiac catheterization during this period, were included. Standard cine-angiograms were done to record the pulmonary artery sizes and associated cardiac defects., Description: A total of 576 patients with Tetralogy of Fallot were catheterized. Pulmonary Artery abnormalities were present in 109 (18.92%) patients. The commonest abnormality was isolated Left Pulmonary Artery stenosis (n = 60, 10.4%) followed by supra-valvular stenosis (n = 9, 1.6%). Left Pulmonary Artery was absent in seven patients(1.2%), while 1 patient (0.2%) had both absent right and left Pulmonary Arteries with segmental branch pulmonary arteries originating directly from Main Pulmonary Artery. Associated cardiac lesions included right aortic arch in 72 (12.5%), additional muscular Ventricular Septal Defect in 31 (5.4%), Patent Ductus Arteriosus in 31 (5.4%), bilateral Superior Vena Cava 36(6.2%), Atrial Septal Defect 4(0.7%) and Major Aortopulmonary Collateral Arteries in 75(13%) patients. Significant coronary artery abnormalities were present in 28(4.9%) children., Conclusion: Pulmonary artery abnormalities were present in 18.92% of patients with Tetralogy of Fallot. Isolated Left Pulmonary Artery origin stenosis was the most common abnormality. Significant associated cardiac lesions including Patent Ductus Arteriosus , additional muscular Ventricular Septal Defect, coronary artery abnormalities, bilateral Superior Vena Cava, Atrial Septal Defect and Major Aortopulmonary Collateral Arteries were present in one-third of the patients.

Ballota limbata (Lamiaceae) has been used for its antispasmodic, antiulcer, diuretic, vermifuge and sedative effects in folk medicine. However, little is known about how does it work to produce these therapeutic actions. Present research investigated phytochemical components and antioxidant properties of methanol extract and different fractions of Ballota limbata. In this study, phytochemical investigation was done by performing different chemical tests. Here, antioxidant property of the extract and fractions was investigated by using 1,1-diphenyl-2-picryl hydrazyl radical scavenging activity, total antioxidant activity by the phosphomolybdenum method, linoleic acid peroxidation, ferric thiocyanate analysis and ferric-reducing antioxidant power. Methanol extract and fractions showed presence of numerous chemical principles including alkaloids, cardiac glycosides, tannins and flavonoids. The ethyl acetate fraction exhibited higher scavenging activity compared to the other fractions under investigation. This fraction displayed 84.16±1.02% 1,1-diphenyl-2-picryl hydrazyl radical inhibition at a dose of 60 μg/ml. IC50 for 1,1-diphenyl-2-picryl hydrazylradical-scavenging activity was 13.53±0.22 μg/ml, relative to the standard, butylatedhydroxytoluene, having IC50 of 12.33±0.88 μg/ml. Thus, Ballota limbata showed significant antioxidant activity, which may contribute in the mechanism of above pharmacological actions.

In the March 2012 issue of The Plant Cell we describe extensive alternative splicing (AS) of Arabidopsis circadian clock genes. Notably these distinct post-transcriptional events associate with different steady-state temperatures and also with plants undergoing temperature transitions leading us to propose that temperature-associated AS is an additional mechanism involved in the operation and control of the plant circadian clock. Here we show that temperature associated AS also extends to REVEILLE 8 (RVE8), demonstrating a hitherto unrecognized link between the expression of this clock associated gene and temperature. Finally we discuss our observations of the plastic nature of clock gene expression at the post-transcriptional level in the context of the ongoing fascination of how plants respond to temperature.

More than 60% of intron-containing genes undergo alternative splicing (AS) in plants. This number will increase when AS in different tissues, developmental stages, and environmental conditions are explored. Although the functional impact of AS on protein complexity is still understudied in plants, recent examples demonstrate its importance in regulating plant processes. AS also regulates transcript levels and the link with nonsense-mediated decay and generation of unproductive mRNAs illustrate the need for both transcriptional and AS data in gene expression analyses. AS has influenced the evolution of the complex networks of regulation of gene expression and variation in AS contributed to adaptation of plants to their environment and therefore will impact strategies for improving plant and crop phenotypes., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Alternative splicing plays crucial roles by influencing the diversity of the transcriptome and proteome and regulating protein structure/function and gene expression. It is widespread in plants, and alteration of the levels of splicing factors leads to a wide variety of growth and developmental phenotypes. The circadian clock is a complex piece of cellular machinery that can regulate physiology and behavior to anticipate predictable environmental changes on a revolving planet. We have performed a system-wide analysis of alternative splicing in clock components in Arabidopsis thaliana plants acclimated to different steady state temperatures or undergoing temperature transitions. This revealed extensive alternative splicing in clock genes and dynamic changes in alternatively spliced transcripts. Several of these changes, notably those affecting the circadian clock genes late elongated hypocotyl (LHY) and pseudo response regulator7, are temperature-dependent and contribute markedly to functionally important changes in clock gene expression in temperature transitions by producing nonfunctional transcripts and/or inducing nonsense-mediated decay. Temperature effects on alternative splicing contribute to a decline in LHY transcript abundance on cooling, but LHY promoter strength is not affected. We propose that temperature-associated alternative splicing is an additional mechanism involved in the operation and regulation of the plant circadian clock.

Alternative splicing (AS) coupled to nonsense-mediated decay (NMD) is a post-transcriptional mechanism for regulating gene expression. We have used a high-resolution AS RT-PCR panel to identify endogenous AS isoforms which increase in abundance when NMD is impaired in the Arabidopsis NMD factor mutants, upf1-5 and upf3-1. Of 270 AS genes (950 transcripts) on the panel, 102 transcripts from 97 genes (32%) were identified as NMD targets. Extrapolating from these data around 13% of intron-containing genes in the Arabidopsis genome are potentially regulated by AS/NMD. This cohort of naturally occurring NMD-sensitive AS transcripts also allowed the analysis of the signals for NMD in plants. We show the importance of AS in introns in 5' or 3'UTRs in modulating NMD-sensitivity of mRNA transcripts. In particular, we identified upstream open reading frames overlapping the main start codon as a new trigger for NMD in plants and determined that NMD is induced if 3'-UTRs were >350 nt. Unexpectedly, although many intron retention transcripts possess NMD features, they are not sensitive to NMD. Finally, we have shown that AS/NMD regulates the abundance of transcripts of many genes important for plant development and adaptation including transcription factors, RNA processing factors and stress response genes.

Gene escape from crops has gained much attention in the last two decades, as transgenes introgressing into wild populations could affect the latter's ecological characteristics. However, different genes have different likelihoods of introgression. The mixture of selective forces provided by natural conditions creates an adaptive mosaic of alleles from both parental species. We investigated segregation patterns after hybridization between lettuce (Lactuca sativa) and its wild relative, L. serriola. Three generations of hybrids (S1, BC1, and BC1S1) were grown in habitats mimicking the wild parent's habitat. As control, we harvested S1 seedlings grown under controlled conditions, providing very limited possibility for selection. We used 89 AFLP loci, as well as more recently developed dominant markers, 115 retrotransposon markers (SSAP), and 28 NBS loci linked to resistance genes. For many loci, allele frequencies were biased in plants exposed to natural field conditions, including over-representation of crop alleles for various loci. Furthermore, Linkage disequilibrium was locally changed, allegedly by selection caused by the natural field conditions, providing ample opportunity for genetic hitchhiking. Our study indicates that when developing genetically modified crops, a judicious selection of insertion sites, based on knowledge of selective (dis)advantages of the surrounding crop genome under field conditions, could diminish transgene persistence.

Twelve different Ty1-copia and Ty3-gypsy group LTR retrotransposons were compared for their usefulness in SSAP marker development in two agriculturally important Vicia species. Three of the retrotransposons, PDR1, Tps19 and Tvf4, yielded useful SSAP marker systems in V. faba, and V. narbonensis. Another, Tvf1 was a good source of SSAP markers in V. narbonensis alone. The optimized SSAP marker systems were applied to the analysis of two diverse Vicia germplasm sets. Two hundred and two polymorphic Tvf1 SSAP markers were scored in 56 V. narbonensis samples and 196 polymorphic markers derived from the other three most useful retrotransposons were scored in a collection of 20 V. faba samples. The marker data were then used to construct phylogenetic trees. The trees for both species tend to show long-branch lengths, with rather little fine structure. Some V. narbonensis accessions cluster by geographical origin but many do not and a given geographical region is often represented by multiple diverse groups in the tree, suggesting a deep and ancient structure for the diversity of V. narbonensis that spans its current geographic range. The tree for the V. faba accessions also shows very limited clustering with geographical origin and no obvious correlation between diversity and morphology-based taxonomic groupings for the species.

Transposable elements are ubiquitous genomic parasites with an ancient history of coexistence with their hosts. A few cases have emerged recently where these genetic elements have been recruited for normal function in the host organism. We have identified an expressed hobo/Ac/Tam (hAT) family transposase-like gene in cereal grasses which appears to represent such a case. This gene, which we have called gary, is found in one or two copies in barley, two diverged copies in rice and two very similar copies in hexaploid wheat. No gary homologues are found in Arabidopsis. In all three cereal species, an apparently complete 2.5 kb transposase-like open reading frame is present and nucleotide substitution data show evidence for positive selection, yet the predicted gary protein is probably not an active transposase, as judged by the absence of key amino acids required for transposase function. Gary is expressed in wheat and barley spikes and gary cDNA sequences are also found in rice, oat, rye, maize, sorghum and sugarcane. The short inverted terminal repeats, flanked by an eight-nucleotide host sequence duplication, which are characteristic of a hAT transposon are absent. Genetic mapping in barley shows that gary is located on the distal end of the long arm of chromosome 2H. Wheat homologues of gary map to the same approximate location on the wheat group 2 chromosomes by physical bin-mapping and the more closely related of the two rice garys maps to the syntenic location near the bottom of rice chromosome 4. These data suggest that gary has resided in a single genomic location for at least 60 Myr and has lost the ability to transpose, yet expresses a transposase-related protein that is being conserved under host selection. We propose that the gary transposase-like gene has been recruited by the cereal grasses for an unknown function.

Molecular markers based upon a novel lettuce LTR retrotransposon and the nucleotide binding site-leucine-rich repeat (NBS-LRR) family of disease resistance-associated genes have been combined with AFLP markers to generate a 458 locus genetic linkage map for lettuce. A total of 187 retrotransposon-specific SSAP markers, 29 NBS-LRR markers and 242 AFLP markers were mapped in an F(2) population, derived from an interspecific cross between a Lactuca sativa cultivar commonly used in Europe and a wild Lactuca serriola isolate from Northern Europe. The cross has been designed to aid efforts to assess gene flow from cultivated lettuce into the wild in the perspective of genetic modification biosafety. The markers were mapped in nine major and one minor linkage groups spanning 1,266.1 cM, with an average distance of 2.8 cM between adjacent mapped markers. The markers are well distributed throughout the lettuce genome, with limited clustering of different marker types. Seventy-seven of the AFLP markers have been mapped previously and cross-comparison shows that the map from this study corresponds well with the previous linkage map.

Multiple copies of transposable elements, inserted at random around the host genome, can be used as molecular markers. Sequence-specific amplification polymorphisms (SSAPs) amplify the region between a PCR primer site near the end of an element and an adjacent restriction site in the flanking genomic DNA. Each amplified insertion is revealed as a band on a sequencing gel or capillary electrophoresis, and a genomic DNA sample produces a characteristic fingerprint of bands. Here, we explain the SSAP marker development method, which can be performed for any species, with recommendations for experimental parameters in several plant species. It takes about 1-2 weeks to complete the whole SSAP marker procedure.

The most popular retrotransposon-based molecular marker system in use at the present time is the sequence-specific amplification polymorphism (SSAP) system . This system exploits the insertional polymorphism of long terminal repeat (LTR) retrotransposons around the genome. Because the LTR sequence is used to design primers for this method, its successful application requires sequence information from the terminal region of the mobile elements . In this study, two LTR sequences were isolated from the cashew genome and used successfully to develop SSAP marker systems. These were shown to have higher levels of polymorphism than amplified fragment length polymorphic markers for this species.

The underlying mechanisms for hybrid vigor or heterosis are elusive. Here we report a population of recombinant inbred lines (RILs), derived from the two ecotypes, Col and Ler, which can serve as a permanent resource for studying the molecular basis of hybrid vigor in Arabidopsis. Using a North Carolina mating design III (NCIII), we determined the additive and dominant nature of gene action in this population. We detected heterosis among crosses of RILs with one of the two parents (Col and Ler) and analyzed genotypes and heterozygosities for RILs and test cross families (RILs crossed to Col and Ler) using a total of 446 published molecular markers. The performance of RILs and additive and dominant components in the test cross families were used to analyze QTLs for 16 traits, using QTL cartographer and composite interval mapping with 1,000 permutations for each trait. Our data suggest that locus-specific and/or genome-wide differential heterozygosity, including epistasis, plays an important role in the generation of the observed heterosis. Furthermore, the hybrid vigor occurred between two closely related ecotypes, and provides a general mechanism for novel variation generated between genetically similar materials.

Cotton, the leading natural fiber crop, is largely produced by two primary cultivated allotetraploid species known as Upland or American cotton ( Gossypium hirsutum L.) and Pima or Egyptian cotton ( G. barbadense L.). The allotetraploid species diverged from each other and from their diploid progenitors (A or D genome) through selection and domestication after polyploidization. To analyze cotton AD genomes and dissect agronomic traits, we have developed a genetic map in an F2 population derived from interspecific hybrids between G. hirsutum L. cv. Acala-44 and G. barbadense L. cv. Pima S-7. A total of 392 genetic loci, including 333 amplified fragment length polymorphisms (AFLPs), 47 simple sequence repeats (SSRs), and 12 restriction fragment length polymorphisms (RFLPs), were mapped in 42 linkage groups, which span 3,287 cM and cover approximately 70% of the genome. Using chromosomal aneuploid interspecific hybrids and a set of 29 RFLP and SSR framework markers, we assigned 19 linkage groups involving 223 loci to 12 chromosomes. Comparing four pairs of homoeologous chromosomes, we found that with one exception linkage distances in the A-subgenome chromosomes were larger than those in their D-subgenome homoeologues, reflecting higher recombination frequencies and/or larger chromosomes in the A subgenome. Segregation distortion was observed in 30 out of 392 loci mapped in cotton. Moreover, approximately 29% of the RFLPs behaved as dominant loci, which may result from rapid genomic changes. The cotton genetic map was used for quantitative trait loci (QTL) analysis using composite interval mapping and permutation tests. We detected seven QTLs for six fiber-related traits; five of these were distributed among A-subgenome chromosomes, the genome donor of fiber traits. The detection of QTLs in both the A subgenome in this study and the D subgenome in a previous study suggests that fiber-related traits are controlled by the genes in homoeologous genomes, which are subjected to selection and domestication. Some chromosomes contain clusters of QTLs and presumably contribute to the large amount of phenotypic variation that is present for fiber-related traits.

The genetic control of 22 quantitative traits, including developmental rates and sizes, was examined in generations of Arabidopsis thaliana derived from the cross between the ecotypes, Columbia (Col) and Landsberg erecta (Ler). The data were obtained from three sets of families raised in the same trial: the 16 basic generations, that is, parents, F(1)'s, F(2)'s, backcrosses, recombinant inbred lines (RILs) and a triple test cross (TTC), the latter produced by crossing the RILs to Col, Ler and their F(1). The data were analysed by two approaches. The first (approach A) involved traditional generation mean and variance component analysis and the second (B), based around the RILs and TTC families, involved marker-based QTL analysis. From (A), genetic differences between Col and Ler were detected for all traits with moderate heritabilities. Height at flowering was the only trait to show heterosis. Dominance was partial to complete for all height traits, and there was no overdominance but there was strong evidence for directional dominance. For most other traits, dominance was ambidirectional and incomplete, with average dominance ratios of around 80%. Epistasis, particularly of the duplicate type that opposes dominance, was a common feature of all traits. The presence of epistasis must imply multiple QTL for all traits. The QTL analysis located 38 significant effects in four regions of chromosomes I, II, IV and V, but not III. QTL affecting rosette size and leaf number were identified in all four regions, with days to maturity on chromosomes IV and V. The only QTL for height was located at the expected position of the erecta gene (chromosome II; 50 cM), but the additive and dominance effects of this single QTL did not adequately explain the generation means. The possible involvement of other interacting height QTL is discussed.