Changes In Genetic Expression Research Articles

Transcriptomic and physiological responses of Quercus acutissima and Quercus palustris to drought stress and rewatering

Establishment of oak seedlings, which is an important factor in forest restoration, is affected by drought that hampers the survival, growth, and development of seedlings. Therefore, it is necessary to understand how seedlings respond to and recover from water-shortage stress. We subjected seedlings of two oak species, Quercus acutissima and Quercus palustris, to drought stress for one month and then rewatered them for six days to observe physiological and genetic expression changes. Phenotypically, the growth of Q. acutissima was reduced and severe wilting and recovery failure were observed in Q. palustris after an increase in plant temperature. The two species differed in several physiological parameters during drought stress and recovery. Although the photosynthesis-related indicators did not change in Q. acutissima, they were decreased in Q. palustris. Moreover, during drought, content of soluble sugars was significantly increased in both species, but it recovered to original levels only in Q. acutissima. Malondialdehyde content increased in both the species during drought, but it did not recover in Q. palustris after rewatering. Among the antioxidant enzymes, only superoxide dismutase activity increased in Q. acutissima during drought, whereas activities of ascorbate peroxidase, catalase, and glutathione reductase increased in Q. palustris. Abscisic acid levels were increased and then maintained in Q. acutissima, but recovered to previous levels after rewatering in Q. palustris. RNA samples from the control, drought, recovery day 1, and recovery day 6 treatment groups were compared using transcriptome analysis. Q. acutissima exhibited 832 and 1076 differentially expressed genes (DEGs) related to drought response and recovery, respectively, whereas Q. palustris exhibited 3947 and 1587 DEGs, respectively under these conditions. Gene ontology enrichment of DEGs revealed “response to water,” “apoplast,” and “Protein self-association” to be common to both the species. However, in the heatmap analysis of genes related to sucrose and starch synthesis, glycolysis, antioxidants, and hormones, the two species exhibited very different transcriptome responses. Nevertheless, the levels of most DEGs returned to their pre-drought levels after rewatering. These results provide a basic foundation for understanding the physiological and genetic expression responses of oak seedlings to drought stress and recovery.

Differentiation of bone marrow mesenchymal stem cells into Leydig-like cells with testicular extract liquid in vitro.

Differentiation of Leydig cells plays a key role in male reproductive function. Bone marrow mesenchymal stem cells (BMSCs) have emerged as a potential cell source for generating Leydig-like cells due to their multipotent differentiation capacity and accessibility. This study aimed to investigate the morphological and genetic expression changes of BMSCs during differentiation into Leydig-like cells. Testicular extract liquid, which simulates the microenvironment in vivo, induced the third passage BMSCs differentiated into Leydig-like cells. Changes in cell morphology were observed by microscopy, the formation of lipid droplets of androgen precursor was identified by Oil Red Staining, and the expression of testicular specific genes 3β-HSD and SF-1 in testicular stromal cells was detected by RT-qPCR. BMSCs isolated from the bone marrow of Sprague-Dawley (SD) rats were cultured for 3 generations and identified as qualified BMSCs in terms of morphology and cell surface markers. After 14 days of induction with testicular tissue lysate, lipid droplets appeared in the cytoplasm of P3 BMSCs by Oil Red O staining. RT-qPCR detection was performed on BMSCs on the 3rd, 7th, 14th, and 21st day after induction. Relative expression levels of 3β-HSD mRNA significantly increased after 14 days of induction, while the relative expression of SF-1 mRNA increased after 14 days of induction but was not significant. BMSCs can differentiate into testicular interstitial cells with reserve androgen precursor lipid droplets after induction by testicular tissue lysate. The differentiation ability of BMSCs provides the potential to reconstruct the testicular microenvironment and is expected to fundamentally improve testicular function and provide new treatment options for abnormal spermatogenesis diseases.

Unique Spatial Transcriptomic Profiling of the Murine Femoral Fracture Callus: A Preliminary Report.

Fracture callus formation is a dynamic stage of bone activity and repair with precise, spatially localized gene expression. Metastatic breast cancer impairs fracture healing by disrupting bone homeostasis and imparting an altered genomic profile. Previous sequencing techniques such as single-cell RNA and in situ hybridization are limited by missing spatial context and low throughput, respectively. We present a preliminary approach using the Visium CytAssist spatial transcriptomics platform to provide the first spatially intact characterization of genetic expression changes within an orthopedic model of impaired fracture healing. Tissue slides prepared from BALB/c mice with or without MDA-MB-231 metastatic breast cancer cells were used. Both unsupervised clustering and histology-based annotations were performed to identify the hard callus, soft callus, and interzone for differential gene expression between the wild-type and pathological fracture model. The spatial transcriptomics platform successfully localized validated genes of the hard (Dmp1, Sost) and soft callus (Acan, Col2a1). The fibrous interzone was identified as a region of extensive genomic heterogeneity. MDA-MB-231 samples demonstrated downregulation of the critical bone matrix and structural regulators that may explain the weakened bone structure of pathological fractures. Spatial transcriptomics may represent a valuable tool in orthopedic research by providing temporal and spatial context.

SNP Analysis of TLR4 Promoter and Its Transcriptional Factor Binding Profile in Relevance to Bovine Subclinical Mastitis.

Bovine mastitis is a complex infectious disease that develops in the mammary gland, predominantly caused by a bacterial infection of mammary tissue. Genetic variability of mastitis is well established and depends upon different quantitative trait loci (QTL) related to mastitis resistance or susceptibility. The susceptibility is often attributed to single-nucleotide polymorphisms (SNPs) in the variable cow breed genomes. Several global investigative attempts have resulted in studies mapping mastitis to the variations in the relevant genes. Reports have been attributed to dramatic genetic expression changes in Toll-Like Receptor 4 (TLR4) genes in mastitis-positive cows. However, the mechanism behind this variable genetic expression of TLR4 genes has been studied poorly. The present study aims to investigate SCM through various screening tests like somatic cell count (SCC), electric conductivity (EC), pH, and California mastitis test (CMT) in milk samples. This study also aims to investigate possible mechanisms behind this variable expression of TLR4 by comparative SNP evaluation and transcriptional factor profile mining. So that the important genetic mutations and effects thereof can be exploited in selecting specific breeds with higher mastitis resistance and milk yield. Seventy Holstein Frisian (HF) crossbred dairy cows were selected in the present study. The animals were screened based on various diagnostic tests (SCC, pH, EC, and CMT). Blood samples (5mL) were collected for extraction of DNA followed by amplification of PPR1 and PPR2 of the promoter region and 5'UTR of the bovine TLR4 gene using specific primers. Sanger's enzymatic DNA sequencing technique sequenced the amplified PCR products. Further, the identification of SNPs was done through various bioinformatic tools used in this study. The findings of the present study revealed that CMT, EC, pH, and SCC could be used for the early detection of subclinical mastitis. In the present study, a significant increase in the EC, pH, and SCC in milk samples of animals affected with SCM was found in comparison to the healthy animals. The present study also revealed 16 SNPs falling in TLR4 promoter and 5' untranslated region (5'UTR) sequences in mastitis-positive genotypes compared to reference genomes. The study also investigates the potential transcriptional factor program deployed in response to variable mastitis development resistance. In the present study, the allelic and genotype frequencies of all SNP variants in the three regions viz., PPR1, PPR2, and 5'UTR, were the same indicating the absence of heterozygous condition at the respective loci. The present study has wide applicability for researchers developing mastitis-resistant breeding programs and the data generated may aid in the selection of better genetic breeds. The transcription factor binding profiles can serve as concrete leads about the studies on bovine mastitis at the molecular level and may also aid global research groups working on transcription factor (TF)-based molecular pathology of mastitis.

Epigenetic Changes Associated with Osteosarcoma: A Comprehensive Review.

Osteosarcoma is the most common malignant primary bone tumor in children and adolescents. While clinical outcomes have improved, the 5-year survival rate is only around 60% if discovered early and can require debilitating treatments, such as amputations. A better understanding of the disease could lead to better clinical outcomes for patients with osteosarcoma. One promising avenue of osteosarcoma research is in the field of epigenetics. This research investigates changes in genetic expression that occur above the genome rather than in the genetic code itself. The epigenetics of osteosarcoma is an active area of research that is still not fully understood. In a narrative review, we examine recent advances in the epigenetics of osteosarcoma by reporting biomarkers of DNA methylation, histone modifications, and non-coding RNA associated with disease progression. We also show how cancer tumor epigenetic profiles are being used to predict and improve patient outcomes. The papers in this review cover a large range of epigenetic target genes and pathways that modulate many aspects of osteosarcoma, including but not limited to metastases and chemotherapy resistance. Ultimately, this review will shed light on the recent advances in the epigenetics of osteosarcoma and illustrate the clinical benefits of this field of research.

Genetic expression changes and pathologic findings associated with hyperhomocysteinemia in human autopsy brain tissue.

Vascular contributions to cognitive impairment and dementia (VCID) are a leading cause of dementia. An underappreciated, modifiable risk factor for VCID is hyperhomocysteinemia (HHcy), defined by elevated levels of plasma homocysteine, most often due to impaired B vitamin absorption in aged persons. Studies aimed at identifying neuropathologic features and gene expression profiles associated with HHcy have been lacking. A subset of research volunteers from the University of Kentucky Alzheimer's Disease Research Center longitudinal cohort came to autopsy and had ante mortem plasma homocysteine levels available. Brain tissue and blood plasma drawn closest to death were used to measure homocysteine and related metabolites in the current pilot study. Genetic expression profiles of inflammatory markers were evaluated using the Human Neuroinflammation NanoString panel. Further analyses included an evaluation of plasma homocysteine effects on amyloid beta, tau, ionized calcium-binding adaptor molecule 1, and glial fibrillary acidic protein immunohistochemistry in the frontal and occipital cortices. Analytes and other study outcomes were evaluated in relation to ante mortem HHcy status: We identified 13 persons with normal ante mortem plasma homocysteine levels (<14µmol/L) and 18 who had high plasma homocysteine levels (≥14µmol/L). Participants with HHcy demonstrated increased levels of several plasma homocysteine cycle metabolites such as total cysteine, S-adenosyl-homocysteine, cystathionine, and choline. Inflammatory gene expression profiles showed a general downregulation in the setting of elevated plasma homocysteine. HHcy was associated with more and longer microglial processes, but smaller and fewer astrocytes, especially in participants of older age at death. HHcy in older participants was also associated with occipital cortex microhemorrhages and increased severity of atherosclerosis throughout the cerebral vasculature. Increased plasma homocysteine and older age were associated with the downregulation of inflammatory gene expression markers in association with significant glial and vascular pathology changes. Impaired immune function is a plausible mechanism by which HHcy increases cerebrovascular damage leading to impaired cognitive function.

Epigenetic Modifications in Plant Development and Reproduction.

Plants are exposed to highly fluctuating effects of light, temperature, weather conditions, and many other environmental factors throughout their life. As sessile organisms, unlike animals, they are unable to escape, hide, or even change their position. Therefore, the growth and development of plants are largely determined by interaction with the external environment. The success of this interaction depends on the ability of the phenotype plasticity, which is largely determined by epigenetic regulation. In addition to how environmental factors can change the patterns of genes expression, epigenetic regulation determines how genetic expression changes during the differentiation of one cell type into another and how patterns of gene expression are passed from one cell to its descendants. Thus, one genome can generate many ‘epigenomes’. Epigenetic modifications acquire special significance during the formation of gametes and plant reproduction when epigenetic marks are eliminated during meiosis and early embryogenesis and later reappear. However, during asexual plant reproduction, when meiosis is absent or suspended, epigenetic modifications that have arisen in the parental sporophyte can be transmitted to the next clonal generation practically unchanged. In plants that reproduce sexually and asexually, epigenetic variability has different adaptive significance. In asexuals, epigenetic regulation is of particular importance for imparting plasticity to the phenotype when, apart from mutations, the genotype remains unchanged for many generations of individuals. Of particular interest is the question of the possibility of transferring acquired epigenetic memory to future generations and its potential role for natural selection and evolution. All these issues will be discussed to some extent in this review.

Abstract 14078: Diabetes Attenuates Leukocyte Inflammatory Transcription Following Sleeve Gastrectomy

Introduction: Individuals with obesity and diabetes have increased risk for atherosclerosis; contributed by chronic systemic inflammation and elevated glycemic variability (GV). Bariatric surgery reduces circulating inflammatory markers. We aimed to determine the differences in GV and the expression of inflammatory genes from circulating white blood cells (WBC) after sleeve gastrectomy (SG) in those with and without non-insulin dependent diabetes. Methods: We conducted a prospective cohort study in subjects with obesity and type 2 diabetes (n=10) and subjects with obesity and no diabetes (n=11). Research visits occurred before SG and 6 months postoperatively. Elevated GV was defined by oral glucose tolerance test derived 1-h plasma glucose ≥155 mg/dL and elevated continuous glucose monitor derived GV index-MAGE (reference range 0-2.8 mmol/l). Bulk RNA-sequencing was performed on total WBCs, isolated neutrophils, monocytes, and lymphocytes to analyze genetic expression changes in chronic 6-month weight loss from baseline. Results: At 6 months, SG caused equivalent weight loss from baseline in both groups (22%). However, HbA1c, 1-h plasma glucose, and MAGE levels were different after SG between both groups. HbA1c decreased by 3.0±1.3% in the diabetes group (p&lt;0.01) but was in the prediabetes range at 6 months. The mean 1-h plasma glucose levels was 228.7± 74.6 mg/dL in the diabetes group versus 137.8 ± 30.5 mg/dL in the no diabetes group, and MAGE remained elevated (4.9 ±1.5 mmol/l) only in the diabetes group at 6 months. Also, total WBC counts decreased significantly at 6 months in both groups (p&lt;0.05). RNA sequencing analysis of these WBCs revealed that SG induced weight loss changed the expression of fewer total and WBCs subset genes in the diabetes group, and the majority of these gene expression changes (&gt;94% of total genes) were different between both groups. Furthermore, our gene set analysis showed downregulated expression of WBC genes enriched in inflammatory pathways primarily in subjects without diabetes. Conclusion: Diabetes dampens the weight-loss induced changes to transcriptomes from WBC subsets that contribute to cardiovascular disease. Elevated GV after SG may contribute to these attenuated changes.

Assessment of Benefits and Risks of Probiotics in Processed Cereal-based Baby Foods Lactobacillus Paracasei ssp. Paracasei F19

The Norwegian Scientific Committee for Food Safety (VKM) has appointed an ad hoc-group of experts to answer a request from the Norwegian Food Safety Authority regarding benefit and risk assessment of Lactobacillus paracasei ssp. paracasei F19 (F19) in processed cerealbased baby foods intended for small children 1-3 years. This assessment is based on the literature provided by the notifier as well as that found by a MEDLINE search. &#x0D; &#x0D; A notification regarding two products of processed cereal-based baby foods (hereafter called cereals), intended for small children and supplemented with the bacterium F19 initiated this work.&#x0D; &#x0D; A daily supply of a monoculture of a particular bacterial strain in large quantities to an age group without a fully established intestinal flora, may have unknown adverse effects. There are however, to our knowledge, no studies investigating possible short or long term adverse health effects of F19 in processed cereal-based baby food given to children 13 months onwards.&#x0D; &#x0D; The documentation and information provided by the notifier regarding the genetic stability of F19 in the two products during processing and storage, is considered insufficient and does not allow any conclusions to be drawn. &#x0D; &#x0D; Moreover, the documentation obtained is not conclusive regarding the antibiotic resistance pattern of the bacterial strain used in the products in question, as the information on different antibiotics is partly inconsistent. The information about specific localization (chromosomal, plasmid) of the resistance genes is not sufficient. &#x0D; &#x0D; Studies demonstrate that F19, as well as other bacterial strains considered probiotic, is able to “crosstalk” with enterocytes in mice and that the result of the “crosstalk” depends upon the microbiota present. Whether F19 has a similar “crosstalk-profile” in humans is unknown. However, as the strain is originally of human origin, it seems reasonable to assume that such “crosstalk” may occur. Thus, before giving F19 daily for months and years, it seems reasonable to ask for additional molecular and physiological studies to unravel the functional impact of possible changes in genetic expression in children. &#x0D; &#x0D; Lactobacillus infections do occasionally occur, mainly as bacteremia, endocarditis and localized infections (e.g. abscesses, peritonitis, and meningitis) in patients with severe underlying diseases. Most of them are elderly, but children are not excluded. The species most often isolated are L. casei and L. rhamnosus, followed by L. paracasei. &#x0D; &#x0D; The increasing use of immunosuppressive therapy and broad spectrum antibiotics which are ineffective against Lactobacillus, might increase the importance of these bacteria as possible pathogens. In order to be able to draw any conclusions regarding beneficial effects of F19, there is a need for randomized placebo-controlled studies in larger populations and in the relevant age group. &#x0D; &#x0D; According to EFSA, Lactobacillus paracasei ssp. paracasei F19 is sufficiently characterized. The documentation provided is, however, not sufficient to claim positive health effects and thus F19 is not proven to be probiotic. &#x0D; &#x0D; There are no published dose-response studies of F19 in children, neither regarding survival of F19 in the gastrointestinal tract, nor possible negative health effects. Thus the potential for negative health effects as e.g. spreading of antimicrobial resistance or unfavourable impact on the genetic expression in children related to the frequency and/or dose of a monoculture of F19 cannot be assessed.

RNAScope in situ Hybridization as a Novel Technique for the Assessment of c-KIT mRNA Expression in Canine Mast Cell Tumor.

RNA is considered as an indicator of the dynamic genetic expression changes in a cell. RNAScope is a commercially available in situ hybridization assay for the detection of RNA in formalin-fixed paraffin-embedded tissue. In this work, we describe the use of RNAScope as a sensitive and specific method for the evaluation of c-KIT messenger RNA (mRNA) in canine mast cell tumor. We investigated the expression of c-KIT mRNA with RNAscope in 60 canine mast cell tumors (MCTs), comparing it with the histological grade and KIT immunohistochemical expression patterns. Our results showed an overall good expression of c-KIT mRNA in neoplastic cells if compared with control probes. We also observed a statistically significant correlation between histological grade and c-KIT mRNA expression. No correlations were found between KIT protein immunohistochemical distribution pattern and c-KIT mRNA expression or histological grade. Our results provide a reference basis to better understand c-KIT mRNA expression in canine MCTs and strongly encourage further studies that may provide useful information about its potential and significant role as a prognostic and predictive biological marker for canine MCTs clinical outcome.

Increased Environment-Related Metabolism and Genetic Expression in the In Vitro Matured Mouse Oocytes by Transcriptome Analysis.

Infertility in humans at their reproductive age is a world-wide problem. Oocyte in vitro maturation (IVM) is generally used in such cases to acquire the embryo in assisted reproductive technology (ART). However, the differences between an in vivo (IVO) and IVM culture environment in the RNA expression profile in oocytes, remains unclear. In this study, we compared the global RNA transcription pattern of oocytes from in vitro and in vivo maturation. Our results showed that 1,864 genes differentially expressed between the IVO and IVM oocytes. Among these, 1,638 genes were up-regulated, and 226 genes were down-regulated, and these changes were mainly divided into environmental adaption, metabolism, and genetic expression. Our detailed analysis showed that the expression of genes that belonged to metabolism-related processes such as energy metabolism, nucleotide metabolism, and carbohydrate metabolism was changed; and these genes also belonged to organismal systems including environmental adaptation and the circulatory system; moreover, we also found that the relative gene expression of genetic expression processes, such as protein synthesis, modification, and DNA replication and repair were also altered. In conclusion, our data suggests that in vitro maturation of mouse oocyte resulted in metabolism and genetic expression changes due to environmental changes compared with in vivo matured oocytes.

Effect of Lepidium meyenii (maca) on spatial memory and brain oxidative damage of ovariectomized-rats exposed to mobile phone

Background: Oxidative stress, genetic expression changes, and decomposition of the blood-brain barrier have been shown to be caused by exposure to radiofrequency radiation (RFR); therefore, the search for drugs or food products that offer some protection from these effects has attracted interest. Lepidium meyenii (maca) is a native Andean plant known for its effects on the female reproductive system as well as its immunomodulating, energizing, antioxidant, and nutritive properties due to its high concentration of alkaloids, amino acids, glucosinolates, fatty acids, and macamides. Objectives: We aim to determine the effect of dietary maca supplementation on spatial memory and cerebral oxidative damage in rats with induced menopause and/or with exposure to mobile phone radiation. Method: Female rats divided into 6 groups (six rats in each group): control or not ovariectomized (O-), ovariectomized (O+), ovariectomized + estrogen (O+E+), ovariectomized + estrogen + irradiated (O+E+I+), ovariectomized + maca (O+M+), and ovariectomized + maca + irradiated (O+M+I). Rat spatial memory was tested using the Morris water navigation task. Rats were sacrificed, and cerebral malondialdehyde was measured. Results: After exposure to mobile phone radiation, the group supplemented with maca showed improved spatial memory and lower levels of malondialdehyde than the estrogenized group. Conclusions: Our results suggest that consumption of maca has a positive effect on the maintenance of memory and decreases oxidative stress caused by mobile phone radiation. However, it is necessary to extend this work using a larger sample size.

Effect of Sutellarin on Neurogenesis in Neonatal Hypoxia-Ischemia Rat Model: Potential Mechanisms of Action.

To investigate the therapeutic efficacy of Scutellarin (SCU) on neurite growth and neurological functional recovery in neonatal hypoxic-ischemic (HI) rats. Primary cortical neurons were cultured to detect the effect of SCU on cell viability of neurons under oxygen-glucose deprivation (OGD). Double immunofluorescence staining of Tuj1 and TUNEL then observed the neurite growth and cell apoptosis in vitro,and double immunofluorescence staining of NEUN and TUNEL was performed to examine the neuronal apoptosis and cell apoptosis in brain tissues after HI in vivo. Pharmacological efficacy of SCU was also evaluated in HI rats by neurobehavioral tests, triphenyl tetrazolium chloride staining, Hematoxylin and eosin staining and Nissl staining. Astrocytes and microglia expression in damaged brain tissues were detected by immunostaining of GFAP and Iba1. A quantitative real-time polymerase chain reaction and western blot were applied to investigate the genetic expression changes and the protein levels of autophagy-related proteins in the injured cortex and hippocampus after HI. We found that SCU administration preserved cell viability, promoted neurite outgrowth and suppressed apoptosis of neurons subjected to OGD both in vitroand in vivo. Meanwhile, 20 mg/kg SCU treatment improved neurological functions and decreased the expression of astrocytes and microglia in the cortex and hippocampus of HI rats. Additionally, SCU treatment depressed the elevated levels of autophagy-related proteins and the p75 neurotrophin receptor (p75NTR) in both cortex and hippocampus. This study demonstrated the potential therapeutic efficacy of SCU by enhancing neurogenesis and restoring long-term neurological dysfunctions, which might be associated with p75NTR depletion in HI rats.

Exercise Heat Exposure Induced Changes In Genetic Expression Before And After Heat Acclimation In Humans

PURPOSE: To evaluate changes in genetic expression of proteins that are implicated in physiological adaptation to exercise heat exposure (Hypoxia Inducible Factor -1α [HIF-1α], Erythropoietin [EPO], and Vascular Endothelial Growth Factor [VEGF]) during systemic adaptation related to Heat Acclimation (HA) in humans. METHODS: Participants (n=18, 13 males, 5 females: 30 ± 7.34 y; 173.1 ± 7.673 cm; 76.25 ±14.17 kg) underwent two Heat Tolerance Tests (HTT 1 & 2; 120 min walking, 5 km/h, 2.0% grade, 40 °C, 40% rh) with 12-14 days between tests. Participants in experimental group (HA) underwent six heat acclimation days between tests, while the control group (CON) avoided exercise heat exposure between HTT’s. Blood was drawn pre- and post- each HTT and isolated into Peripheral Blood Mononuclear Cells, then further isolated into RNA. Then, cDNA was synthesized for Quantitative Real-Time Polymerase Chain Reaction to quantify gene expression. The data was then analyzed using the ΔΔCT to acquire fold change. RESULTS: No statistical difference in resting rectal temperature was observed before HTT2 in HA (-0.13±0.36 °C) vs. CON (-.08±0.47 °C; P=0.80). No significant changes were observed between HTT1 and HTT2 in the control group for HIF-1α, EPO, or VEGF. However, it was observed that acute EPO fold change increased 10.6x; (P=0.14) from pre- to post- in HTT1 for each group. An increased fold change was also observed in both HIF-1α and EPO between HTT1 and HTT2 (3.24x; P=0.04) & (7.19x; P=0.03) respectively in the HA group. No significant changes in VEGF were found in either group. CONCLUSION: Although the HA protocol utilized in this investigations was not stressful enough to induce observable rectal temperature changes, genetic expression of HIF-1α and EPO was significantly upregulated in response to chronic exercise heat stress. Grant Info: This publication was supported by the Mountain and Plains - Educational Research Center (MAP-ERC) Pilot Grant & the High Plains Intermountain Center for Agricultural Health & Safety (HICAHS) Pilot Grant.

The Rapid Regenerative Response of a Model Sea Anemone Species Exaiptasia pallida Is Characterised by Tissue Plasticity and Highly Coordinated Cell Communication.

Regeneration of a limb or tissue can be achieved through multiple different pathways and mechanisms. The sea anemone Exaiptasia pallida has been observed to have excellent regenerative proficiency, but this has not yet been described transcriptionally. In this study, we examined the genetic expression changes during a regenerative timecourse and reported key genes involved in regeneration and wound healing. We found that the major response was an early (within the first 8h) upregulation of genes involved in cellular movement and cell communication, which likely contribute to a high level of tissue plasticity resulting in the rapid regeneration response observed in this species. We find the immune system was only transcriptionally active in the first 8h post-amputation and conclude, in accordance with previous literature, that the immune system and regeneration have an inverse relationship. Fifty-nine genes (3.8% of total) differentially expressed during regeneration were identified as having no orthologues in other species, indicating that regeneration in E. pallida may rely on the activation of species-specific novel genes. Additionally, taxonomically restricted novel genes, including species-specific novels, and highly conserved genes were identified throughout the regenerative timecourse, showing that both may work in concert to achieve complete regeneration.

Non-coding RNAs as therapeutic targets in spinal cord injury

Spinal cord injury (SCI) may be followed by persistent motor dysfunction and somatosensory disturbances that negatively influences the quality of life of patients and creates a significant economic burden. Analysis of secondary biological processes associated with changes in genetic expression is becoming increasingly important every day in understanding the pathophysiology of spinal cord injury. The results of international sequencing of the human genome were analyzed in 2004. These data revealed about 20,000 protein-coding genes covering near 2% of the total genomic sequence. The vast majority of gene transcripts are actually characterized as non-coding RNAs (ncRNAs). These RNA clusters do not encode functional proteins and ensure post-transcriptional regulation of gene expression. The clusters may be small (approximately 20 nucleotides) known as miRNAs or the transcripts can enroll over 200 nucleotides defined as long non-coding RNAs (lncRNAs). Some modern studies describe transient expression of microRNA in case of spinal cord injury. These RNAs are associated with inflammation and apoptosis, functional recovery and regeneration. Large-scale genomic analysis has demonstrated the existence of multiple lncRNAs whose expression is associated with some processes of spinal cord injury. lncRNA can be divided into two categories depending on the position in relation to the coding genes: intergenic and intragenic. Intergenic lncRNAs is currently the most studied class. Intragenic lncRNAs can be subdivided depending on the overlap of the coding genes (antisense, intron, etc.). According to recent studies, long non-coding RNAs are abundantly present in the tissues of central nervous system and may be crucial in the pathogenesis of certain diseases of nervous system. At the cellular level, it has been shown that lncRNAs regulate the expression of protein-coding RNAs. Moreover, these molecules are involved into such processes as neuronal death, demyelination and glia activation. This review is devoted to the role of ncRNAs in the pathogenesis of spinal cord injury and their potential use as targets for the treatment of consequences of spinal cord injury.

Genetic Gene Expression Changes during Environmental Adaptations Tend to Reverse Plastic Changes Even after the Correction for Statistical Nonindependence.

Organismal adaptations to new environments often begin with plastic phenotypic changes followed by genetic phenotypic changes, but the relationship between the two types of changes is controversial. Contrary to the view that plastic changes serve as steppingstones to genetic adaptations, recent transcriptome studies reported that genetic gene expression changes more often reverse than reinforce plastic expression changes in experimental evolution. However, it was pointed out that this trend could be an artifact of the statistical nonindependence between the estimates of plastic and genetic phenotypic changes, because both estimates rely on the phenotypic measure at the plastic stage. Using computer simulation, we show that indeed the nonindependence can cause an apparent excess of expression reversion relative to reinforcement. We propose a parametric bootstrap method and show by simulation that it removes the bias almost entirely. Analyzing transcriptome data from a total of 34 parallel lines in 5 experimental evolution studies of Escherichia coli, yeast, and guppies that are amenable to our method confirms that genetic expression changes tend to reverse plastic changes. Thus, at least for gene expression traits, phenotypic plasticity does not generally facilitate genetic adaptation. Several other comparisons of statistically nonindependent estimates are commonly performed in evolutionary genomics such as that between cis- and trans-effects of mutations on gene expression and that between transcriptional and translational effects on gene expression. It is important to validate previous results from such comparisons, and our proposed statistical analyses can be useful for this purpose.

Gene expression profiling reveals upregulated FUT1 and MYBPC1 in children with pancreaticobiliary maljunction.

Pancreaticobiliary maljunction (PBM) is associated with high risk of epithelial atypical growth and malignant transformation of the bile duct or gallbladder. However, overall changes in genetic expression have not been examined in children with PBM. Genome-wide expression was analyzed using peripheral blood samples from 10 children with PBM and 15 pediatric controls. Differentially expressed genes (DEGs) were identified using microarray. Bioinformatics analysis was conducted using Gene Ontology and KEGG analyses. The top 5 in the up-regulated genes in PBM were verified with qRT-PCR. Receiver operator characteristic curve analysis was conducted to evaluate the predictive accuracy of selected genes for PBM. The microarray experiments identified a total of 876 DEGs in PBM, among which 530 were up-regulated and the remaining 346 were down-regulated. Verification of the top 5 up-regulated genes (TYMS, MYBPC1, FUT1, XAGE2, and GREB1L) by qRT-PCR confirmed the up-regulation of MYBPC1 and FUT1. Receiver operating characteristic curve analysis suggested that FUT1 and MYBPC1 up-regulation could be used to predict PBM, with the area under the curve of 0.873 (95%CI=0.735−1.000) and 0.960 (95%CI=0.891−1.000), respectively. FUT1 and MYBPC1 were up-regulated in children with PBM, and could be used as potential biomarkers for PBM.

The role of EGFR overexpression on the recurrence of basal cell carcinomas with positive surgical margins

BackgroundEpidermal growth factor receptor (EGFR) expression may have role on recurrence of basal cell carcinoma (BCC) with positive surgical margin(s). ObjectiveThe aim was to investigate the role of genetic expression changes of EGFR on recurrence rates in patients in follow up with surgically excised BCC with positive surgical margin(s). MethodsThirty-four surgical margin–positive BCC lesions that were closely followed up without an immediate reoperation were included in this study. Real-time polymerase chain reaction (PCR) was performed from the both healthy and tumoral tissue samples. ResultsEGFR was expressed at a significantly higher rate in tumoral tissues compared to healthy tissues (p < 0,05). In patients with recurrence lesions, EGFR expression was 6,66 times higher compared to patients with non-recurrent. Also, there was statistically significant difference EGFR expression for infiltrative subtypes (p < 0,05). ConclusionOur study focuses on the role of EGFR overexpression specifically and outcomes for recurrent and infiltrative subtyped lesions are significant for both clinic and pathogenesis of BCC. Similar studies have to be performed with high numbered patient groups.

Heberprot-P’s Effect on Gene Expression in Healing Diabetic Foot Ulcers

NTRODUCTION Diabetic foot ulcers are a chronic complication in patients with diabetes mellitus. They appear as a result of the combination of diabetic polyneuropathy and angiopathy, and in many cases require amputation of the affected extremity. Clinical trials have demonstrated that repeated local infiltration with Heberprot-P can improve healing of chronic diabetic foot ulcers. Although there is evidence of its effects as a granulation stimulator and on cell migration and proliferation, genetic control mechanisms explaining its anti-inflammatory and oxidative stress reduction properties are not yet thoroughly understood. OBJECTIVE Analyze changes in expression of genes involved in healing after treatment of diabetic foot ulcers with Heberprot-P. METHODS Biopsies were collected from diabetic foot ulcers of 10 responding patients before and after 2 weeks' treatment with Heberprot-P (75-μg applied intralesionally 3 times per week). Total RNA was obtained and quantitative PCR used to determine expression of 26 genes related to inflammation, oxidative stress, cell proliferation, ngiogenesis and extracellular matrix formation. Genetic expression was quantified before and after treatment using REST 2009 v2.0.13. RESULTS After treatment, there was a statistically significant increase in expression of genes related to cell proliferation, angiogenesis and formation of extracellular matrix (PDGFB, CDK4, P21, TP53, ANGPT1, COL1A1, MMP2 and TIMP2). A significant decrease was observed in gene expression related to inflammatory processes and oxidative stress (NFKB1, TNFA and IL-1A). CONCLUSIONS Our findings suggest that Heberprot-P's healing action on diabetic foot ulcers is mediated through changes in genetic expression that reduce hypoxia, inflammation and oxidative stress, and at the same time increase cell proliferation, collagen synthesis and extracellular matrix remodeling. The kinetics of expression of two genes related to extracellular matrix formation needs further exploration. KEYWORDS Epidermal growth factor, EGF, diabetic foot ulcer, wound healing, quantitative real-time PCR, gene expression, Cuba.