Regulated Gene Family Research Articles

Role of the type-B authentic response regulator gene family in fragrant rice under alkaline salt stress.

Globally, rice is being consumed as a main staple food and faces different kinds of biotic and abiotic stresses such drought, salinity, and pest attacks. Through the cytokinin signaling, Type-B authentic response regulators (ARR-Bs) respond positively towards the environmental stimuli. ARR-Bs are involved in abiotic stress tolerance and plant development but their molecular mechanisms in fragrant rice are still not fully explored. The current study showed the genome-wide characterization of OsARR-B genes under alkaline salt stress. Results showed that in total, 24 OsARR-B genes were found and divided into four subgroups on the basis of a phylogenetic analysis. These genes were located on all rice chromosomes except 8 and 10. Analysis of gene duplications, gene structure, cis-elements, protein-protein interactions, and miRNA were performed. Gene ontology analysis showed that OsARR-B genes are involved in plant development through the regulation of molecular functions, biological processes, and cellular components. Furthermore, 117 and 192 RNA editing sites were detected in chloroplast and mitochondrial genes, respectively, encoding proteins of OsARR-B. In chloroplast and mitochondrial genes, six and nine types of amino acid changes, respectively, were caused by RNA editing, showing that RNA editing has a role in the alkaline salt stress tolerance in fragrant rice. We also used a comparative transcriptome approach to study the gene expression changes in alkaline tolerant and susceptible genotypes. Under alkaline salt stress, OsARR-B5, OsARR-B7, OsARR-B9, OsARR-B10, OsARR-B16, OsARR-B22, and OsARR-B23 showed higher transcript levels in alkaline salt tolerant genotypes as compared to susceptible ones. Quantitative RT-PCR showed upregulation of gene expression in the alkaline tolerant genotypes under alkaline stress. Our study explored the gene expression profiling and RESs of two rice contrasting genotypes, which will help to understand the molecular mechanisms of alkaline salt tolerance in fragrant rice.

Aberrant Regenerating‐Islet Derived (Reg) Gene Expression is an Early Indicator of Colonic Dysplasia in Heterogeneous Nuclear Ribonucleoprotein (Hnrnp I) Knockout Mice

ObjectivesReg is an evolutionarily conserved family of proteins with anti‐inflammatory and antimicrobial functions, is mainly involved in the defense of intestinal epithelial cells (IEC). Recent studies indicate that the attenuation of colitis depends on the functions of Reg3b. Here, knockout mice with an IEC‐specific ablation of the Hnrnp I gene (KO) were examined, which exhibited an increased risk of developing spontaneous colitis. The objective of this study is to examine the gene expression of the Reg genes in the KO mice.HypothesisWe hypothesize that epithelial ablation of Hnrnp I in the colon of the KO mice leads to early aberrant expression of Reg3b and Reg3g.MethodsSix weeks old WT and KO mice were sampled for body weight, colon weight and length. Whole colon was opened and jelly‐rolled from distal to proximal end for embedding. Total RNA was extracted for quantification of gene expression using qPCR. Colon tissue sections were examined by hematoxylin‐eosin staining (H&E) for colon morphology and colonic crypt length measurements. Colon localization of Reg proteins was analyzed using immunofluorescent staining. Results were analyzed using the Mann‐Whitney test. Spearman test was used to analyze the correlation. P less than 0.05 is considered significant.ResultsThe expression levels of Reg3b, Reg3g, and Il‐6 in KO mice were significantly lower than WT mice. Furthermore, expression levels of Reg3b and Reg3g are correlated in both WT and KO groups (R=0.95). It is worth mentioning that, in 30% of KO mice, the expression levels of Reg3b and Reg3g are significantly higher than the rest of the KO mice, exhibiting significant dichotomy. Histological analysis showed that the crypt lengths of KO mice were significantly longer than those in the WT mice both in the distal end and proximal colon. More importantly, the KO mice with elevated Reg gene expressions had longer crypt lengths in the distal end. Moreover, KO mice with elongated crypts also exhibited invasive dysplasia in the colon sections.ConclusionsOur results indicate that IECs‐specific Hnrnp I knockout abolished the expression of the Regfamily genes. Further investigations are warranted to determine the potentially detrimental effects from the diminished Reg3 to the overall protection against microbial invasion in the colon. The contradictory upregulation of Reg3b and Reg3g in a subset of the KO mice indicates the extreme responsiveness to the perturbation from the Hnrnp I knockout and may serve as an early indicator of colon dysplasia.

Annotation survey and life cycle transcriptomics of transcription factors in rust fungi (Pucciniales) identify a possible role for cold shock proteins in dormancy exit

Fungi of the order Pucciniales are obligate plant biotrophs causing rust diseases. They exhibit a complex life cycle with the production of up to five spore types, infection of two unrelated hosts and an overwintering stage. Transcription factors (TFs) are key regulators of gene expression in eukaryote cells. In order to better understand genetic programs expressed during major transitions of the rust life cycle, we surveyed the complement of TFs in fungal genomes with an emphasis on Pucciniales. We found that despite their large gene numbers, rust genomes have a reduced repertoire of TFs compared to other fungi. The proportions of C2H2 and Zinc cluster - two of the most represented TF families in fungi - indicate differences in their evolutionary relationships in Pucciniales and other fungal taxa. The regulatory gene family encoding cold shock protein (CSP) showed a striking expansion in Pucciniomycotina with specific duplications in the order Pucciniales. The survey of expression profiles collected by transcriptomics along the life cycle of the poplar rust fungus revealed TF genes related to major biological transitions, e.g. response to environmental cues and host infection. Particularly, poplar rust CSPs were strongly expressed in basidia produced after the overwintering stage suggesting a possible role in dormancy exit. Expression during transition from dormant telia to basidia confirmed the specific expression of the three poplar rust CSP genes. Their heterologous expression in yeast improved cell growth after cold stress exposure, suggesting a probable regulatory function when the poplar rust fungus exits dormancy. This study addresses for the first time TF and regulatory genes involved in developmental transition in the rust life cycle opening perspectives to further explore molecular regulation in the biology of the Pucciniales.

Assessing the anticancer effects of metformin

Background: Metformin is an antihyperglycemic biguanide that is used as the first-line treatment for type 2 diabetes mellitus (T2DM). Metformin use helps control T2DM which is one of the many risk factors for cancer and is proposed to have multiple antagonistic actions against cancer cells. Metformin induces adenosine monophosphate-activated protein kinase (AMPK)-driven cascades, involving two pathways, a direct and an indirect one. This leads to a decrease in the mechanistic activity of mammalian target of rapamycin (mTOR), folate level, c-MYC (a family of regulator genes and proto-oncogenes), NF-κB (nuclear factor kappa of B cell), and also increases tumor suppressor P53 phosphorylation. These cascades will also decrease cyclin D1, reactive oxygen species (ROS), and increase mTOR complex1 (mTORC1) concentrations, apoptosis, and autophagy. Metformin also exerts anti-inflammatory effects through reducing interleukins 6 (IL6) and 8 (IL8), inhibition of protein translation via LKB1 (liver kinase B1), increasing expression of GPD1 (glycerol-3-phosphate dehydrogenase 1) which suppresses cancer by inhibiting mitochondria, inducing cell apoptosis, and inhibiting leptin while increasing adiponectin production. We would like to assess the anticancer effect of metformin on various types of malignancies. Methods: The 266 cancer patients diagnosed in 2018–2019 in King Fahd Hospital of the University (KFHU) were divided into non-diabetic and diabetic cancer patients (with or without metformin). The data includes age, gender, body mass index (BMI), type of cancer with grades and stages, T2DM, with or without metformin, complications, and fate etc. of each case. Results: Out of 300, 266 were selected for the analysis. The results showed the statistical significance (p value 0.022) of metformin use on the cancer grade at diagnosis that favorably influences the morbidity/mortality. Conclusions: Metformin might have an anti-cancer effect on the grade of cancer at the time of diagnosis regardless of its dosage, and this might improve the prognosis of malignancy.

Pancreas Whole Tissue Transcriptomics Highlights the Role of the Exocrine Pancreas in Patients With Recently Diagnosed Type 1 Diabetes.

Although type 1 diabetes (T1D) is primarily a disease of the pancreatic beta-cells, understanding of the disease-associated alterations in the whole pancreas could be important for the improved treatment or the prevention of the disease. We have characterized the whole-pancreas gene expression of patients with recently diagnosed T1D from the Diabetes Virus Detection (DiViD) study and non-diabetic controls. Furthermore, another parallel dataset of the whole pancreas and an additional dataset from the laser-captured pancreatic islets of the DiViD patients and non-diabetic organ donors were analyzed together with the original dataset to confirm the results and to get further insights into the potential disease-associated differences between the exocrine and the endocrine pancreas. First, higher expression of the core acinar cell genes, encoding for digestive enzymes, was detected in the whole pancreas of the DiViD patients when compared to non-diabetic controls. Second, In the pancreatic islets, upregulation of immune and inflammation related genes was observed in the DiViD patients when compared to non-diabetic controls, in line with earlier publications, while an opposite trend was observed for several immune and inflammation related genes at the whole pancreas tissue level. Third, strong downregulation of the regenerating gene family (REG) genes, linked to pancreatic islet growth and regeneration, was observed in the exocrine acinar cell dominated whole-pancreas data of the DiViD patients when compared with the non-diabetic controls. Fourth, analysis of unique features in the transcriptomes of each DiViD patient compared with the other DiViD patients, revealed elevated expression of central antiviral immune response genes in the whole-pancreas samples, but not in the pancreatic islets, of one DiViD patient. This difference in the extent of antiviral gene expression suggests different statuses of infection in the pancreas at the time of sampling between the DiViD patients, who were all enterovirus VP1+ in the islets by immunohistochemistry based on earlier studies. The observed features, indicating differences in the function, status and interplay between the exocrine and the endocrine pancreas of recent onset T1D patients, highlight the importance of studying both compartments for better understanding of the molecular mechanisms of T1D.

Correlation of REG1A, Claudin 7 and Ki67 expressions with tumor recurrence and prognostic factors in superficial urothelial urinary bladder carcinomas.

Superficial urothelial urinary bladder tumors are neoplasms that frequently recur and have a potential for invasion and metastasis. REG gene family is composed of various acute phase reactants, lectins, antiapoptotic factors, and growth factors that are effective on pancreatic island cells, neural cells, and epithelial cells. REG1A and REG1B are two forms of the human REG1 gene. It is reported that they are expressed in several cancers and are correlated with the prognosis of the patient. Claudins are integral transmembrane proteins that interconnect cells. However, their role in human tumorigenesis is extremely controversial. The aim of this study is to evaluate the relationship of REG1A, claudin 7 protein expressions, and Ki67 proliferation index in superficial urothelial urinary bladder tumors with well-known parameters of prognosis and tumor recurrence, and also to clarify whether these parameters are independent prognostic factors or not. A hundred and eleven patients diagnosed with superficial urothelial carcinoma between 2011 and 2016 years in our hospital and followed up in our urology clinic were included in this study. The slides prepared from paraffin blocks were immunohistochemically stained with REG1A, claudin 7, and Ki67 antibodies. REG1A showed positive staining in 37 (33%) and negative staining in 74 (67%) of urothelial tumors. Claudin 7 was positive in 24 (22%) and negative in 87 (78%) cases. REG1A expression showed a positive correlation with tumor stage and tumor recurrence; a high Ki67 proliferation index was positively correlated with tumor stage and grade. The loss of claudin 7 expression was related to tumor recurrence. Besides, tumors with REG1A expression and claudin 7 loss had a shorter survival independent of recurrence. In urothelial tumors, REG1A expression and loss of claudin 7 might be significant markers of prognosis that predict tumor recurrence.

In silico analysis of the regulatory gene families for proanthocyanidins biosynthesis in the genus Gossypium L.

The flavonoid pigments provide cotton cultivars with various shades of the naturally colored fiber. Despite of the deep knowledge about the flavonoids biosynthesis pathway in cotton, the genetic features underlying its control are not fully understood. Particularly, data on regulatory genes for the proanthocyanidins (PAs) branch are incomplete for the genus Gossypium L. Here we report results of comprehensive in silico analysis of the R2R3-Myb, bHLH-Myc and WD40 regulatory gene families, involved in the biosynthesis of flavonoid pigment PAs in cotton. For the first time, we identified regulatory genes R2R3-Myb, bHLH-Myc and WD40, including paralogous and homoeologous copies, among all sequenced diploid and allotetraploid cotton species: G. hirsutum L., G. barbadence L., G. raimondii L. and G. arboreum L. All duplication events occurred in the genome of the common diploid ancestor of the genus Gossypium and were supported by a negative evolution (Ka/Ks < 1). However, the GhTTG1/GhTTG3 genes are proved to be the most conservative and predominantly supported by selection, while GhTT2/GhMYB10 and GhTT8 are more variable and suitable for further analysis. The thorough study has suggested that all genes, with the exception of GhTT8-A2, possibly involved in the PAs biosynthesis. Therefore, information about structural organization and functionality of the all MBW genes in cotton genome is represented here. Revealing of the allelic diversities among identified genes, associating with contrast phenotype, may be useful for marker-assisted selection or genome editing for creation of naturally colored cotton cultivars with agriculturally valuable traits.

The molecular characteristics of soybean ARR-B transcription factors

The Type-B authentic response regulator (ARR-Bs) gene family is one of the important plant-specific transcription factor families involved in variety of physiological processes. However, study of ARR-Bs gene family in soybean is limited. Genome-wide analysis and expression profiling of the ARR-Bs gene family were performed in the soybean genome. 31 ARR-Bs genes (namely GmARR-B1-31) were identified, containing conserved catalytic domains with protein lengths and molecular weights ranging from 246 to 699 amino acids (aa) and 28.30 to 76.86 kDa, respectively. Phylogenetic analysis grouped ARR-Bs genes into three clusters—Cluster I, Cluster II, and Cluster III—which included 15, 12, and 4 genes, respectively, and were asymmetrically distributed on 17 chromosomes. Tissue specific expression analysis of GmARR-Bs family revealed a high transcription level in flowers, roots and seeds. The subcellular localization of GmARR5, GmARR14 were observed in the nucleus, and the promoter region of them included low-temperature responsive element (LTR), the C-repeat/dehydration responsive element (DRE), MBS, ABRE, MYB, MEJA and TCA-elements, which possibly participate in abiotic stress and hormones responses. qRT-PCR analysis showed that the expression of GmARR-B genes were affected by different abiotic stresses, especially cold stress and salt stress, and GmARR-B5 and GmARR-B14 were significantly induced by cold stress. This suggested that ARR-Bs genes were involved in multiple abiotic stress response pathways and acted as a positive factor under cold stress.

The evolution and function of the PSEUDO RESPONSE REGULATOR gene family in the plant circadian clock.

PSEUDO-RESPONSE PROTEINS (PRRs) are a gene family vital for the generation of rhythms by the circadian clock. Plants have circadian clocks, or circadian oscillators, to adapt to a rhythmic environment. The circadian clock system can be divided into three parts: the core oscillator, the input pathways, and the output pathways. The PRRs have a role in all three parts. These nuclear proteins have an N-terminal pseudo receiver domain and a C-terminal CONSTANS, CONSTANS-LIKE, and TOC1 (CCT) domain. The PRRs can be identified from green algae to monocots, ranging from one to >5 genes per species. Arabidopsis thaliana, for example, has five genes: PRR9, PRR7, PRR5, PRR3 and TOC1/PRR1. The PRR genes can be divided into three clades using protein homology: TOC1/PRR1, PRR7/3, and PRR9/5 expanded independently in eudicots and monocots. The PRRs can make protein complexes and bind to DNA, and the wide variety of protein-protein interactions are essential for the multiple roles in the circadian clock. In this review, the history of PRR research is briefly recapitulated, and the diversity of PRR genes in green and recent works about their role in the circadian clock are discussed.

An upstream deletion polymorphism within the goat Period circadian regulator 1 (PER1) gene was associated with growth traits

The Period circadian regulator (PER) gene family, including PER1, PER2 and PER3, codes transcriptional repressors which could accurately control biological rhythms. PER1/2 gene was proved to be associated with bone mass and PER1 gene was associated with insulin-like growth factor binding proteins 3 (IGFBP3) levels in serum. However, it was few studies reported genetic effects of PER gene on growth traits at the individual level. In this study, we identified the potential insertion/deletion (indel) loci in PER1/2/3 gene, and then explored the relationship between goat growth traits and the frequency of genotype in Shaanbei white cashmere goats (n = 827). As a result, a 9 bp indel within PER1 gene (g.27528003-27528011 del.TGCTGCTGC; rs642467689) was identified using molecular biology techniques. In addition, there existed significant correlation between the 9 bp indel and body height, height at hip cross, chest depth, body length index and cannon circumference index of goats. These results suggested that the 9 bp indel variation in PER1 gene was associated with goat growth traits, providing the theoretical basic for the role of PER1 gene in goat breeding.

Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome.

The growth of complexity in evolution is a most intriguing phenomenon. Using gene phylostratigraphy, we showed this growth (as reflected in regulatory mechanisms) in the human genome, tracing the path from prokaryotes to hominids. Generally, the different regulatory gene families expanded at different times, yet only up to the Euteleostomi (bony vertebrates). The only exception was the expansion of transcription factors (TF) in placentals; however, we argue that this was not related to increase in general complexity. Surprisingly, although TF originated in the Prokaryota while chromatin appeared only in the Eukaryota, the expansion of epigenetic factors predated the expansion of TF. Signaling receptors, tumor suppressors, oncogenes, and aging- and disease-associated genes (indicating vulnerabilities in terms of complex organization and strongly enrichment in regulatory genes) also expanded only up to the Euteleostomi. The complexity-related gene properties (protein size, number of alternative splicing mRNA, length of untranslated mRNA, number of biological processes per gene, number of disordered regions in a protein, and density of TF–TF interactions) rose in multicellular organisms and declined after the Euteleostomi, and possibly earlier. At the same time, the speed of protein sequence evolution sharply increased in the genes that originated after the Euteleostomi. Thus, several lines of evidence indicate that molecular mechanisms of complexity growth were changing with time, and in the phyletic lineage leading to humans, the most salient shift occurred after the basic vertebrate body plan was fixed with bony skeleton. The obtained results can be useful for evolutionary medicine.

N-myc downstream regulated family member 1 (NDRG1) is enriched in myelinating oligodendrocytes and impacts myelin degradation in response to demyelination.

The N-myc downstream regulated gene family member 1 (NDRG1) is a gene whose mutation results in peripheral neuropathy with central manifestations. While most of previous studies characterized NDRG1 role in Schwann cells, the detection of central nervous system symptoms and the identification of NDRG1 as a gene silenced in the white matter of multiple sclerosis brains raise the question regarding its role in oligodendrocytes. Here, we show that NDRG1 is enriched in oligodendrocytes and myelin preparations, and we characterize its expression using a novel reporter mouse (TgNdrg1-EGFP). We report NDRG1 expression during developmental myelination and during remyelination after cuprizone-induced demyelination of the adult corpus callosum. The transcriptome of Ndrg1-EGFP+ cells further supports the identification of late myelinating oligodendrocytes, characterized by expression of genes regulating lipid metabolism and bioenergetics. We also generate a lineage specific conditional knockout (Olig1cre/+ ;Ndrg1fl/fl ) line to study its function. Null mice develop normally, and despite similar numbers of progenitor cells as wild type, they have fewer mature oligodendrocytes and lower levels of myelin proteins than controls, thereby suggesting NDRG1 as important for the maintenance of late myelinating oligodendrocytes. In addition, when control and Ndrg1 null mice are subject to cuprizone-induced demyelination, we observe a higher degree of demyelination in the mutants. Together these data identify NDRG1 as an important molecule for adult myelinating oligodendrocytes, whose decreased levels in the normal appearing white matter of human MS brains may result in greater susceptibility of myelin to damage.

Differential expression and hypoxia-mediated regulation of the N-myc downstream regulated gene family.

Many organisms rely on oxygen to generate cellular energy (adenosine triphosphate or ATP). During severe hypoxia, the production of ATP decreases, leading to cell damage or death. Conversely, excessive oxygen causes oxidative stress that is equally damaging to cells. To mitigate pathological outcomes, organisms have evolved mechanisms to adapt to fluctuations in oxygen levels. Zebrafish embryos are remarkably hypoxia‐tolerant, surviving anoxia (zero oxygen) for hours in a hypometabolic, energy‐conserving state. To begin to unravel underlying mechanisms, we analyze here the distribution of the N‐myc Downstream Regulated Gene (ndrg) family, ndrg1‐4, and their transcriptional response to hypoxia. These genes have been primarily studied in cancer cells and hence little is understood about their normal function and regulation. We show here using in situ hybridization that ndrgs are expressed in metabolically demanding organs of the zebrafish embryo, such as the brain, kidney, and heart. To investigate whether ndrgs are hypoxia‐responsive, we exposed embryos to different durations and severity of hypoxia and analyzed transcript levels. We observed that ndrgs are differentially regulated by hypoxia and that ndrg1a has the most robust response, with a ninefold increase following prolonged anoxia. We further show that this treatment resulted in de novo expression of ndrg1a in tissues where the transcript is not observed under normoxic conditions and changes in Ndrg1a protein expression post‐reoxygenation. These findings provide an entry point into understanding the role of this conserved gene family in the adaptation of normal cells to hypoxia and reoxygenation.

The Potential Role of REG Family Proteins in Inflammatory and Inflammation-Associated Diseases of the Gastrointestinal Tract

Regenerating gene (REG) family proteins serve as multifunctional secretory molecules with trophic, antiapoptotic, anti-inflammatory, antimicrobial and probably immuno-regulatory effects. Since their discovery, accumulating evidence has clarified the potential roles of the REG family in the occurrence, progression and development of a wide range of inflammatory and inflammation-associated diseases of the gastrointestinal (GI) tract. However, significant gaps still exist due to the undefined nature of certain receptors, regulatory signaling pathways and possible interactions among distinct Reg members. In this narrative review, we first describe the structural features, distribution pattern and purported regulatory mechanisms of REG family proteins. Furthermore, we summarize the established and proposed roles of REG proteins in the pathogenesis of various inflammation-associated pathologies of the GI tract and the body as a whole, focusing particularly on carcinogenesis in the ulcerative colitis—colitic cancer sequence and gastric cancer. Finally, the clinical relevance of REG products in the context of diagnosis, treatment and prognostication are also discussed in detail. The current evidence suggests a need to better understanding the versatile roles of Reg family proteins in the pathogenesis of inflammatory-associated diseases, and their broadened future usage as therapeutic targets and prognostic biomarkers is anticipated.

Transcriptome Analysis Reveals Differentially Expressed Genes and Long Non-coding RNAs Associated With Fecundity in Sheep Hypothalamus With Different FecB Genotypes.

Small-tailed Han sheep, with different FecB genotypes, manifest distinct ovulation rates and fecundities, which are due to differences in reproductive hormones secreted by the hypothalamic–pituitary–ovarian axis. Nevertheless, the function of the hypothalamus against a FecB mutant background on increasing ovulation rate is rarely reported. Therefore, we determined the expression profiles of hypothalamus tissue collected from six wild-type (WW) and six FecB mutant homozygous (BB) ewes at the follicular and luteal phases by whole-transcriptome sequencing. We identified 53 differentially expressed mRNAs (DEGs) and 40 differentially expressed long non-coding RNAs (DELs) between the two estrus states. Functional annotation analysis revealed that one of the DEGs, PRL, was particularly enriched in the hypothalamic function, hormone-related, and reproductive pathways. The lncRNA–target gene interaction networks and KEGG analysis in combination suggest that the lncRNAs LINC-676 and WNT3-AS cis-acting on DRD2 and WNT9B in different phases may induce gonadotropin-releasing hormone (GnRH) secretion. Furthermore, there were differences of regulatory elements and WNT gene family members involved in the follicular–luteal transition in the reproductive process between wild-type (WNT7A) and FecB mutant sheep (WNT9B). We combined the DEG and DEL data sets screened from different estrus states and genotypes. The overlap of these two sets was identified to select the mRNAs and lncRNAs that have major effects on ovulation. Among the overlapping molecules, seven DEGs and four DELs were involved in the follicular–luteal transition regulated by FecB mutation. Functional annotation analysis showed that two DEGs (FKBP5 and KITLG) were enriched in melanogenesis, oxytocin, and GnRH secretion. LINC-219386 and IGF2-AS were highly expressed in the BB ewes compared with WW ewes, modulating their target genes (DMXL2 and IGF2) to produce more GnRH during follicular development, which explains why mutated ewes produced more mature follicles. These results from expression profiling of the hypothalamus with the FecB mutation at different estrus states provide new insights into how the hypothalamus regulates ovulation under the effect of the FecB mutation.

Genome-wide characterization and expression analysis of pseudo-response regulator gene family in wheat.

Pseudo-response regulator (PRR) gene family members play a significant role in plant circadian clocks, flowering time inflorescence architecture development during transition from vegetative growth phase to reproductive phase. In current study, we analyzed the expression profiling, phylogenetic relationship, and molecular characterization of PRR gene family members of common wheat by using IWGSC Ref seq v1.1 wheat genome database with a coverage rate of 90%. By using bioinformatic approach total 20 candidate gene sequences were identified and divided into six groups and four clades. It was found that mostly genes have same number of exons and introns showed similar features because they originated through duplication events during evolution processes. Although all the proteins have conserved PRR domains, but some are distinct in their sequences suggesting functional divergence. By comparative synteny analysis it was revealed that Group 1, 2, 3 and 11-D of group 4 have duplication events while group 5 and TaPRR9-B,10-D showed conservation with previously identified PRR members from rice. While expression variation of six groups from each analysis matches with each other. Five groups highly expressed in leaf, spike, and roots in pattern like leaf > spike > root at all three stages booting, heading and anthesis of spike development. This suggests that TaPRR genes play important roles in different photoperiod signaling pathways in different organs at different stages of spike development and flowering via unknown pathway. These findings will also provide comprehensive knowledge about future investigations on wheat PRR family members involved in complex network of circadian system for plant development.

High expression of NDRG3 in osteoarthritis patients

BackgroundOsteoarthritis (OA), as a common disease, seriously affects the quality of life of the victims, but its pathogenesis remains unclear. It has been confirmed that hypoxia-induced factor (HIF)-mediated hypoxia response plays an important role in the development and progression of OA. As a member of the N-myc downstream regulatory gene families, NDRG3 has been reported to independently regulate the hypoxic response of tumour cells, but the relationship between NDRG3 and OA development has not been reported so far.MethodsIn this study, seven OA patients were admitted to Guizhou Provincial People’s Hospital from January 2017 to December 2018. The OA group included 5 patients clinically diagnosed with hip/knee OA, which required arthroplasty. The normal group included 2 patients with no previous history of OA and rheumatoid arthritis, which required amputation due to trauma or tumour. The articular cartilage samples were collected to detect the expression of HIF-1α, HIF-2α and NDRG3 using immunohistochemical (IHC), haematoxylin and eosin (HE) and toluidine blue (TB) staining.ResultsHE and TB staining indicated that the cartilage surface of the normal group was smooth and intact, with a columnar arrangement of hyaline chondrocytes, while the cartilage surface of the OA group was discontinuous, with cartilage missing and fibrous soft tissue growing into the defect site. HIF-1α staining was positive in both groups. Moreover, HIF-2α and NDRG3 staining was weakly positive in the normal group, but were uniformly and strongly positive in the OA group. The positively stained areas and integral optical density for NDRG3 were significantly greater in OA group than in the normal group (p < 0.05).ConclusionsNDRG3 might be closely related to the development and progression of OA. However, the relationship between NDRG3 and OA, which is independent of the HIF pathway, warrants further research.

Expression of the apoptosis regulatory gene family in the long-term in vitro cultured human cumulus cells

Abstract Human cumulus cells (CCs) play a key role in the regulation of ovarian follicle maturation and oocyte fertilization. They influence the oocyte development by transferring the various molecules via the specific gap junction proteins, also known as the connexins, which provide a direct transmembrane connection between the oocyte and CCs. The human CCs were obtained in the patients diagnosed with infertility, who underwent the procedure of the controlled ovarian stimulation, and the following in vitro fertilization to elucidate the possible involvement of the CCs in the regulation of the fertilization and oocyte aging. Collected samples were long-term cultured and harvested after 7, 15, and 30 days of cultivation. Afterward, we assessed the relative expression of the following apoptosis regulatory genes - BAX, CASP9, and TP53 - using the RT-qPCR method. We noted a decrease in the expression of all above-mentioned genes in the samples harvested after 15 and 30 days, in reference to 7 days in vitro cultured CCs. In summary, our results provide precious insight into the dynamics of changes and confirm the continuous expression of the proapoptotic genes – BAX, CASP9, and TP53 in the long-term cultured CCs. Running title: Apoptotic gene expression in the human cumulus cells

Re-expression of REG family and DUOXs genes in CRC organoids by co-culturing with CAFs

Organoids derived from epithelial tumors have recently been utilized as a preclinical model in basic and translational studies. This model is considered to represent the original tumor in terms of 3D structure, genetic and cellular heterogeneity, but not tumor microenvironment. In this study, we established organoids and paired cancer-associated fibroblasts (CAFs) from surgical specimens of colorectal carcinomas (CRCs), and evaluated gene expression profiles in organoids with and without co-culture with CAFs to assess interactions between tumor cells and CAFs in tumor tissues. We found that the expression levels of several genes, which are highly expressed in original CRC tissues, were downregulated in organoids but re-expressed in organoids by co-culturing with CAFs. They comprised immune response- and external stimulus-related genes, e.g., REG family and dual oxidases (DUOXs), which are known to have malignant functions, leading tumor cells to proliferative and/or anti-apoptotic states and drug resistant phenotypes. In addition, the degree of differential induction of REG1 and DUOX2 in the co-culture system varied depending on CAFs from each CRC case. In conclusion, the co-culture system of CRC organoids with paired CAFs was able to partially reproduce the tumor microenvironment.

Identification and characterisation of single nucleotide polymorphisms in interferon regulatory factor-5 gene of Nigerian local chickens

Abstract The interferon regulatory factor gene family encodes transcription factors with multiple biological functions, which include reproduction, cell differentiation and immunity. Interferon regulatory factor-5 (IRF-5) gene is involved in immune defence against virus, stress response, activation of type I interferon genes, cell differentiation and growth. This experiment was conducted to identify and characterise single nucleotide polymorphisms in exons 3, 4, 5 and 7 of IRF-5 gene in Nigerian local chickens. Exons 3, 4, 5 and 7 of IRF-5 gene were amplified and sequenced. Single nucleotide polymorphisms (SNPs) present in exons 3, 4, 5 and 7 of IRF-5 gene were identified and analysed using Clustal W, DnaSp and SNAP2 software packages. Four SNPs, rs317511101, rs312902332, rs315149141 and rs739389464, were identified in exon 3 of IRF-5 gene in all the three genotypes. Exon 4 of the gene was conserved while three of the SNPs (rs736423928, 170C&gt;T and rs740736761) identified in exon 7 were shared among the three genotypes. Linkage disequilibrium of 1.00 existed between rs317511101 and rs315149141 polymorphisms identified in exon 3 of normal feathered and frizzle feathered chickens. Mutation rs740736761 identified in exon 7 had the highest polymorphism information content obtainable for any biallelic marker. Most of the SNPs identified in exons 3, 5 and 7 were synonymous and singletons which could not be used for association study. The study concluded that only haplotypes in exons 3 and 7 of IRF-5 gene can be used in marker-assisted selection when improving Nigerian local chickens.