Relative Expression Analysis Research Articles

MTOR signaling and endometrial receptivity in infertile women with intramural uterine leiomyomas

BackgroundReceptive endometrium is a restraining factor in the establishment of pregnancy in several estrogen-dependent gynecological disorders including uterine leiomyomas. Recently, data are beginning to accrue suggesting negative impact of non-cavity distorting intramural fibroids on molecular mediators of endometrial receptivity. The potential importance of the mammalian target of rapamycin (mTOR) signaling pathway has been suggested during embryo implantation. However, its exact role in fibroid-associated endometrium during the window of implantation is poorly defined. The objective of the study was to examine the expression and cellular distribution of key components of the mTOR signaling pathway during window of implantation in infertile women with non-cavity distorting intramural uterine leiomyomas (n = 24) as compared to fertile controls (n = 17). Relative gene expression analysis of mTOR, TSC1, and TSC2 was performed by real-time PCR. Immunohistochemistry was used to evaluate the expression of mTOR, phospho-mTOR (Serine 2448), TSC1, TSC2, phospho-TSC2 (Threonine 1462), and phospho-S6 ribosomal protein (Serines 235 and 236) and Ki67.ResultsIn comparison to fertile controls, statistically significant upregulation of mTOR (8.97-fold; p < 0.001) and downregulation of TSC2 mRNA (− 6.01-fold; p < 0.01) levels and cell-specific upregulation of proteins phospho-mTOR, phospho-TSC2, and phospho-S6 and downregulation of TSC1 and TSC2 were observed in infertile women. The ratio of p-mTOR/mTOR and p-TSC2/TSC2 was significantly higher in infertile women. Pearson’s correlation analysis revealed significant negative correlation between p-mTOR and TSC2 and positive correlation between p-mTOR and p-S6 in the infertile group. Increased Ki67 labelling index was observed in the glandular epithelium (GE) and stroma of endometrium from infertile women as compared to controls.ConclusionsLoss of TSC2 function and enhanced expression of activated mTOR and its downstream targets, observed in the infertile group, indicate heightened mTOR signaling which might contribute to impaired endometrial receptivity. Increased number of Ki67-positive nuclei suggests that enhanced mTOR signaling may help drive dysregulated proliferation of midsecretory endometrium leading to compromised fertility in women with non-cavity distorting intramural uterine leiomyomas. The present findings provide avenues for future investigation of mTOR pathway as a nonsurgical alternative for treatment of infertility in these patients.

Green cabbage supplementation influences the gene expression and fatty acid levels of adipose tissue in Chinese Wanxi White geese.

Dietary green cabbage was evaluated for its impact on fatty acid synthetic ability in different adipose tissues during fattening of Wanxi White geese. A total of 256 Wanxi White geese at their 70 days were randomly allocated into 4 groups with 4 replicates and fed 0%, 15%, 30%, and 45% fresh green cabbage (relative to dry matter), respectively, in each group. Adipose tissues (subcutaneous and abdominal fat), liver and blood were collected from 4 birds in each replicate at their 70, 80, 90, and 100 days for fatty acid composition, relative gene expression and serum lipid analysis. Two-way or three-way analysis of variance was used for analysis. The contents of palmitic acid (C16:0), palmitoleic acid (C16:1), linoleic acid (C18:2), and alpha-linolenic acid (C18:3) were feeding time dependently increased. The C16:0 and stearic acid (C18:0) were higher in abdominal fat, while C16:1, oleic acid (C18:1), and C18:2 were higher in subcutaneous fat. Geese fed 45% green cabbage exhibited highest level of C18:3. Geese fed green cabbage for 30 d exhibited higher level of C16:0 and C18:0 in abdominal fat, while geese fed 30% to 45% green cabbage exhibited higher C18:3 in subcutaneous fat. The expression of Acsl1 (p = 0.003) and Scd1 (p<0.0001) were decreased with green cabbage addition. Interaction between feeding time and adipose tissue affected elongation of long-chain fatty acids family member 6 (Elovl6), acyl-CoA synthetase longchain family member 1 (Acsl1), and stearoly-coA desaturase 1 (Scd1) gene expression levels (p = 0.013, p = 0.003, p = 0.005). Feeding time only affected serum lipid levels of free fatty acid and chylomicron. Higher contents of C16:0, C18:1, and C18:3 were associated with greater mRNA expression of Scd1 (p<0.0001), while higher level of C18:2 was associated with less mRNA expression of Scd1 (p<0.0001). Considering content of C18:2 and C18:3, 30% addition of green cabbage could be considered for fattening for 30 days in Wanxi White geese.

Abstract #1406834: Study of Methylation Status and Expression of Vitamin D Receptor Gene in Polycystic Ovarian Syndrome Patients of Kashmiri Population

Downregulation of Vitamin D Receptor (VDR) gene expression resulting from epigenetics events, like methylation in promoter of VDR gene play an important role in pathogenesis, clinical and bio-chemical parameters of polycystic ovary syndrome, but the results from different studies are inconsistent. We aim to determine the methylation status of promoter of VDR gene and VDR gene expression analysis in addition to the co-relation between promoter methylation and expression profile of VDR genes in PCOS patients in Kashmiri Population. This study was a case control, comprising of 100 women with PCOS and 100 normal healthy control women aged between 15-45 years. PCOS patients were selected after proper diagnosis using Rotterdam criteria (2004) and obtaining written consent. DNA extraction was carried out by the non-enzymatic Salting out method and extracted DNA samples were subjected to bisulphite treatment using EZ DNA Methylation-Gold Kit (Zymo Research, Irvine, California) to produces a chemical conversion of unmethylated cytosine to uracil, which is detected as a thymine after PCR. Methylation specific PCR (MS-PCR) was performed following the bisulfite conversion, using pre-designed sets of methylated and unmethylated primers to confirm the prominence of methylation in the promoter VDR region and to specially acknowledge methylated and unmethylated VDR fragments. The VDR expression analysis was carried out following RNA extraction from the blood sample and processed ahead for cDNA synthesis using reverse transcriptase reaction and then relative expression analysis by RT-PCR using SYBR Green fluorescent dye. We found that vitamin D level among test group was significantly lower compared to controls (13.95±9.60 VS. 16.63±7.46; p=0.026). Methylation was significantly higher in test group compared to controls (84% vs 62%; p<0.0001) with OR of 3.21. Furthermore, there exists a significant difference between the average cyclic threshold (CT) value of VDR gene among test and control groups (24.64 vs. 26.14;p <0.0001). The average CT value corresponding to GAPDH (glyceraldehyde phosphate dehydrogenase) is 29.76 in test group and 32.11 in control group. The expression of VDR gene was 0.55 times down regulated in test group in comparison to controls. In the present study, we have comprehensively shown that VDR hypermethylation is significantly associated with reduced vitamin D level and decreased expression level of VDR gene among PCOS women. Increased VDR methylation in response to decreased vitamin D levels could be involved in the impairment of VDR mediated effects resulting in the peculiar clinical and bio-chemical derangements in patients of polycystic ovary syndrome. However, the enhanced ligand availability results in decreased receptor expression to maintain homeostasis of vitamin D signalling. Hence, this, inverse association could have a significant role in the altered gene expression of VDR and thereby effecting the cell response in PCOS patients.

Using RNA-seq to identify suitable housekeeping genes for hypoxia studies in human adipose-derived stem cells

BackgroundHypoxic culture conditions have been used to study the impact of oxygen deprivation has on gene expression in a number of disease models. However, hypoxia response elements present in the promoter regions of some commonly used housekeeping genes, such as GAPDH and PGK1, can confound the relative gene expression analysis. Thus, there is ongoing debate as to which housekeeping gene is appropriate for studies investigating hypoxia-induced cell responses. Specifically, there is still contradicting information for which housekeeping genes are stable in hypoxia cultures of mesenchymal stem cells. In this study, candidate housekeeping genes curated from the literature were matched to RNAseq data of normoxic and hypoxic human adipose-derived stem cell cultures to determine if gene expression was modulated by hypoxia or not. Expression levels of selected candidates were used to calculate coefficient of variation. Then, accounting for the mean coefficient of variation, and normalised log twofold change, genes were ranked and shortlisted, before validating with qRT-PCR. Housekeeping gene suitability were then determined using GeNorm, NormFinder, BestKeeper, comparativeDelta Ct, RefFinder, and the Livak method.ResultsGene expression levels of 78 candidate genes identified in the literature were analysed in the RNAseq dataset generated from hADSC cultured under Nx and Hx conditions. From the dataset, 15 candidates with coefficient of variation ≤ 0.15 were identified, where differential expression analysis results further shortlisted 8 genes with least variation in expression levels. The top 4 housekeeping gene candidates, ALAS1, RRP1, GUSB, and POLR2B, were chosen for qRT-PCR validation. Additionally, 18S, a ribosomal RNA commonly used as housekeeping gene but not detected in the RNAseq method, was added to the list of housekeeping gene candidates to validate. From qRT-PCR results, 18S and RRP1 were determined to be stably expressed in cells cultured under hypoxic conditions.ConclusionsWe have demonstrated that 18S and RRP1 are suitable housekeeping genes for use in hypoxia studies with human adipose-derived stem cell and should be used in combination. Additionally, these data shown that the commonly used GAPDH and PGK1 are not suitable housekeeping genes for investigations into the effect of hypoxia in human adipose-derived stem cell.

Mercury remediation potential of mercury-resistant strain Rheinheimera metallidurans sp. nov. isolated from a municipal waste dumping site

A novel mercury-resistant bacterium, designated strain DCL_24T, was isolated from the legacy waste at the Daddu Majra dumping site in Chandigarh, India. It showed resistance up to 300 µM of inorganic mercury (mercuric chloride). The isolate was found to be a Gram-negative, facultative anaerobic, motile, and rod-shaped bacterium that can grow at 4 – 30 °C (optimum 25 °C), pH 6.0 – 12.0 (optimum 7.0), and 0 – 4.0 % (w/v) NaCl (optimum 0.5 – 2.0 %). The 16 S rRNA gene-based phylogenetic analysis showed that DCL_ 24 T shared a 97.53 % similarity with itsºlosest type strain Rheinheimera muenzenbergensis E-49T. Insilico DNA-DNA hybridization and average nucleotide identity values were found to be 18.60 % and 73.77 %, respectively, between the genomes of DCL_24T and R. muenzenbergensis E-49T. The strain DCL_24T has 44.33 DNA G+C content (mol %). Based on the phenotypic, chemotaxonomic, and genotypic data, the strain DCL_24T represents a novel species within the genus Rheinheimera, for which the name Rheinheimera metallidurans sp. nov is proposed. The type strain is DCL_24T (MTCC13203T = NBRC115780T = JCM 35551 T). The isolate was found to volatilize and remove mercury efficiently, as demonstrated by X-ray film and dithizone-based colorimetric methods. Around 92 % of mercury removal was observed within 48 h. The mercury-resistant determinant mer operon consisting of merA, encoding the mercuric reductase enzyme, and transport and regulatory genes (merT, merP, merD, and merR) were found in the isolate. Relative expression analysis of merA at increasing concentrations of HgCl2 was confirmed by quantitative real-time PCR. These data indicate the merA-mediated reduction of toxic Hg2+ into a non-toxic volatile Hg0. The phytotoxicity assay performed using Arabidopsis thaliana seeds further demonstrated the mercury toxicity reduction potential of DCL_24T. The study shows that this novel isolate, DCL_24T, is an interesting candidate for mercury bioremediation. However, further studies are required to assess the bioremediation efficacy of the strain under the harsh environmental conditions prevailing in polluted sites.

Early gonadal differentiation is associated with the antagonistic action of Foxl2 and Dmrt1l in the Pacific oyster.

As the second largest phylum in the zoological kingdom next to arthropods, the mechanism of gonadal differentiation in mollusca is quite complex. Currently, although much has been carried out on gonadal differentiation in the Pacific oyster, there is still unknown information that needs to be further explored. Here, analysis of the Foxl2 and Dmrt1l expression in samples at different development periods of male and female gonads as well as in annual gonad samples revealed that Log10 (Foxl2/Dmrt1l) values were an effective method for sex identification in oysters. In differentiated gonadal tissue, Log10 (Foxl2/Dmrt1l) values greater than 2 were females and less than 1 for males. Subsequent sequential sampling of the same individuals verified that Log10 (Foxl2/Dmrt1l) values greater than 2 for resting gonads would develop as females and less than 1 would develop as males in the future. Relative expression analysis of Foxl2 and Dmrt1l in the annual samples revealed a negative correlation between Log10 (Foxl2) and Log10 (Dmrt1l). Double fluorescence reporter validation results showed that DMRT1L protein was able to bind the Foxl2 promoter and repress its activity with a weak dosage effect. Antagonism between Dmrt1l and Foxl2 is therefore not restricted to vertebrates, and the competing regulatory networks are of great significance in the maintenance of gonadal sex in oysters after sexual differentiation. This study provides novel ideas and insights into the study of early gonadal differentiation in the adult oyster.

No-stain protein labeling as a potential normalization marker for small extracellular vesicle proteins

Western blot analysis of relative protein expression relies on appropriate reference proteins for data normalization. Small extracellular vesicles (sEVs), or exosomes, are increasingly recognized as potential indicators of the physiological state of cells due to their protein composition. Therefore, accurate relative sEVs protein quantification is crucial for disease detection and prognosis applications. Currently, no documented ubiquitous reference proteins are identified for precise normalization of a protein of interest in sEVs. Here we showed the use of total protein staining method for sEVs protein normalization in western blots of samples where conventional housekeeping proteins like β-actin and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) are not always detected in the sEVs western blots. The No-Stain™ Protein Labeling (NSPL) method showed high sensitivity in sEVs-protein labeling and facilitated quantitative evaluation of changes in the expression pattern of the protein of interest. Further, to show the robustness of NSPL for expression analysis, the results were compared with quantitative mass spectroscopy analysis results. Here, we outline a comprehensive method for protein normalization in sEVs that will increase the value of protein expression study of therapeutically significant sEVs.

Epoxy Triglyceride Enhances Intestinal Permeability via Caspase-1/NLRP3/GSDMD and cGAS-STING Pathways in Dextran Sulfate Sodium-Induced Colitis Mice.

Oxidized triglyceride monomers are the main cytotoxic products of deep-frying oil. However, its impact on the intestinal barrier, the first health guardian, remains unknown. In this study, HPLC-MS/MS analysis revealed that the epoxy group is the main oxidation product, indicating that it may be the main cytotoxic factor. Therefore, 1-9,10-epoxystearic ester, 2,3-dioleic acid (EGT) and glycerol trioleate (GT) were used to reveal the effect of the epoxy group on the intestinal barrier of dextran sulfate sodium-induced colitis. Characteristics analysis showed that EGT could aggravate intestinal damage. The relative mRNA expression analysis suggested that EGT could activate Caspase-1/NLRP3/GSDMD, thereby inducing pyroptosis. The proinflammatory cytokines activated by pyroptosis and the cGAS-STING pathway were released through the pores, thus inducing the disintegration of the tight junction between the intestinal epithelial cells and enhancing intestinal permeability. Metabonomics further confirmed that EGT can change the composition and content of phospholipids on the cell membrane, indicating the morphological changes of the intestinal epithelial cell membrane. In conclusion, this study highlights that EGT induced intestinal dysfunction via Caspase-1/NLRP3/GSDMD and cGAS-STING pathways.

Prevalence of Polymorphism and Post-Training Expression of ACTN3 (R/X) and ACE (I/D) Genes in CrossFit Athletes

CrossFit is known as a functional fitness training high-intensity exercise to improve physical performance. The most studied polymorphisms are the ACTN3 R577X gene, known for speed, power, and strength, and ACE I/D, related to endurance and strength. The present investigation analyzed the effects of training on ACTN3 and ACE gene expression in CrossFit athletes for 12 weeks. the studies included 18 athletes from the Rx category, where ACTN3 (RR, RX, XX) and ACE (II, ID, DD) characterization of genotypes and tests of maximum strength (NSCA), power (T-Force), and aerobic endurance (Course Navette) were performed. The technique used was the reverse transcription-quantitative PCR real-time polymerase chain reaction (RT-qPCR) for the relative expression analysis. the relative quantification (RQ) values for the ACTN3 gene increased their levels 2.3 times (p = 0.035), and for ACE, they increased 3.0 times (p = 0.049). there is an overexpression of the ACTN3 and ACE genes due to the effect of training for 12 weeks. Additionally, the correlation of the expression of the ACTN3 (p = 0.040) and ACE (p = 0.030) genes with power was verified.

Effects of dietary yeast cell wall supplementation on growth performance, intestinal Campylobacter jejuni colonization, innate immune response, villus height, crypt depth, and slaughter characteristics of broiler chickens inoculated with Campylobacter jejuni at d 21

A study was conducted to assess the effects of a dietary yeast cell wall (YCW) with and without a Campylobacter jejuni (CJ) challenge. A total of 2,240-day-old Ross 708 males were randomly assigned within 8 treatments with a 4×2 factorial design, with 4 diets (negative control, positive control, YCW constant dose (400 g/ton), and YCW step-down dose (800/400/200 g/ton in the starter/grower/finisher diets, respectively) and with and without d 21 CJ oral gavage challenge at 5.2×107 CFU/mL. At d 0, 14, 28, and 41 body weights and feed consumption were measured to determine performance. At d 14, 28, and 42, 8 jejunal and ileal histology samples per treatment were collected for villi morphology measurements. At d 22 and 28 (1- and 7-days postinoculation), 24 ileal tissue samples per treatment were collected for relative gene expression analysis. At d 42, 24 cecal content samples per treatment were collected for CJ enumeration. Finally, on d 44, 96 birds per treatment were processed to determine carcass yield and 16 carcass rinses per treatment were collected to determine CJ prevalence after processing. Diet or inoculation did not impact broiler performance (P > 0.05). Limited differences were observed in intestinal morphology, and villus height and crypt depth were different only in the ileum at d 42 (P=0.0280 and P=0.0162, respectively). At d 1 postinoculation, differences between treatments inoculated with CJ and PBS were observed in the expression of avian beta defensin 10 (AvBD10), interleukin 1ß (IL-1ß), and interleukin 10 (IL-10) (P < 0.05). At d 7 postinoculation, expression of AvBD10, IL-1ß, and IL-10 was similar among all treatments (P > 0.05). At d 42, all birds, regardless the inoculation, had similar levels of CJ recovered from cecal contents (P > 0.05). After processing, carcass yield and CJ prevalence postchilling was similar in all treatments (P > 0.05). Overall, under the conditions of this study, the addition of YCW during a CJ challenge did not have an impact in growth performance, innate immune response, cecal colonization, carcass yield, or CJ prevalence after processing.

MYB Transcription Factor Family in Pearl Millet: Genome-Wide Identification, Evolutionary Progression and Expression Analysis under Abiotic Stress and Phytohormone Treatments.

Transcription factors (TFs) are the regulatory proteins that act as molecular switches in controlling stress-responsive gene expression. Among them, the MYB transcription factor family is one of the largest TF family in plants, playing a significant role in plant growth, development, phytohormone signaling and stress-responsive processes. Pearl millet (Pennisetum glaucum L.) is one of the most important C4 crop plants of the arid and semi-arid regions of Africa and Southeast Asia for sustaining food and fodder production. To explore the evolutionary mechanism and functional diversity of the MYB family in pearl millet, we conducted a comprehensive genome-wide survey and identified 279 MYB TFs (PgMYB) in pearl millet, distributed unevenly across seven chromosomes of pearl millet. A phylogenetic analysis of the identified PgMYBs classified them into 18 subgroups, and members of the same group showed a similar gene structure and conserved motif/s pattern. Further, duplication events were identified in pearl millet that indicated towards evolutionary progression and expansion of the MYB family. Transcriptome data and relative expression analysis by qRT-PCR identified differentially expressed candidate PgMYBs (PgMYB2, PgMYB9, PgMYB88 and PgMYB151) under dehydration, salinity, heat stress and phytohormone (ABA, SA and MeJA) treatment. Taken together, this study provides valuable information for a prospective functional characterization of the MYB family members of pearl millet and their application in the genetic improvement of crop plants.

Identification of a survival associated gene trio in chemical induced breast cancer

Sporadic cases of breast cancer being more prevalent than the hereditary cases, can be largely attributed to environmental pollutants like polycyclic aromatic hydrocarbons (PAHs). The aim of the present study was to identify gene dysregulations and the associations in DMBA (a PAH) induced breast cancer. A breast cancer model was developed in Wistar rats (n = 40), using DMBA. Serum proteomics (2D electrophoresis and MALDI-TOF MS) followed by relative gene expression analysis in mammary glands were conducted to reach to the differential gene signatures. The candidate genes were subjected to survival analysis (by GEPIA2 and KM plotter) and infiltration analysis (by ImmuCellAI) for correlating gene expression with patient survival and immune cell infiltration respectively. Further, the regulatory network investigation (by Cytoscape) was performed to find out the transcription factors (TFs) and miRNAs of the concerned genes. A gene trio (ANXA5, MTG1, PPP2R5B), expressing differentially in early mammary carcinogenesis at 4 months (precancerous stage) till full-fledged cancerous stage (post 6 months) was identified. The altered gene expression was associated with less survival among breast cancer patients (n = 4019). The dysregulated expression also has a correlation with enhanced mammary infiltration of immune cells. Moreover, a regulatory network (comprising of 77 transcription factors and 50 miRNAs) involved in the regulation of candidate genes was also deciphered. The deregulated target genes can therefore be explored for reregulation via identified TFs and miRNAs, and survival thereby improved.

Cytokine supplemented maturation medium improved development to term following somatic cell nuclear transfer (SCNT) in cattle.

In vitro maturation is an important process in the production of embryos. It has been shown that three cytokines, fibroblast growth factor 2, leukemia inhibitory factor and insulin-like growth factor 1 (FLI), increased efficiency of in vitro maturation, somatic cell nuclear transfer (SCNT) blastocyst production, and in vivo development of genetically engineered piglets. Assess effects of FLI on oocyte maturation, quality of oocytes, and embryo development in bovine in vitro fertilisation (IVF) and SCNT. Cytokine supplementation resulted in significant increases in maturation rates and decreased levels of reactive oxygen species. Oocytes matured in FLI had increased blastocyst rates when used in IVF (35.6%vs 27.3%, P <0.05) and SCNT (40.6%vs 25.7%, P <0.05). SCNT blastocysts contained significantly more inner cell mass and trophectodermal cells when compared to the control group. Importantly, SCNT embryos derived from oocytes matured in FLI medium resulted in a four-fold increase in full-term development compared to control medium (23.3%vs 5.3%, P <0.05). Relative mRNA expression analysis of 37 genes associated with embryonic and fetal development revealed one gene had differential transcript abundance in metaphase II oocytes, nine genes at the 8-cell stage, 10 genes at the blastocyst stage in IVF embryos and four genes at the blastocyst stage in SCNT embryos. Cytokine supplementation increased efficiency of in vitro production of IVF and SCNT embryos and in vivo development of SCNT embryos to term. Cytokine supplementation is beneficial to embryo culture systems, which may shed light on requirements of early embryo development.

Lactiplantibacillus plantarum PGB02 Improved Serum Cholesterol Profile by Tweaking Genes Involved in Cholesterol Homeostasis in Male Swiss Albino Mice.

The effect of Lactiplantibacillus plantarum PGB02 isolated from buttermilk on serum cholesterol profile of normal and hypercholesterolemic mice was evaluated. Further changes in the expression of mice genes were determined. The hypercholesterolemia was induced in experimental mice by feeding high cholesterol and fat diet. Serum cholesterol parameters, physical parameters, cholic acid excretion, and cholesterol metabolism related gene expression analysis was carried out. L. plantarum PGB02 efficiently reduced total cholesterol, triglycerides, and LDL-cholesterol and improved HDL-cholesterol in hypercholesterolaemic mice. Body weight was reduced and fecal cholic acid increased in probiotic treatment groups. Gene expression analysis revealed that L. plantarum PGB02 up-regulated the expression of LDL receptors, CYP7A1, ABCA1, ABCG5, ABCG8, and down-regulated the expression of FXR and NPC1L1 genes. Summarizing the mechanism, L. plantarum PGB02 improved hypercholesterolemia by increasing bile acid synthesis and excretion, reducing exogeneous cholesterol absorption from the intestine, and increased LDL clearance through upregulation of LDL-receptors. The present study has given insight into the mechanism of serum cholesterol reduction by bile salt hydrolase positive L. plantarum PGB02 in mice. L. plantarum PGB02 reduced the serum cholesterol level through increased bile acid synthesis and deconjugation and reduced absorption of cholesterol in the intestine. Isolate PGB02 shown cholesterol removal potential as good as statin.

Identification and fine mapping of a fertility restorer gene for wild abortive cytoplasmic male sterility in the elite indica rice non-restorer line 9311

The wild abortive (WA)-type cytoplasmic male sterility (CMS) derived from the wild rice species Oryza rufipogon Griff. is used widely in three-line indica hybrids. The identification and mapping of restorer of fertility (Rf) genes aided in the development of WA-type hybrids. Here we report that testcross F1 plants from the WA-type CMS line and 9311 exhibited stainable pollen grains with no seed set, indicating that 9311 carries minor-effect Rfs for WA-type CMS. We developed an advanced backcross population consisting of plants harboring small regions of donor chromosomal segments from 9311 in the WA-TianfengA genetic background with moderate seed setting rates. Genetic analysis showed that the pollen fertility levels of the backcross individuals are governed by a single gene from 9311 that we named Rf19(t). By use of the RICE 40 K gene chip, three introduced segments were identified in the fertile lines, and a candidate region spanning 4.37–8.29 Mb on chromosome 1 was identified for Rf19(t). Finally, Rf19(t) was fine-mapped to a region of 90 kb between the DNA marker loci STS1-163 and STS1-183, in which eight ORFs were predicted. Also, using relative expression analyses, comparative sequence analyses and functional domain analyses, we identified LOC_Os01g10530 as the most likely candidate gene for Rf19(t). Furthermore, Rf19(t) was found to function in fertility restoration, most probably by regulating the degradation of mRNA transcribed from the mitochondrial gene WA352. These results increase our knowledge of fertility restoration in WA-type CMS lines and will facilitate the development of high-quality pairs of WA-type CMS and maintainer lines.

Erythrocyte type 1 equilibrative nucleoside transporter expression in sickle cell disease and sickle cell trait.

Hypoxia-mediated red blood cell (RBC) sickling is central to the pathophysiology of sickle cell disease (SCD). The signalling nucleoside adenosine is thought to play a significant role in this process. This study investigated expression of the erythrocyte type 1 equilibrative nucleoside transporter (ENT1), a key regulator of plasma adenosine, in adult patients with SCD and carriers of sickle cell trait (SCT). Relative quantitative expression analysis of erythrocyte ENT1 was carried out by Western blot and flow cytometry. Patients with SCD with steady state conditions, either with SS or SC genotype, untreated or under hydroxycarbamide (HC) treatment, exhibited a relatively high variability of erythrocyte ENT1, but with levels not significantly different from normal controls. Most strikingly, expression of erythrocyte ENT1 was found to be significantly decreased in patients with SCD undergoing painful vaso-occlusive episode and, unexpectedly, also in healthy SCT carriers. Promoting hypoxia-induced adenosine signalling, the reduced expression of erythrocyte ENT1 might contribute to the pathophysiology of SCD and to the susceptibility of SCT individuals to altitude hypoxia or exercise to exhaustion.

Identification of a genomic region linked with sex determination of Undaria pinnatifida (Alariaceae) through genomic resequencing and genetic linkage analyses of a segregating gametophyte family.

Different from the traditional knowledge about kelp, three sexual phenotypes (female, male, and monoecious) exist in the haploid gametophytes of Undaria pinnatifida. However, the sex-determining mechanisms remain unknown. Genetic linkage mapping is an efficient tool to identify sex-linked regions. In the present study, we resequenced a segregating gametophyte family based on the male genome of U. pinnatifida. A high-density genetic linkage map was constructed using 9887 SNPs, with an average distance of 0.41 cM between adjacent SNPs. On the basis of this genetic map and using the composite interval mapping method, we identified 62 SNPs significantly linked with the sexual phenotype. They were located at a position of 67.67 cM on the linkage group 23, corresponding to a physical range of 14.67 Mbp on the HiC_Scaffold_23 of the genome. Reanalysis of the previous specific length amplified fragment sequencing data according to the reference genome led to the identification of a sex-linked genomic region that encompassed the above-mentioned 14.67 Mbp region. Hence, this overlapped genomic range was likely the sex-determining region. Within this region, 129 genes were retrieved and 39 of them were annotated with explicit function, including the potential male sex-determining gene-encoding high mobility group (HMG) domain protein. Relative expression analysis of the HMG gene showed that its expression was higher in male gametophytes during the vegetative phase and monoecious gametophytes during both the vegetative and gametogenesis phases, but significantly lower in male gametophytes during the gametogenesis phase. These results provide a foundation for deciphering the sex-determining mechanism of U. pinnatifida.

Characterization of qPL5: a novel quantitative trait locus (QTL) that controls panicle length in rice (Oryza sativa L.).

The online version contains supplementary material available at 10.1007/s11032-022-01339-z.

Molecular characterization, targeting and expression analysis of chloroplast and mitochondrion protein import components in Nicotiana benthamiana.

Improved bioinformatics tools for annotating gene function are becoming increasingly available, but such information must be considered theoretical until further experimental evidence proves it. In the work reported here, the genes for the main components of the translocons of the outer membrane of chloroplasts (Toc) and mitochondria (Tom), including preprotein receptors and protein-conducting channels of N. benthamiana, were identified. Sequence identity searches and phylogenetic relationships with functionally annotated sequences such as those of A. thaliana revealed that N. benthamiana orthologs mainly exist as recently duplicated loci. Only a Toc34 ortholog was found (NbToc34), while Toc159 receptor family was composed of four orthologs but somewhat different from those of A. thaliana. Except for NbToc90, the rest (NbToc120, NbToc159A and NbToc159B) had a molecular weight of about 150 kDa and an acidic domain similar in length. Only two orthologs of the Tom20 receptors, NbTom20-1 and NbTom20-2, were found. The number of the Toc and Tom receptor isoforms in N. benthamiana was comparable to that previously reported in tomato and what we found in BLAST searches in other species in the genera Nicotiana and Solanum. After cloning, the subcellular localization of N. benthamiana orthologs was studied, resulting to be identical to that of A. thaliana receptors. Phenotype analysis after silencing together with relative expression analysis in roots, stems and leaves revealed that, except for the Toc and Tom channel-forming components (NbToc75 and NbTom40) and NbToc34, functional redundancy could be observed either among Toc159 or mitochondrial receptors. Finally, heterodimer formation between NbToc34 and the NbToc159 family receptors was confirmed by two alternative techniques indicating that different Toc complexes could be assembled. Additional work needs to be addressed to know if this results in a functional specialization of each Toc complex.

Evaluation and validation of reference genes in Cymbidium faberi for real-time quantitative PCR.

For all organs at all Cymbidium faberi stages, ACT, UBQ3 and GAPDH can be selected as reference genes. For organs of the vegetative stage, UBQ2 and UBQ3 can be chosen for analysis of normalized gene expression. For the bud stage, ACT and UBQ3 can be used for analysis of gene expression. For the full blossom stage, ACT, UBQ3 and UBQ2 can be introduced into relative gene expression analysis. For vegetative organs, UBQ2 and ACT can be used as reference genes. For reproductive organs, ACT, UBQ3 and UBQ2 can be used as a reference for data processing. CfAG1 gene expression is more consistent when UBQ3, GAPDH and ACT are used as reference genes.