Expression Patterns Of Multiple Genes Research Articles

Functional analysis reveals calcium-sensing receptor gene regulating cell-cell junction in renal tubular epithelial cells.

Calcium-sensing receptor (CASR) influences the expression pattern of multiple genes in renal tubular epithelial cells. The objective of this inquiry was to explore the molecular mechanisms of CASR in renal tubular epithelial cells and nephrolithiasis. HK-2 cells were transfected with lentiviruses carrying either CASR (named CASR) or an empty vector negative control (named NC), as well as shRNA intended to target CASR (named shCASR) or its corresponding negative control (named shNC). CCK-8 assay was used to detect the effect of CASR on the proliferation of HK-2 cells. RNA-Sequencing was applied to explore potential pathways regulated by CASR in HK-2 cells. PCR and western blot results showed that CASR expression was significantly increased in CASR cells and was decreased in shCASR cells when compared to their corresponding negative control, respectively. CCK-8 assay revealed that CASR inhibited the proliferation of HK-2 cells. RNA-Sequencing results suggested that the shCASR HK-2 cells exhibited a significant up-regulation of 345 genes and a down-regulation of 366 genes. These differentially expressed genes (DEGs) were related to cell apoptosis and cell development. In CASR HK-2 cells, 1103 DEGs primarily functioned in mitochondrial energy metabolism, and amino acid metabolism. With the Venn diagram, 4 DEGs (Clorf116, ENPP3, IL20RB, and CLDN2) were selected as the hub genes regulated by CASR. Enrichment analysis revealed that these hub genes were involved in cell-cell junction, and epithelial cell development. In summary, our investigation has the potential to offer novel perspectives on CASR regulating cell-cell junction in HK-2 cells.

Multiple approaches revealed MGc80-3 as a somatic hybrid with HeLa cells rather than a gastric cancer cell line.

The short-tandem-repeats (STR) profiles of MGc80-3 and HeLa partially overlap, raising suspicion of contamination in the MGc80-3 cell line. However, there has not been any relevant study demonstrating whether MGc80-3 was fully replaced by HeLa cells, just mixed with HeLa cells (co-existing), or was a somatic hybrid with HeLa cells. In addition to STR profiling, various approaches, including single nucleotide polymorphisms genotyping, polymerase chain reaction, screening for human papillomaviruses type 18 (HPV-18) fragment, chromosome karyotyping, pathological examination of xenografts, tissue-specific-90-gene expression signature and high-throughput RNA sequencing were used to determine the nature of MGc80-3. Our study found that the abnormal STR profile, partially overlapping with that of HeLa cells (64.62% to 71.64%), could not verify MGc80-3 as a HeLa cell line. However, the STR 13.3 repeat allele in the D13S317 locus that seemed to be unique to HeLa cells was detected in MGc80-3. Almost all the MGc80-3 cells exhibited HPV-18 fragments in the genome as well as certain HeLa marker chromosomes, such as M7 and M12. The molecular assay of the 90-gene expression signature still considered MGc80-3 as a stomach cancer using an algorithmic analysis. The expression pattern of multiple genes in MGc80-3 was quite different from that in HeLa cells, which showed that certain characteristics belonged to gastric cancer cell lines. High throughput RNA sequencing showed the distinct patterns of gene expression in MGc80-3. In conclusion, MGc80-3 cell line is a somatic hybrid with HeLa cells rather than a pure gastric cancer cell line.

Transcriptome and hypoxia-responsive gene expression analyses reveal the physiological reaction to acute hypoxia and reoxygenation in Epinephelus coioides

Dissolved oxygen (DO) is crucial for fish farming, and when fish experience hypoxic stress, negative effects such as the disruption of normal physiological activities, a decline in aerobic swimming ability, and feeding restriction will occur. In this study, healthy Epinephelus coioides individuals were subjected to hypoxic (DO = 0.6 ± 0.1 mg/L) and reoxygenation treatments (DO = 6.0 ± 0.1 mg/L), with a normoxic group (DO = 6.0 ± 0.1 mg/L) set as the control. Transcriptome sequencing (RNA-seq) was performed on the brains of E. coioides in hypoxia-sensitive (EBW), hypoxia-tolerant (EBS), and normoxic control (CB) groups. In total, 1174 differentially expressed genes (DEGs) were screened from the three groups. KEGG analysis revealed several pathways, including the HIF-1 signaling pathway, and immune-related pathways such as MAPK signaling, microRNAs (miRNAs), and oxidative phosphorylation pathways enriched in the EBS group, and cAMP signaling pathway enriched in the EBW group. Moreover, a variety of significant hypoxia-responsive DEGs involved in energy metabolism and immune reactions were identified in the EBS and EBW groups. qRTPCR analysis showed that the key DEGs HIF-1α, LDH-A, PPARα, PNP, RAB13, DDIT4, TNF-1, and ALDOA were significantly upregulated in the brain tissues of E. coioides under acute hypoxic stress and that their expression returned to normoxic levels after reoxygenation, indicating that they provided energy to the organism and regulated severe damage and lesions appearing in the brains of E. coioides during hypoxic stress to prolong the survival time of the organism. Altogether, these results suggest that hypoxia disrupts the expression patterns of multiple genes in E. coioides and that these genes may participate in resistance and adaptation to hypoxia in the organisms by regulating apoptosis, proliferation, differentiation, and energy metabolism.

The circadian clock in the piriform cortex intrinsically tunes daily changes of odor-evoked neural activity

The daily activity in the brain is typically fine-tuned by the circadian clock in the local neurons as well as by the master circadian clock in the suprachiasmatic nucleus (SCN) of the hypothalamus. In the olfactory response, odor-evoked activity in the piriform cortex (PC) and olfactory behavior retain circadian rhythmicity in the absence of the SCN, yet how the circadian rhythm in the PC is achieved independently of the SCN remains elusive. Here, to define neurons regulating the circadian rhythm of the odor-evoked activity in the PC, we knocked out the clock gene Bmal1 in a host of specific neurons along the olfactory circuit. We discovered that Bmal1 knockout in the PC largely abolishes the circadian rhythm of the odor-evoked activity. We further showed that isolated PC exhibits sustained circadian rhythms of the clock gene Per2 expression. Quantitative PCR analysis revealed that expression patterns of multiple genes involved in neural activity and synaptic transmission exhibit circadian rhythm in the PC in a BMAL1-dependent manner. Our findings indicate that BMAL1 acts intrinsically in the PC to control the circadian rhythm of the odor-evoked activity in the PC, possibly through regulating expression patterns of multiple genes involved in neural activity and transmission.

CRISPR/Cas9-Mediated Multi-Locus Promoter Engineering in ery Cluster to Improve Erythromycin Production in Saccharopolyspora erythraea

Erythromycins are a group of macrolide antibiotics produced by Saccharopolyspora erythraea. Erythromycin biosynthesis, which is a long pathway composed of a series of biochemical reactions, is precisely controlled by the type I polyketide synthases and accessary tailoring enzymes encoded by ery cluster. In the previous work, we have characterized that six genes representing extremely low transcription levels, SACE_0716-SACE_0720 and SACE_0731, played important roles in limiting erythromycin biosynthesis in the wild-type strain S. erythraea NRRL 23338. In this study, to relieve the potential bottlenecks of erythromycin biosynthesis, we fine-tuned the expression of each key limiting ery gene by CRISPR/Cas9-mediated multi-locus promoter engineering. The native promoters were replaced with different heterologous ones of various strengths, generating ten engineered strains, whose erythromycin productions were 2.8- to 6.0-fold improved compared with that of the wild-type strain. Additionally, the optimal expression pattern of multiple rate-limiting genes and preferred engineering strategies of each locus for maximizing erythromycin yield were also summarized. Collectively, our work lays a foundation for the overall engineering of ery cluster to further improve erythromycin production. The experience of balancing multiple rate-limiting factors within a cluster is also promising to be applied in other actinomycetes to efficiently produce value-added natural products.

Identification, Characterization and Functional Analysis of Fibroblast Growth Factors in Black Rockfish (Sebastes schlegelii)

Fibroblast growth factors (FGFs) are short polypeptides that play essential roles in various cellular biological processes, including cell migration, proliferation, and differentiation, as well as tissue regeneration, immune response, and organogenesis. However, studies focusing on the characterization and function of FGF genes in teleost fishes are still limited. In this study, we identified and characterized expression patterns of 24 FGF genes in various tissues of embryonic and adult specimens of the black rockfish (Sebates schlegelii). Nine FGF genes were found to play essential roles in myoblast differentiation, as well as muscle development and recovery in juvelines of S. schlegelii. Moreover, sex-biased expression pattern of multiple FGF genes was recorded in the species' gonads during its development. Among them, expression of the FGF1 gene was recorded in interstitial and sertoli cells of testes, promoting germ-cell proliferation and differentiation. In sum, the obtained results enabled systematic and functional characterization of FGF genes in S. schlegelii, laying a foundation for further studies on FGF genes in other large teleost fishes.

Identification of Adipogenesis Subgroups and Immune Infiltration Characteristics in Diabetic Peripheral Neuropathy.

Dysregulation of adipogenesis is related to diabetic peripheral neuropathy (DPN) pathogenesis, which may be mediated by immune infiltration. Nevertheless, the expression patterns of multiple adipogenesis-related genes and the differences of immune infiltration in different lipid metabolism levels remain unknown. GSE95849, a gene expression matrix containing DPN patients and healthy participants, was downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed adipogenesis-related genes (DEARGs) were screened by overlapping the adipogenesis-related genes with differentially expressed genes (DEGs). DPN patients from GSE24290 and GSE148059 were divided into two adipogenesis subgroups according to the expression of DEARGs. The single-sample gene set enrichment analysis (ssGSEA) was used to estimate the abundance of the immune cells between two subgroups. The analysis of immune infiltration suggested that a variety of immune cells and immune processes were elevated in the high expression group of DEARGs. The differentially expressed genes of the two subgroups were mainly enriched in biological processes and signaling pathways related to lipid metabolism. PPARG, FABP4, LIPE, FASN, SCD, DGAT2, PNPLA2, ADIPOQ, LEP, and CEBPA were identified as the hub genes of the two subgroups, whose related transcription factors (TFs) and miRNAs were predicted. An immunohistochemical assay was used to verify the expression of hub genes in DPN nerve tissues. Our comprehensive analysis of adipogenesis subgroups in DPN illustrated that different expression patterns of DEARGs may lead to different immune and inflammatory states. The identification of DEARGs may help to further distinguish the different characteristics of DPN patients and lay the foundation for targeted treatment. Our findings may bring a novel perspective to the diagnosis and treatment of DPN patients.

Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of Egr1, Rxra and Max in kidney stone disease.

Nephrolithiasis is one of the most common and frequent urologic diseases worldwide. The molecular mechanism of kidney stone formation is complex and remains to be illustrated. Transcript factors (TFs) that influenced the expression pattern of multiple genes, as well as microRNAs, important posttranscriptional modulators, play vital roles in this disease progression. Datasets of nephrolithiasis mice and kidney stone patients were acquired from Gene Expression Omnibus repository. TFs were predicted from differentially expressed genes by RcisTarget. The target genes of differential-expressed microRNAs were predictedby miRWalk. MicroRNA-mRNA network and PPI network were constructed. Functional enrichment analysis was performed via Metascape and Cytoscape identified hub genes. The assay of quantitative real-time PCR (q-PCR) and immunochemistry and the datasets of oxalate diet-induced nephrolithiasis mice kidneys and kidney stone patients' samples were utilized to validate the bioinformatic results. We identified three potential key TFs (Egr1, Rxra, Max), which can be modulated by miR-181a-5p, miR-7b-3p and miR-22-3p, respectively. The TFs and their regulated hub genes influenced the progression of nephrolithiasis via altering the expression of genes enriched in the functions of fibrosis, cell proliferation and molecular transportation and metabolism. The expression changes of transcription factors were consistent in q-PCR and immunochemistry results. For regulated hub genes, they showed consistent expression changes in oxalate diet-induced nephrolithiasis mice model and human kidneys with stones. The identified and verified three TFs, which may be modulated by microRNAs in nephrolithiasis disease progression, mainly influence biological processes responding to fibrosis, proliferation and molecular transportation and metabolism. The transcript influence showed consistency in multiple nephrolithiasis mice models and kidney stone patients.

Combined targeting of KRT23 and NCCRP1 as a potential novel therapeutic approach for the treatment of triple-negative breast cancer.

Breast cancers characterized by triple-negative status tend to be more malignant and have a poorer prognosis. A risk model for predicting breast cancer risk should be developed. We obtained gene expression and clinical characteristics data using the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and The Cancer Genome Atlas (TCGA) database. Differential gene screening between patients with triple-negative breast cancer (TNBC) and non-triple-negative breast cancers (NTNBC) was performed according to the "edgeR" filter criteria. Univariate and multivariate Cox regression analyses were used to construct a risk model and identify prognosis-related genes. XCELL, TIMER, EPIC, QUANTISEQ, MCPCOUNTER, EPIC, CIBERSORT-ABS, and CIBERSORT software programs were used to determine the extent of tumor immune cell infiltration. To evaluate the clinical responses to breast cancer treatment, the half maximal inhibitory concentration (IC50s) of common chemotherapeutics were calculated using "pRRophetic" and "ggplot2". Cell proliferation was assayed using cell counting kit-8 (CCK8) and 5-Ethynyl-2'-deoxyuridine (EdU) Cell Proliferation Kit. A dual-luciferase reporter assay confirmed the gene regulatory relationship of sex determining region Y-box 10 (SOX10). An assessment model was established for Keratin23 (KRT23) and non-specific cytotoxic cell receptor 1 (NCCRP1) using the univariate and multivariate Cox regression analyses. In addition, high expression levels of KRT23 and NCCRP1 indicated high proliferation and poor prognosis. We also found that the gene expression patterns of multiple genes were significantly more predictive of risks and have a higher level of consistency when assessing risk. In vitro experiments showed that the expressions of KRT23 and NCCRP1 were increased in TNBCs and promoted cell proliferation. Mechanically, the dual-luciferase reporter assay confirmed that SOX10 regulated the expressions of KRT23 and NCCRP1. The risk score model revealed a close relationship between the expressions of KRT23 and NCCRP1, the tumor immune microenvironment, and chemotherapeutics. In conclusion, we constructed a risk assessment model to predict the risk of TNBC patients, which acted as a potential predictor for chemosensitivity.

Organic Anion Transporters (OAT) and Other SLC22 Transporters in Progression of Renal Cell Carcinoma.

Simple SummaryKidney cancer diagnoses make up over 2% of newly identified cancers each year. SoLute Carrier 22 (SLC22) genes are expressed in normal functioning kidneys and are responsible for transport of myriad metabolites, xenobiotics, antioxidants and other small molecules, but their role in kidney cancer is not well understood. We assessed the relationship between the expression of SLC22 genes and survival in patients with kidney cancer and found expression patterns of multiple SLC22 genes to be associated with overall survival as well as with disease progression. We sought to interpret this data in the context of physiological information from previous studies by us and others. Furthermore, network analysis indicated the importance of SLC22 genes and identified additional genes that might be therapeutic targets.(1) Background: Many transporters of the SLC22 family (e.g., OAT1, OAT3, OCT2, URAT1, and OCTN2) are highly expressed in the kidney. They transport drugs, metabolites, signaling molecules, antioxidants, nutrients, and gut microbiome products. According to the Remote Sensing and Signaling Theory, SLC22 transporters play a critical role in small molecule communication between organelles, cells and organs as well as between the body and the gut microbiome. This raises the question about the potential role of SLC22 transporters in cancer biology and treatment. (2) Results: In two renal cell carcinoma RNA-seq datasets found in TCGA, KIRC and KIRP, there were multiple differentially expressed (DE) SLC22 transporter genes compared to normal kidney. These included SLC22A6, SLC22A7, SLC22A8, SLC22A12, and SLC22A13. The patients with disease had an association between overall survival and expression for most of these DE genes. In KIRC, the stratification of patient data by pathological tumor characteristics revealed the importance of SLC22A2, SLC22A6, and SLC22A12 in disease progression. Interaction networks combining the SLC22 with ADME genes supported the centrality of SLC22 transporters and other transporters (ABCG2, SLC47A1) in disease progression. (3) Implications: The fact that many of these genes are uric acid transporters is interesting because altered uric acid levels have been associated with kidney cancer. Moreover, these genes play key roles in processing metabolites and chemotherapeutic compounds, thus making them potential therapeutic targets. Finally, our analyses raise the possibility that current approaches may undertreat certain kidney cancer patients with low SLC22 expression and only localized disease while possibly overtreating more advanced disease in patients with higher SLC22 expression. Clinical studies are needed to investigate these possibilities.

Stochastic population dynamics of cancer stemness and adaptive response to therapies.

Intratumoral heterogeneity can exist along multiple axes: Cancer stem cells (CSCs)/non-CSCs, drug-sensitive/drug-tolerant states, and a spectrum of epithelial-hybrid-mesenchymal phenotypes. Further, these diverse cell-states can switch reversibly among one another, thereby posing a major challenge to therapeutic efficacy. Therefore, understanding the origins of phenotypic plasticity and heterogeneity remains an active area of investigation. While genomic components (mutations, chromosomal instability) driving heterogeneity have been well-studied, recent reports highlight the role of non-genetic mechanisms in enabling both phenotypic plasticity and heterogeneity. Here, we discuss various processes underlying phenotypic plasticity such as stochastic gene expression, chromatin reprogramming, asymmetric cell division and the presence of multiple stable gene expression patterns ('attractors'). These processes can facilitate a dynamically evolving cell population such that a subpopulation of (drug-tolerant) cells can survive lethal drug exposure and recapitulate population heterogeneity on drug withdrawal, leading to relapse. These drug-tolerant cells can be both pre-existing and also induced by the drug itself through cell-state reprogramming. The dynamics of cell-state transitions both in absence and presence of the drug can be quantified through mathematical models. Such a dynamical systems approach to elucidating patterns of intratumoral heterogeneity by integrating longitudinal experimental data with mathematical models can help design effective combinatorial and/or sequential therapies for better clinical outcomes.

Akirin2 plays an important role in protecting Megalobrama amblycephala from Aeromonas hydrophila infection

Akirins are highly conserved, small, nuclear proteins that have been recognized as key regulators of multiple gene expression patterns and play important roles in immune responses. Previous studies on Akirins have mainly focused on the model species Drosophila and mice, while there have been few studies on fish. In the present study, two Akirin genes, Akirin1 and Akirin2, were identified from Megalobrama amblycephala. The open reading frames (ORFs) of M. amblycephala Akirin1 and Akirin2 were 570 bp and 558 bp in length, encoding 189 and 185 amino acids, respectively. Quantitative real-time PCR analysis indicated that both Akirin1 and Akirin2 mRNA were ubiquitously expressed in all 10 examined tissues with different expression patterns. After Aeromonas hydrophila infection, the mRNA levels of Akirin1, Akirin2, nuclear factor κB subunit p50 (NF-κB p50) and nuclear factor κB subunit p65 (NF-κB p65) were significantly induced in the liver and spleen. Knockdown and overexpression of Akirins in L8824 cells showed that Akirin2 positively regulated the expression of NF-κB p50, NF-κB p65, liver-expressed antimicrobial peptide 1 (LEAP-1) and liver-expressed antimicrobial peptide 1 (LEAP-2), while Akirin1 had no significant effect on the expression of these genes above. In addition, the recombinant M. amblycephala Akirin1 (rAkirin1) and Akirin2 (rAkirin2) proteins were successfully obtained and intraperitoneal injection of them could help protect M. amblycephala from A. hydrophila infection, with rAkirin2 having a better protective effect than rAkirin1. Furthermore, in vitro glutathione S-Transferase (GST) pull-down assays showed that M. amblycephala Akirin2 could bind to the IPT domain of NF-κB p50 and luciferase assays showed that NF-κB p65 could promote the activities of LEAP-1 and LEAP-2 promoters, which suggested that Akirin2, rather than Akirin1, could interact with the IPT domain of NF-κB p50 and induce the transcription of downstream antimicrobial peptides LEAP-1 and LEAP-2 though NF-κB p65 to enhance the immunity of M. amblycephala to A. hydrophila infection. All the above results indicated that M. amblycephala Akirin2 plays an essential role in the defense against A. hydrophila via the NF–κB signaling pathway, providing a theoretical basis for in-depth study of the innate immune mechanism of fish and promotion of healthy aquaculture.

Ethylene-Inducible AP2/ERF Transcription Factor Involved in the Capsaicinoid Biosynthesis in Capsicum.

Ethylene is very important in the process of plant development and regulates the biosynthesis of many secondary metabolites. In these regulatory mechanisms, transcription factors (TFs) that mediate ethylene signals play a very important role. Capsaicinoids (CAPs) are only synthesized and accumulated in Capsicum species, causing their fruit to have a special pungent taste, which can protect against attack from herbivores and pathogens. In this study, we identified the TF CcERF2, which is induced by ethylene, and demonstrated its regulatory effect on CAPs biosynthesis. Transcriptome sequencing analysis revealed that the expression patterns of CcERF2 and multiple genes associated with CAPs biosynthesis were basically the same. The spatiotemporal expression results showed CcERF2 was preferentially expressed in the placenta of the spicy fruit. Ethylene can induce the expression of CcERF2 and CAPs biosynthesis genes (CBGs). CcERF2 gene silencing and 1-methylcyclopropene (1-MCP) and pyrazinamide (PZA) treatments caused a decrease in expression of CBGs and a sharp decrease in content of CAPs. The results indicated that CcERF2 was indeed involved in the regulation of structural genes of the CAPs biosynthetic pathway.

The More, the Merrier? Multiple Myoglobin Genes in Fish Species, Especially in Gray Bichir (Polypterus senegalus) and Reedfish (Erpetoichthys calabaricus).

The members of the globin superfamily are a classical model system to investigate gene evolution and their fates as well as the diversity of protein function. One of the best-known globins is myoglobin (Mb), which is mainly expressed in heart muscle and transports oxygen from the sarcolemma to the mitochondria. Most vertebrates harbor a single copy of the myoglobin gene, but some fish species have multiple myoglobin genes. Phylogenetic analyses indicate an independent emergence of multiple myoglobin genes, whereby the origin is mostly the last common ancestor of each order. By analyzing different transcriptome data sets, we found at least 15 multiple myoglobin genes in the polypterid gray bichir (Polypterus senegalus) and reedfish (Erpetoichthys calabaricus). In reedfish, the myoglobin genes are expressed in a broad range of tissues but show very different expression values. In contrast, the Mb genes of the gray bichir show a rather scattered expression pattern; only a few Mb genes were found expressed in the analyzed tissues. Both, gray bichir and reedfish possess lungs which enable them to inhabit shallow and swampy waters throughout tropical Africa with frequently fluctuating and low oxygen concentrations. The myoglobin repertoire probably reflects the molecular adaptation to these conditions. The sequence divergence, the substitution rate, and the different expression pattern of multiple myoglobin genes in gray bichir and reedfish imply different functions, probably through sub- and neofunctionalization during evolution.

Molecular characterization of stress tolerance genes associated with D. indicus strain under extreme environment conditions.

Deinococcus indicus is a novel bacteria isolated from West Bengal, India known for its UV radiation and heavy metal tolerance. Since, this organism is reported from a region known for heavy metal contamination and earlier investigations demonstrated its radiation resistance, our study focused on the multiple stress responsive and DNA repair mechanisms. Though, most of the members of the genus Deinococcus are Gram positive cocci, D. indicus postures Gram negative rod shaped cells. Hence, the objectives were framed precisely to understand DNA repair pathway and stress responsive genes expression with a broader perspective. Based on available whole genome sequence of D. indicus, quantitative real time PCR (qPCR) was done to determine the expression pattern of multiple stress responsive genes upon various environmental extremities. Among them, UV responsive genes like UvrD and UvsE showed elevated expression when subjected to UV-C radiation at different time intervals. Similarly, when supplemented with arsenic and chromium, ArsR and ArsB exhibited considerably higher level of expression. While all the genes were subsequently analyzed in-silico, depicted that most of them were with N-glycosylation site, GPI anchor sites, N-terminal trans-membrane helix region besides putative signal peptides. Overall, this study opined the functional information onstress tolerance genes that aid to understand the DNA damage recovery mechanism towards elucidation of DNA repair pathways.

In Vivo Simultaneous Analysis of Gene Expression by Dual-Color Luciferases in Caenorhabditis elegans.

Both fluorescent and luminescent observation are widely used to examine real-time gene expression patterns in living organisms. Several fluuorescent and luminescent proteins with specific optical properties have been developed and applied for simultaneous, multi-color observation of more than two gene expression profiles. Compared to fluorescent proteins, however, the application of multi-color luminescent imaging in living organisms is still limited. In this study, we introduced two-color luciferases into the soil nematode C. elegans and performed simultaneous analysis of two gene expression profiles. Using a green-emitting luciferase Eluc (emerald luciferase) and red-emitting luciferase SLR (stable luciferase red), the expression patterns of two genes were simultaneously observed in single animals from embryonic to adult stages over its whole life span. In addition, dual gene activities were observed at the single embryo level, with the simultaneous observation of morphological changes. These are the first application of a two-color luciferase system into a whole animal and suggest that precise relationship of expression patterns of multiple genes of interest can be analyzed over the whole life of the animal, dependent on the changes in genetic and/or environmental conditions.

Comparative transcriptome analysis of defense response of rice to Nilaparvata lugens and Chilo suppressalis infestation

The brown planthopper (BPH, Nilaparvata lugens) and striped stem borer (SSB, Chilo suppressalis) are two of the most devastating insect pests in rice, causing significant losses of rice yield. Plants evolve multiple defense responses in the process of coexisting with pests. According to different pest infestation, the plants selectively activate related pathways and downstream gene expression. However, there are very few reports of differences in defense signaling pathways after rice was attacked by BPH or SSB. We determined the transcriptional responses of rice infested with BPH and SSB for 3 and 6 h using Illumina sequencing. By comparing the difference in gene changes caused by BPH and SSB infestation in rice, multiple signal pathways and gene expression patterns, including phytohormones, secondary metabolites, plant-pathogen interaction, reactive oxygen species, defense response, transcription factors, protease inhibitor and chitinase were found significantly different. Our results provide a basis for further exploring the molecular mechanism of rice defense response caused by BPH and SSB infestation, which will add to further understanding the interactions between plants and insects, and could provide valuable resources that could be applied in insect-resistant crop breeding.

Analysis of Micro Array Gene Expression Data Using Multi-Objective Binary Particle Swarm Optimization with Fuzzy Weighted Clustering (MOBPSO-FWC) Technique

In the rapidly advancing field of genomics, microarray technologies have turned into a ground-breaking system on simultaneous monitoring the expression patterns of multiple genes under various arrangements of constraints. A fundamental errand is to propose diagnostic techniques to distinguish cluster of genes comparative expression designs and are initiated by comparative conditions. And furthermore, the relating investigation has issue is to cluster multi-condition gene expression data. To overcome these issues, the vast measure of data obtained by this technology, resort to clustering methods that distinguish clusters of genes of share similar expression profiles. The motivation of this work is to introduce a clustering method in microarray gene expression data analysis. Multi-Objective Binary Particle Swarm Optimization with Fuzzy Weighted Clustering (MOBPSOFWC) algorithm is proposed to analyze gene expression data. In high dimensionality, a quick heuristic based pre-processing technique is employed to diminish some of the basic domain features from the initial feature set. Since these pre-processed and reduced features are still high dimensional, the proposed MOBPSO algorithm is implemented in MATLAB tool used for finding further feature subsets. The investigative are directed to distinguish the execution of the proposed work with existing clustering approaches.

Genes dysregulated in the blood of people with Williams syndrome are enriched in protein-coding genes positively selected in humans.

Williams syndrome is a complex condition resulting from the heterozygous deletion of nearly 30 genes in chromosome 7. However, precise genotype-to-phenotype mappings are not available for most of its distinctive features. Because WS entails changes in the expression patterns of multiple genes outside the WS region, it can be expected that many other genes besides the deleted genes contribute to this condition. In this paper, we hypothesise that genes that have changed recently in our history could account for some key aspects of the WS phenotype, because of the robust link that exists between human evolution and complex, human-specific diseases. Supporting this view, we have found that protein-coding genes that are dysregulated in the blood of subjects with WS are significantly enriched in protein-coding genes that have been positively selected in our species compared to extinct hominins. These genes play biological roles and are expressed in body regions of relevance for the WS phenotype. We conclude that the genes we highlight in the paper should be regarded as important etiological factors of the WS clinical profile.

Nonfluorescent RNA In Situ Hybridization Combined with Antibody Staining to Visualize Multiple Gene Expression Patterns in the Embryonic Brain of Drosophila.

In Drosophila, the brain arises from about 100 neural stem cells (called neuroblasts) per hemisphere which originate from the neuroectoderm. Products of developmental control genes are expressed in spatially restricted domains in the neuroectoderm and provide positional cues that determine the formation and identity of neuroblasts. Here, we present a protocol for nonfluorescent double in situ hybridization combined with antibody staining which allows the simultaneous representation of gene expression patterns in Drosophila embryos in up to three different colors. Such visible multiple stainings are especially useful to analyze the expression and regulatory interactions of developmental control genes during early embryonic brain development. We also provide protocols for wholemount and flat preparations of Drosophila embryos, which allow a more detailed analysis of gene expression patterns in relation to the cellular context of the early brain (and facilitate the identification of individual brain neuroblasts) using conventional light microscopy.