Ion Transport Genes Research Articles

Carbonate Apatite Nanoparticles-Facilitated Intracellular Delivery of siRNA(s) Targeting Calcium Ion Channels Efficiently Kills Breast Cancer Cells.

Specific gene knockdown facilitated by short interfering RNA (siRNA) is a potential approach for suppressing the expression of ion channels and transporter proteins to kill breast cancer cells. The overexpression of calcium ion channels and transporter genes is seen in the MCF-7 breast cancer cell line. Since naked siRNA is anionic and prone to nuclease-mediated degradation, it has limited permeability across the cationic cell membrane and short systemic half-life, respectively. Carbonate apatite (CA) nanoparticles were formulated, characterized, loaded with a series of siRNAs, and delivered into MCF-7 and 4T1 breast cancer cells to selectively knockdown the respective calcium and magnesium ion channels and transporters. Individual knockdown of TRPC6, TRPM7, TRPM8, SLC41A1, SLC41A2, ORAI1, ORAI3, and ATP2C1 genes showed significant reduction (p < 0.001) in cell viability depending on the cancer cell type. From a variety of combinations of siRNAs, the combination of TRPC6, TRPM8, SLC41A2, and MAGT1 siRNAs delivered via CA produced the greatest cell viability reduction, resulting in a cytotoxicity effect of 57.06 ± 3.72% (p < 0.05) and 59.83 ± 2.309% (p = 0.09) in 4T1 and MCF-7 cell lines, respectively. Some of the combinations were shown to suppress the Akt pathway in Western Blot analysis when compared to the controls. Therefore, CA-siRNA-facilitated gene knockdown in vitro holds a high prospect for deregulating cell proliferation and survival pathways through the modulation of Ca2+ signaling in breast cancer cells.

Genome-wide identification of genes regulated by RcsA, RcsB, and RcsAB phosphorelay regulators in Klebsiella pneumoniae NTUH-K2044

Rcs phosphorelay system is a two-component signal transduction system, which can regulate the transcription of capsule polysaccharide and biofilm related genes in Enterobacteriaceae. In this study, microarray technology was used to investigate the overall genes regulated by RcsA, RcsB, and RcsAB and the regulation mechanism in Klebsiella pneumoniae, then COG analysis was performed to explore the functions of the differentially expressed genes. According to the microarray data result, a total of 45, 223 and 217 genes regulated by RcsA, RcsB, and RcsAB were screened. The result of COG analysis suggested that inorganic ion transport and metabolism related genes have a majority in RcsA regulating genes. Most of RcsB regulated genes were showed involved in energy production and conversion process. Besides Carbohydrate transport and metabolism genes were identified as the major components of the RcsAB regulated genes. 15 differentially expressed genes were confirmed by quantitative real-time PCR (RT-qPCR). The RT-qPCR results indicated that 13 genes consistent with microarray data. The results of this study provided important evidence for further research to investigate the influence of RcsA, RcsB, RcsAB regulators and further efforts to address the diseased caused by K.pneumoniae, such as pneumonia, bacteremia, and urinary tract infection.

Four-dimensional, dynamic mosaicism is a hallmark of normal human skin that permits mapping of the organization and patterning of human epidermis during terminal differentiation

Recent findings of mosaicism (DNA sequence variation) challenge the dogma that each person has a stable genetic constitution. Copy number variations, point mutations and chromosome abnormalities in normal or diseased tissues have been described. We studied normal skin mosaicism of a single nucleotide polymorphism (SNP) [rs1426654, p.Thr111Ala] in SLC24A5, an ion transporter gene. This SNP is unusual in that more than 90% of people of European descent have homozygous germline A/A alleles, while more than 90% of East Asians and Blacks have homozygous germline G/G alleles. We found mosaicism in neonatal foreskins as well as in 69% of nearly 600 skin surface scraping samples from 114 donors of different ages. Strikingly, donors with germline (buccal or blood) A/A, A/G or G/G genotypes had all three sequences (A/A, A/G or G/G) in the skin surface scrapings. SNP sequence differences extended within the epidermis in the vertical dimension from basal cell layer to the stratum corneum at the surface, as well as across the two-dimensions of the skin surface. Furthermore, repeated scrapings in the same location revealed variation in the sequences in the same individuals over time, adding a fourth dimension to this variation. We then used this mosaicism to track the movement of epidermal cells during normal differentiation and characterize the patterning of epidermal cells during terminal differentiation. In this coordinated proliferation model of epidermal differentiation, the skin surface is alternatively populated by synchronous, cycling of waves of cells, with each group having a different DNA sequence. These groups of cells abruptly flatten into large sheets at the surface providing patches of uniform SNP sequence. This four-dimensional mosaicism is a normal, previously unrecognized form of dynamic mosaicism in human skin.

A tomato proline-, lysine-, and glutamic-rich type gene SpPKE1 positively regulates drought stress tolerance

Plant abiotic resistance in cultivated species features limited variability. Using genes of wild species serves as a valid approach for improving abiotic resistance of cultivated plants. In this study, we uncovered a previously uncharacterized proline-, lysine-, and glutamic-rich protein gene (SpPKE1), which was isolated from drought-resistant wild tomato species Solanum pennellii (LA0716). When M82, which is a drought-sensitive tomato cultivar, was engineered to overexpress SpPKE1, its tolerance under drought stress was significantly improved by the accumulation of more chlorophyll, proline, and limited malondialdehyde compared with that in RNA interference (RNAi)-suppression lines, which were more sensitive than the wild-type plants. Several ion transporter genes, abiotic-related transcriptional factors, and reactive oxygen species-scavenging genes were upregulated in PKE1 overexpression (OE) lines but downregulated in RNAi plants. OE of SpPKE1 enhanced drought tolerance in tobacco. Screening results of yeast two-hybrid protein–protein interaction revealed that SpPKE1 can bind to an F-box protein that plays an important role in plant drought resistance. We posited that PKE1 enhanced drought tolerance by modulating the expressions of stress-responsive genes and interacting with the F-box protein.

Association of sodium ion transporter gene polymorphisms with essential hypertension among ethnic Koreans from Mudanjiang

OBJECTIVE To assess the association of SLC12A3 and SCNN1B gene polymorphisms (rs11643718 and rs12447134) with essential hypertension among ethnic Koreans from Mudanjiang, China. METHODS For 204 patients with essential hypertension and 186 healthy controls, the genotypes of rs11643718 and rs12447134 loci were determined with an improved multiplex ligase detection reaction (iMLDR) method. RESULTS Allelic and genotypic frequencies of rs11643718 of SLC12A3 gene are associated with the onset of disease hypertension (P <0.05) as well as systolic blood pressure (P < 0.01, under a recessive model). No association was found between rs12447134 of SCNN1B gene with the onset of disease (P > 0.05) but diastolic blood pressure (P < 0.05, under a recessive model). CONCLUSION The polymorphisms of rs11643718 locus is associated with the susceptibility for essential hypertension among ethnic Koreans from Mudanjiang area and can be used as a predictor for the disease.

Rutin as a Potent Antioxidant: Implications for Neurodegenerative Disorders.

A wide range of neurodegenerative diseases (NDs), including Alzheimer's disease, Parkinson's disease, Huntington's disease, and prion diseases, share common mechanisms such as neuronal loss, apoptosis, mitochondrial dysfunction, oxidative stress, and inflammation. Intervention strategies using plant-derived bioactive compounds have been offered as a form of treatment for these debilitating conditions, as there are currently no remedies to prevent, reverse, or halt the progression of neuronal loss. Rutin, a glycoside of the flavonoid quercetin, is found in many plants and fruits, especially buckwheat, apricots, cherries, grapes, grapefruit, plums, and oranges. Pharmacological studies have reported the beneficial effects of rutin in many disease conditions, and its therapeutic potential in several models of NDs has created considerable excitement. Here, we have summarized the current knowledge on the neuroprotective mechanisms of rutin in various experimental models of NDs. The mechanisms of action reviewed in this article include reduction of proinflammatory cytokines, improved antioxidant enzyme activities, activation of the mitogen-activated protein kinase cascade, downregulation of mRNA expression of PD-linked and proapoptotic genes, upregulation of the ion transport and antiapoptotic genes, and restoration of the activities of mitochondrial complex enzymes. Taken together, these findings suggest that rutin may be a promising neuroprotective compound for the treatment of NDs.

Genomic Characteristics of Gender Dysphoria Patients and Identification of Rare Mutations in RYR3 Gene

Gender dysphoria (GD) is characterized by an incongruence between the gender assigned at birth and the gender with which one identifies. The biological mechanisms of GD are unclear. While common genetic variants are associated with GD, positive findings have not always been replicated. To explore the role of rare variants in GD susceptibility within the Han Chinese population, whole-genome sequencing of 9 Han female-to-male transsexuals (FtMs) and whole-exome sequencing of 4 Han male-to-female transsexuals (MtFs) were analyzed using a pathway burden analysis in which variants are first collapsed at the gene level and then by Gene Ontology terms. Novel nonsynonymous variants in ion transport genes were significantly enriched in FtMs (P- value, 2.41E-10; Fold enrichment, 2.8) and MtFs (P- value, 1.04E-04; Fold enrichment, 2.3). Gene burden analysis comparing 13 GD cases and 100 controls implicated RYR3, with three heterozygous damaging mutations in unrelated FtMs and zero in controls (P = 0.001). Importantly, protein structure modeling of the RYR3 mutations indicated that the R1518H mutation made a large structural change in the RYR3 protein. Overall, our results provide information about the genetic basis of GD.

Effect of seed priming with spermine/spermidine on transcriptional regulation of stress-responsive genes in salt-stressed seedlings of an aromatic rice cultivar

Gobindobhog, the indigenous aromatic rice cultivar from West Bengal, India, is well-known for its magnificent flavor and intense pleasant aroma. Earlier observation established the highly salt-susceptible nature of this cultivar and the potential role of exogenous spermidine (Spd) and spermine (Spm) in the amelioration of salt stress. In the present study, the effect of seed priming with Spd and Spm on salt-stressed Gobindobhog seedlings has been studied with respect to the regulation of expression of genes involved in multiple metabolic pathways controlling salt tolerance. The expression profiling of key genes encoding non-enzymatic and enzymatic antioxidants (ANS, CAT, SOD, APX, GR), osmolyte (P5CS, PDH, BADH1), ABA biosynthetic enzyme (NCED3), transcription factors (TRAB-1, WRKY-71), LEA (Osem), ion transporter (NHX1), PA metabolic enzymes (SAMDC, SPDS, SPMS, DAO, PAO), enzyme for RuBisCo (RbcS), and content of endogenous PAs, responsible for stress tolerance were studied both in the shoots and roots of Gobindobhog seedlings. Both Spm and Spd priming enhanced the expression of antioxidant genes in shoots and roots with respect to stressed seedlings. However, the enhanced expression was more pronounced with Spm priming. The genes for osmolyte and ABA biosynthesis were significantly enhanced by both the PAs, together with increased expression of ABA-inducible transcription factors and LEA gene in shoots and roots of stressed seedlings. However, better expression was noted with Spm. Priming also altered the expression of ion transporter gene NHX1 during stress. Salt stress did not increase the (Spm+Spd)/Put ratio; however, Spm pre-treatment slightly altered this ratio and also led to increased expression of PA biosynthetic genes and decreased expression of PA catabolic genes like DAO and PAO in shoots. Seed pre-treatment with Spd however decreased the (Spm+Spd)/Put ratio, as well as leading to higher expression of PAO in shoots, thereby indicating that the overall levels of Spm and Spd did not increase and that the biosynthesis and degradation processes were mutually regulated. However, the expression of DAO and PAO was decreased in roots. The metabolic readjustment in the seedlings brought about by the coordinated expression of a diverse array of genes during pre-treatment could significantly restore the down regulated RbcS expression noted under stress. Our results highlight the potentiality of priming technique in improving the overall performance of the aromatic cultivar during salt stress by controlling stress-tolerant determinants of multiple metabolic pathways.

The Reaumuria trigyna transcription factor RtWRKY1 confers tolerance to salt stress in transgenic Arabidopsis

Reaumuria trigyna (R. trigyna) is an endangered small shrub endemic to the Eastern Alxa–Western Ordos area in Inner Mongolia, China. Based on R. trigyna transcriptome data, the Group I WRKY transcription factor gene RtWRKY1 was cloned from R. trigyna. The full-length RtWRKY1 gene was 2100bp, including a 1261-bp open reading frame (ORF) encoding 573 amino acids. RtWRKY1 was mainly expressed in the stem and was induced by salt, cold stress, and ABA treatment. Overexpression of RtWRKY1 in Arabidopsis significantly enhanced the chlorophyll content, root length, and fresh weight of the transgenic lines under salt stress. RtWRKY1 transgenic Arabidopsis exhibited higher proline content, GSH-PX, POD, SOD, and CAT activities, and lower MDA content, Na+ content, and Na+/K+ ratio than wild-type Arabidopsis under salt stress conditions. Salt stress affected the expression of ion transport, proline biosynthesis, and antioxidant related genes, including AtAPX1, AtCAT1, AtSOD1, AtP5CS1, AtP5CS2, AtPRODH1, AtPRODH2, and AtSOS1 in transgenic lines. RtWRKY1 confers tolerance to salt stress in transgenic Arabidopsis by regulating plant growth, osmotic balance, Na+/K+ homeostasis, and the antioxidant system.

Breaking barrier integrity in alveolar epithelial cells leads to modification in the expression profile of tight junction and ion transporter genes

Acute lung injury is associated with epithelial disruption and abnormal transepithelial Na+ transport affecting lung oedema clearance and injury recovery. In the past, we reported that ENaC expression is downregulated in alveolar epithelial cells in presence of pro‐inflammatory conditions. However, the impact of loss of barrier integrity on ion channels and genes important for barrier integrity in these cells is not known. In the present work, we determined if loss of barrier integrity, in absence of inflammation, would have an impact on the gene expression profile of rat alveolar epithelial cells in primary culture, focussing on ion transporter and tight junction genes. We found that mechanical wounding (MW), induces a ~60% decrease of α,β and γENaC mRNA expression at 6h and 24h and ~40% decrease of αNa/K‐ATPase mRNA expression. ENaC short‐circuit current (Isc) recorded in Ussing chamber was decreased by 80% at 6h following MW and was correlated to αENaC mRNA expression (R=0,8379). Beside ENaC and Na/K‐ATPase, the expression profile of genes important for restauration of barrier integrity or epithelial differentiation was investigated at 6h following MW. There was an upregulation of tight junction genes (Cldn3 (171%), Cldn4 (288%), but not of Cldn5 and Cldn18. Integrin (Itgb3 (160%)) and epithelial markers (Ker8 (153%), Ker18 (209%)) were upregulated at 6h along with Ker14 (279%). While Cldn 3 and Cldn4 expressions were back to normal after 24h, αENaC gene expression was normalized only after 48h. This expression profile was also observed if we disrupt tight junction with a short EDTA treatment. Altogether the present data suggest that breaking epithelial barrier integrity leads to a change in epithelial cells phenotype where the cells prepare themselves to repair and restore tight junctions and cell polarity. Our results show that disruption of barrier integrity also affects ENaC expression and activity. These data will help to better understand the consequences of alveolar epithelial injury in the resolution of edema following lung injury.

Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife.

Comparative approaches in physiological genomics offer an opportunity to understand the functional importance of genes involved in niche exploitation. We used populations of Alewife (Alosa pseudoharengus) to explore the transcriptional mechanisms that underlie adaptation to fresh water. Ancestrally anadromous Alewives have recently formed multiple, independently derived, landlocked populations, which exhibit reduced tolerance of saltwater and enhanced tolerance of fresh water. Using RNA-seq, we compared transcriptional responses of an anadromous Alewife population to two landlocked populations after acclimation to fresh (0ppt) and saltwater (35ppt). Our results suggest that the gill transcriptome has evolved in primarily discordant ways between independent landlocked populations and their anadromous ancestor. By contrast, evolved shifts in the transcription of a small suite of well-characterized osmoregulatory genes exhibited a strong degree of parallelism. In particular, transcription of genes that regulate gill ion exchange has diverged in accordance with functional predictions: freshwater ion-uptake genes (most notably, the 'freshwater paralog' of Na+ /K+ -ATPase α-subunit) were more highly expressed in landlocked forms, whereas genes that regulate saltwater ion secretion (e.g. the 'saltwater paralog' of NKAα) exhibited a blunted response to saltwater. Parallel divergence of ion transport gene expression is associated with shifts in salinity tolerance limits among landlocked forms, suggesting that changes to the gill's transcriptional response to salinity facilitate freshwater adaptation.

Ischaemic exercise enhances mitochondrial and ion transport gene adaptations in trained human skeletal muscle: Role of cellular redox state, AMPK and CaMKII signalling

Ischaemic exercise enhances mitochondrial and ion transport gene adaptations in trained human skeletal muscle: Role of cellular redox state, AMPK and CaMKII signalling

Cold stress increases salt tolerance of the extremophytes Eutrema salsugineum (Thellungiella salsuginea) and Eutrema (Thellungiella) botschantzevii

A comparative study was performed to analyze the effect of cold acclimation on improving the resistance of Arabidopsis thaliana, Eutrema salsugineum and Eutrema botschantzevii plants to salt stress. Shoot FW, sodium and potassium accumulation, metabolite content, expression of proton pump genes VAB1, VAB2,VAB3, VP2, HA3 and genes encoding ion transporters SOS1, HKT1, NHX1, NHX2, NHX5 located in the plasma membrane or tonoplast were determined just after the cold treatment and the onset of the salt stress. In the same cold-acclimated E. botschantzevii plants, the Na+ concentration after salt treatment was around 80% lower than in non-acclimated plants, whereas the K+ concentration was higher. As a result of cold acclimation, the expression of, VAB3, NHX2, NHX5 genes and of SOS1, VP2, HA3 genes was strongly enhanced in E. botschantzevii and in E. salsugineum plants correspondently. None of the 10 genes analyzed showed any expression change in A. thaliana plants after cold acclimation. Altogether, the results indicate that cold-induced adaptation to subsequent salt stress exists in the extremophytes E. botschantzevii and to a lesser extend in E. salsugineum and is absent in Arabidopsis. This phenomenon may be attributed to the increased expression of ion transporter genes during cold acclimation in the Eutrema species.

Neonatal cardiac dysfunction and transcriptome changes caused by the absence of Celf1.

The RNA binding protein Celf1 regulates alternative splicing in the nucleus and mRNA stability and translation in the cytoplasm. Celf1 is strongly down-regulated during mouse postnatal heart development. Its re-induction in adults induced severe heart failure and reversion to fetal splicing and gene expression patterns. However, the impact of Celf1 depletion on cardiac transcriptional and posttranscriptional dynamics in neonates has not been addressed. We found that homozygous Celf1 knock-out neonates exhibited cardiac dysfunction not observed in older homozygous animals, although homozygous mice are smaller than wild type littermates throughout development. RNA-sequencing of mRNA from homozygous neonatal hearts identified a network of cell cycle genes significantly up-regulated and down-regulation of ion transport and circadian genes. Cell cycle genes are enriched for Celf1 binding sites supporting a regulatory role in mRNA stability of these transcripts. We also identified a cardiac splicing network coordinated by Celf1 depletion. Target events contain multiple Celf1 binding sites and enrichment in GU-rich motifs. Identification of direct Celf1 targets will advance our knowledge in the mechanisms behind developmental networks regulated by Celf1 and diseases where Celf1 is mis-regulated.

Haplotype distribution and association of candidate genes with salt tolerance in Indian wild rice germplasm.

The association of natural genetic variations of salt-responsive candidate genes belonging to different gene families with salt-tolerance phenotype and their haplotype variation in different geographic regions. Soil salinity covers a large part of the arable land of the world and is a major factor for yield losses in salt-sensitive crops, such as rice. Different gene families that respond to salinity have been identified in rice, but limited success has been achieved in developing salt-tolerant cultivars. Therefore, 21 salt stress-responsive candidate genes belonging to different gene families were re-sequenced to analyse their genetic variation and association with salt tolerance. The average single nucleotide polymorphism (SNP) density was 16 SNPs per kbp amongst these genes. The identified nucleotide and haplotype diversity showed comparatively higher genetic variation in the transporter family genes. Linkage disequilibrium (LD) analysis showed significant associations of SNPs in BADH2, HsfC1B, MIPS1, MIPS2, MYB2, NHX1, NHX2, NHX3, P5CS1, P5CS2, PIP1, SIK1, SOS1, and SOS2 genes with the salt-tolerant phenotype. A combined analysis of SNPs in the 21 candidate genes and eight other HKT transporter genes produced two separate clusters of tolerant genotypes, carrying unique SNPs in the ion transporter and osmoticum-related genes. Haplotype network analysis showed all the major and few minor alleles distributed over distant geographic regions. Minor haplotypes may be recently evolved alleles which migrated to distant geographic regions and may represent recent expansion of Indian wild rice. The analysis of genetic variation in different gene families identified the relationship between adaptive variations and functional significance of the genes. Introgression of the identified alleles from wild relatives may enhance the salt tolerance and consequently rice production in the salinity-affected areas.

Salinity-induced changes in gene expression from anterior and posterior gills of Callinectes sapidus (Crustacea: Portunidae) with implications for crustacean ecological genomics

Decapods represent one of the most ecologically diverse taxonomic groups within crustaceans, making them ideal to study physiological processes like osmoregulation. However, prior studies have failed to consider the entire transcriptomic response of the gill – the primary organ responsible for ion transport – to changing salinity. Moreover, the molecular genetic differences between non-osmoregulatory and osmoregulatory gill types, as well as the hormonal basis of osmoregulation, remain underexplored. Here, we identified and characterized differentially expressed genes (DEGs) via RNA-Seq in anterior (non-osmoregulatory) and posterior (osmoregulatory) gills during high to low salinity transfer in the blue crab Callinectes sapidus, a well-studied model for crustacean osmoregulation. Overall, we confirmed previous expression patterns for individual ion transport genes and identified novel ones with salinity-mediated expression. Notable, novel DEGs among salinities and gill types for C. sapidus included anterior gills having higher expression of structural genes such as actin and cuticle proteins while posterior gills exhibit elevated expression of ion transport and energy-related genes, with the latter likely linked to ion transport. Potential targets among recovered DEGs for hormonal regulation of ion transport between salinities and gill types included neuropeptide Y and a KCTD16-like protein. Using publically available sequence data, constituents for a “core” gill transcriptome among decapods are presented, comprising genes involved in ion transport and energy conversion and consistent with salinity transfer experiments. Lastly, rarefication analyses lead us to recommend a modest number of sequence reads (~10–15M), but with increased biological replication, be utilized in future DEG analyses of crustaceans.

KMT2D regulates specific programs in heart development via histone H3 lysine 4 di-methylation.

KMT2D, which encodes a histone H3K4 methyltransferase, has been implicated in human congenital heart disease in the context of Kabuki syndrome. However, its role in heart development is not understood. Here, we demonstrate a requirement for KMT2D in cardiac precursors and cardiomyocytes during cardiogenesis in mice. Gene expression analysis revealed downregulation of ion transport and cell cycle genes, leading to altered calcium handling and cell cycle defects. We further determined that myocardial Kmt2d deletion led to decreased H3K4me1 and H3K4me2 at enhancers and promoters. Finally, we identified KMT2D-bound regions in cardiomyocytes, of which a subset was associated with decreased gene expression and decreased H3K4me2 in mutant hearts. This subset included genes related to ion transport, hypoxia-reoxygenation and cell cycle regulation, suggesting that KMT2D is important for these processes. Our findings indicate that KMT2D is essential for regulating cardiac gene expression during heart development primarily via H3K4 di-methylation.

Osmoregulation in larvae and juveniles of two recently separated Macrobrachium species: Expression patterns of ion transporter genes

In this comparative study, osmoregulatory mechanisms were analyzed in two closely related species of palaemonid shrimp from Brazil, Macrobrachium pantanalense and Macrobrachium amazonicum. A previous investigation showed that all postembryonic stages of M. pantanalense from inland waters of the Pantanal are able to hyper-osmoregulate in fresh water, while this species was not able to hypo-osmoregulate at high salinities. In M. amazonicum originating from the Amazon estuary, in contrast, all stages are able to hypo-osmoregulate, but only first-stage larvae, late juveniles and adults are able to hyper-osmoregulate in fresh water. The underlying molecular mechanisms of these physiological differences have not been known. We therefore investigated the expression patterns of three ion transporters (NKA α-subunit, VHA B-subunit and NHE3) following differential salinity acclimation in different ontogenetic stages (stage-V larvae, juveniles) of both species. Larval NKAα expression was at both salinities significantly higher in M. pantanalense than in M. amazonicum, whereas no difference was noted in juveniles. VHA was also more expressed in larvae of M. pantanalense than in those of M. amazonicum. When NHE3 expression is compared between the larvae of the two species, further salinity-related differences were observed, with generally higher expression in the inland species. Overall, a high expression of ion pumps in M. pantanalense suggests an evolutionary key role of these transporters in freshwater invasion.

Transcriptome profiling of Kentucky bluegrass (Poa pratensis L.) accessions in response to salt stress.

BackgroundKentucky bluegrass (Poa pratensis L.) is a prominent turfgrass in the cool-season regions, but it is sensitive to salt stress. Previously, a relatively salt tolerant Kentucky bluegrass accession was identified that maintained green colour under consistent salt applications. In this study, a transcriptome study between the tolerant (PI 372742) accession and a salt susceptible (PI 368233) accession was conducted, under control and salt treatments, and in shoot and root tissues.ResultsSample replicates grouped tightly by tissue and treatment, and fewer differentially expressed transcripts were detected in the tolerant PI 372742 samples compared to the susceptible PI 368233 samples, and in root tissues compared to shoot tissues. A de novo assembly resulted in 388,764 transcripts, with 36,587 detected as differentially expressed. Approximately 75 % of transcripts had homology based annotations, with several differences in GO terms enriched between the PI 368233 and PI 372742 samples. Gene expression profiling identified salt-responsive gene families that were consistently down-regulated in PI 372742 and unlikely to contribute to salt tolerance in Kentucky bluegrass. Gene expression profiling also identified sets of transcripts relating to transcription factors, ion and water transport genes, and oxidation-reduction process genes with likely roles in salt tolerance.ConclusionsThe transcript assembly represents the first such assembly in the highly polyploidy, facultative apomictic Kentucky bluegrass. The transcripts identified provide genetic information on how this plant responds to and tolerates salt stress in both shoot and root tissues, and can be used for further genetic testing and introgression.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2379-x) contains supplementary material, which is available to authorized users.

Orchestrated regulation of energy supply and energy expenditure: Transcriptional coexpression of metabolism, ion homeostasis, and sarcomeric genes in mammalian myocardium

During the development of heart failure, the myocardium undergoes profound electrical remodeling, characterized by prolongation of action potential duration, changes in Ca(2+) homeostasis, and slowing of conduction. We tested the hypothesis that the electrical remodeling, indexed by the expression of ion channel and transporter genes, occurs in the context of a coordinated regulation of metabolism and signaling processes observed in heart failure. A meta-analysis of myocardial murine and human microarray data sets was performed. We identified transcripts that were coordinately expressed with 132 myocardial ion channel and transporter genes in 18 murine and human myocardial microarray data sets. The genes coexpressed with ion channels were subsequently grouped into Gene Ontology (GO) categories, revealing 4 major, mutually exclusive GO clusters: 55 ion channel and transporter genes were coexpressed with major bioenergetic pathways (oxidative phosphorylation, citric acid cycle, glycolysis, and fatty acid metabolism) and contractile processes (muscle contraction, sarcomere, and Z disc), while 36, 16, and 25 ion channel transcripts were associated with the GO clusters of signal transduction, transcription/translation, and a nonspecified cluster, respectively. Myocardial expression of ion channel genes coexpressed with metabolic processes was >10-fold higher than that of ion channels associated with the other 3 clusters. In addition to transcriptional coexpression, major myocardial ion channels were found to physically interact with metabolic pathways based on protein-protein interaction data. Electromechanical and metabolic remodeling processes are intricately linked at the transcriptional level, suggesting an orchestrated regulation of energy supply (metabolism) and energy expenditure (muscle contraction and ion homeostasis) in mammalian myocardium.