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• We screened the expression profiles of miRNAs in the late stage of RBC preservation. • We identified miRNAs that changed during different storage times as well as potential target genes. • We predicted the potential regulatory effects of these differential miRNAs through bioinformatics. To detect the differentially expressed regulatory miRNAs in the late stage of red blood cell (RBC) preservation and predict their roles. Suspended RBCs with different storage periods of 35 day, 42 day, and 50 day were collected for routine blood tests, RNA extraction, and preparation of small RNA sequencing libraries. The constructed libraries were sequenced and the biological functions of differential miRNAs in RBCs in the late storage were analyzed by bioinformatics. Routine indicators of RBCs in the late stage were not significantly affected by preservation time. The Pearson correlation analysis performing on RBC miRNAs with different storage days revealed that RBC miRNAs changed with the increase of storage days. RBC miRNAs from day 35 (D35), day 42 (D42) and day 50 (D50) showed significant differences (P < 0.05). Compared RBC miRNAs from D42 with these from D35, there were 690 up-regulated miRNAs and 82 down-regulated miRNAs; compared RBC miRNAs from D50 with these from D35, there were 638 up-regulated miRNAs and 123 down-regulated miRNAs; compared RBC miRNAs from D42 with these from D50, there were 271 up-regulated miRNAs and 515 down-regulated miRNAs. GO enrichment analysis of target genes of differential miRNAs were mainly involved in cell metabolism, biosynthesis, protein modification, gene expression and transcriptional regulation of biological processes. KEGG pathway enrichment analysis of miRNA target genes showed that differential miRNA target genes were closely related to pathways in cancer. MiRNAs were differentially expressed in the late stage of RBC preservation, and may be involved in various biological processes, especially cancer. [ABSTRACT FROM AUTHOR]

Research indicates that long noncoding RNAs (lncRNAs) contribute significantly to fibrotic diseases. Although lncRNAs may play a role in hypertrophic scars after burns, its mechanisms remain poorly understood. Using chip technology, we compared the lncRNA expression profiles of burn patients and healthy controls (HCs). Microarray results were examined by quantitative reverse-transcription polymerase chain reaction (RT-PCR) to verify their reliability. The biological functions of differentially expressed mRNAs and the relationships between genes and signaling pathways were investigated by Gene Ontology (GO) and pathway analyses, respectively. In contrast with HCs, it was found that 2738 lncRNAs (1628 upregulated) and 2166 mRNAs (1395 upregulated) were differentially expressed in hypertrophic scars after burn. Results from RT-PCR were consistent with those from microarray. GO and pathway analyses revealed that the differentially expressed mRNAs are mainly associated with processes related to cytokine secretion in the immune system, notch signaling, and MAPK signaling. The lncRNA expression profiles of hypertrophic scars after burn changed significantly compared with HCs. It was believed that the transcripts could be used as potential targets for inhibiting abnormal scar formation in burn patients. ● Chip technology was used to detect the differences in lncRNAs and mRNAs expression. ● The lncRNAs and mRNAs expression profiles of hypertrophic scars after burn differed. ● Processes presented in hypertrophic scars related to immune system、signaling pathway. ● The study may provide ideas for the treatment of hypertrophic scar after burn. [ABSTRACT FROM AUTHOR]

Celiac disease (CD) a complex immune disease that affects duodenal mucosa. Identification of tissue specific biomarkers is expected to improve the existing biopsy based CD diagnosis. To investigate the differentially expressed genes (DEGs) in duodenal mucosa tissue to identify clinically relevant gene expression pattern in CD. Whole RNA extracted from the duodenal biopsies of three CD patients and four non-CD controls were sequenced. Significant DEGs were identified. Prioritized DEGs were validated using qRT-PCR in an independent group (CD=23; Control=26). Enriched pathways were analyzed, protein-protein interaction networks were evaluated. 923 DEGs comprising of 135 up-regulated, and 788 down-regulated genes, with p -value≤0.05; log2FC>2 or <-2 were identified. A novel down-regulated gene CDH18 (p = 0.03; log2FC=−0.74) was identified. Previously known CXCL9 was replicated. CDH18, a trans-membrane protein was found to interact with other CDH proteins, α/β catenins, and other membrane transporters such as SLC and ABCB. Pathways and protein networks contributing in channel activity (p = 2.15E-12), membrane transporters (p = 2.15E-12), and cellular adhesion (p = 8.05E-6) were identified. CDH18 , a novel DEG identified in the present study is a pivotal gene involved in maintaining epithelial membrane organization and integrity. The functional significance of lower expression of CDH18 in pathogenesis of CD warranted to be investigated. CDH18 expression could be tested for its effectiveness in diagnostic, prognostic and therapeutic purposes. [ABSTRACT FROM AUTHOR]

• qtc isoforms in Drosophila show testis-specific or ovary-specific expression. • qtc gene uses multiple promoters and splicing, creating tissue-specific isoforms. • Testis-specific qtc transcripts are conserved across Drosophila , implying importance. The quick-to-court (qtc) gene is expressed in both males and females but affects only the mating behavior of males, probably due to the different composition of isoforms between the sexes. We tested this hypothesis and examined the sex-specific expression of qtc transcripts in the tissues of male and female Oregon-R flies. It was found that some qtc transcripts, such as qtc-RM and qtc-RN, are testis-specific, while others like qtc-RH are found in ovaries but absent in testes. No sex-specific transcripts were identified in the brain, suggesting further investigation into specific brain structures may be needed. There is likely a complex regulation of qtc gene expression, which is potentially influenced by various factors in different tissues. [ABSTRACT FROM AUTHOR]

Small heat shock proteins (sHSPs) are conserved proteins that play key roles in organismal adaptation to adversity stressors. However, little is known about sHSPs during summer diapause. Three sHSP genes: PmHSP19.5 , PmHSP19.9 , and PmHSP20.0 were identified and cloned from Pieris melete. Sequence alignment and phylogenetic analysis revealed that the three sHSPs have a typical, conserved α-crystallin domain. PmHSP19.5 and PmHSP20.0 were both upregulated in summer diapause (SD) and winter diapause (WD), compared to non-diapause (ND) pupae. All three sHSPs were upregulated and showed similar trends in response to thermal stress. The 0 °C chilling treatment slightly affected sHSP transcripts in ND pupae, whereas both PmHSP19.5 and PmHSP19.9 were upregulated and PmHSP20.0 was downregulated after chilling at 0 °C for 24–96 h in both SD and WD pupae. The transcripts of PmHSP19.5 and PmHSP19.9 were significantly induced at 31 °C for 30 d in SD and WD pupae. The PmHSP20.0 transcript gradually decreased during the SD and WD programs. This is the first time that sHSPs have been linked to both overwintering and summer diapause processes. These findings suggest that sHSPs are involved in both summer and winter diapause maintenance and play a possible key role in temperature stress. [ABSTRACT FROM AUTHOR]

Cancer genomic, transcriptomic, and proteomic profiling has generated extensive data that necessitate the development of tools for its analysis and dissemination. We developed UALCAN to provide a portal for easy exploring, analyzing, and visualizing these data, allowing users to integrate the data to better understand the gene, proteins, and pathways perturbed in cancer and make discoveries. UALCAN web portal enables analyzing and delivering cancer transcriptome, proteomics, and patient survival data to the cancer research community. With data obtained from The Cancer Genome Atlas (TCGA) project, UALCAN has enabled users to evaluate protein-coding gene expression and its impact on patient survival across 33 types of cancers. The web portal has been used extensively since its release and received immense popularity, underlined by its usage from cancer researchers in more than 100 countries. The present manuscript highlights the task we have undertaken and updates that we have made to UALCAN since its release in 2017. Extensive user feedback motivated us to expand the resource by including data on a) microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and promoter DNA methylation from TCGA and b) mass spectrometry-based proteomics from the Clinical Proteomic Tumor Analysis Consortium (CPTAC). UALCAN provides easy access to pre-computed, tumor subgroup-based gene/protein expression, promoter DNA methylation status, and Kaplan-Meier survival analyses. It also provides new visualization features to comprehend and integrate observations and aids in generating hypotheses for testing. UALCAN is accessible at http://ualcan.path.uab.edu [ABSTRACT FROM AUTHOR]

Long non-coding RNAs (lncRNAs) play pivot roles in regulating mRNA expression in eukaryotic organisms without coding any proteins. In the current study, a comprehensive analysis of 260 published RNA-Seq datasets collected from different tissues (fruits, leaves, stems, and roots) of Coffea arabica L. was performed to discover potential lncRNAs. A total of 10,564 unique lncRNAs were identified. Our results showed that 77.14% of the lncRNAs were intergenic and 60.39% of them are located within 5 Kbp from the partner gene. In general, all the identified lncRNAs showed shorter lengths, fewer number of exons, and lower expression levels as compared to mRNAs in different studied tissues. Several lncRNAs were determined as differentially expressed (DE) in fruits as compared to leaves, stems, or roots. The functional characterization of the DE lncRNAs revealed their roles in regulating significant biological processes in different tissues of C. arabica. The current study provides a comprehensive analysis and dataset of lncRNAs in C. arabica that could be utilized in further studies concerning the roles of these molecules in plant cells. [ABSTRACT FROM AUTHOR]

Ameloblastoma is an odontogenic neoplasm of the mandible and maxilla with various histological types and subtypes. It has been reported that some ameloblastomas could arise from dentigerous cyst walls; thus, the development of ameloblastoma from dentigerous cysts may be due to differential protein expression. Our aim was to identify a membrane protein that is differentially expressed in ameloblastomas with respect to dentigerous cysts. We analyzed the SDS-PAGE profiles of membrane proteins from ameloblastomas and dentigerous cysts. The protein in a band present in the ameloblastoma sample, but apparently absent in the dentigerous cyst sample was identified via mass spectrometry as the chaperonin Hsp60. We used western blotting and immunohistochemistry to analyze its overexpression and localization in ameloblastoma. We found a differential band of 95 kDa in the membrane proteins of ameloblastoma. In this band, the chaperonin Hsp60 was identified, and its overexpression was corroborated using western blotting and immunohistochemistry. Hsp60 was localized in the plasma membrane of all ameloblastoma samples studied; in addition, it was found in the cell nucleus of the plexiform subtype of conventional ameloblastoma. Our results suggest that Hsp60 may be involved in ameloblastoma development, and could therefore be a potential therapeutic target for ameloblastoma treatment. [Display omitted] • Hsp60 is overexpressed in ameloblastoma respect to dentigerous cyst. • Hsp60 is detected in plasma membrane of ameloblastoma. • Hsp60 is located in nucleus of conventional amleloblastoma subtype plexiform. [ABSTRACT FROM AUTHOR]

Defensins are a prominent family of antimicrobial peptides. They play sophisticated roles in the defense against pathogens in all living organisms, but few works address their expression under different conditions and plant tissues. The present work prospected defensins of Manihot esculenta Crantz, popularly known as cassava. Five defensin candidates (MeDefs) were retrieved from the genome sequences and characterized. Considering chromosome distribution, only MeDef1 and 2 occupy adjacent positions in the same chromosome arm. All 3D structures had antiparallel ß-sheets, an α-helix, and amphipathic residues distributed throughout the peptides with a predominance of cationic surface charge. MeDefs expression was validated by RT-qPCR, including two stress types (biotic: fungus Macrophomina pseudophaseolina , and abiotic: mechanical injury) and a combination of both stresses (fungus+injury) in three different tissues (root, stem, and leaf). For this purpose, ten reference genes (RGs) were tested, and three were chosen to characterize MeDef expression. MeDef3 was up-regulated at roots in all stress situations tested. MeDef1 and MeDef5 were induced in leaves under biotic and abiotic stresses, but not in both stress types simultaneously. Only MeDef2 was down-regulated in the stem tissue also with biotic/abiotic combined stresses. These results indicate that although defensins are known to be responsive to pathogen infection, they may act as preformed defense or, still, have tissue or stress specificities. Aspects of their structure, stability and evolution are also discussed. [Display omitted] • Cassava genome presents 5 defensins (MeDefs) with predicted antimicrobial activity. • MeDefs are transcriptionally modulated under biotic and abiotic stresses. • Higher expression was observed in roots and leaves. • MeDefs differed in sequence but their structures were conserved. • MeDefs 3D models were flexible with fluctuations converging to a more stable state. [ABSTRACT FROM AUTHOR]

Liver biotransformation enzymes have long been thought to enable animals to feed on diets rich in xenobiotic compounds. However, despite decades of pharmacological research in humans and rodents, little is known about hepatic gene expression in specialized mammalian herbivores feeding on toxic diets. Leveraging a recently identified population of the desert woodrat (Neotoma lepida) found to be highly tolerant to toxic creosote bush (Larrea tridentata), we explored the expression changes of suites of biotransformation genes in response to diets enriched with varying amounts of creosote resin. Analysis of hepatic RNA-seq data indicated a dose-dependent response to these compounds, including the upregulation of several genes encoding transcription factors and numerous phase I, II, and III biotransformation families. Notably, elevated expression of five biotransformation families — carboxylesterases, cytochromes P450, aldo-keto reductases, epoxide hydrolases, and UDP-glucuronosyltransferases — corresponded to species-specific duplication events in the genome, suggesting that these genes play a prominent role in N. lepida 's adaptation to creosote bush. Building on pharmaceutical studies in model rodents, we propose a hypothesis for how the differentially expressed genes are involved in the biotransformation of creosote xenobiotics. Our results provide some of the first details about how these processes likely operate in the liver of a specialized mammalian herbivore. [Display omitted] • Creosote resin induces a dose-dependent hepatic response in Neotoma lepida. • Biotransformation genes are primarily regulated by CAR, PXR, and NRF2. • Duplications are present in many upregulated biotransformation genes. • Biotransformation is accompanied by disrupted lipid and glucose metabolism. [ABSTRACT FROM AUTHOR]

Coccidiosis, a protozoan disease that substantially impacts poultry production, is characterized by an intracellular parasite. The study utilized 48 one-day-old Horro chickens, randomly divided into the infected (I) and control (C) groups. The challenge group of chickens were administered Eimeria maxima oocysts via oral gavage at 21-days-old, and each chicken received 2 mL containing 7×104 sporulated oocysts. The total RNAs of chicken jejunum and cecum tissues were isolated from three samples, each from I and C groups. Our study aimed to understand the host immune-parasite interactions and compare immune response mRNA profiles in chicken jejunum and cecum tissues at 4 and 7 days postinfection with Eimeria maxima. The results showed that 823 up- and 737 down-regulated differentially expressed mRNAs (DEmRNAs) in jejunum at 4 d infection and control (J4I vs. J4C), and 710 up- and 368 down-regulated DEmRNAs in jejunum at 7 days infection and control (J7I vs. J7C) were identified. In addition, DEmRNAs in cecum tissue, 1424 up- and 1930 down-regulated genes in cecum at 4 days infection and control (C4I vs. C4C), and 77 up- and 191 down-regulated genes in cecum at 7 days infection and control (C7I vs. C7C) were detected. The crucial DEmRNAs, including SLC7A5, IL1R2, GLDC, ITGB6, ADAMTS4, IL1RAP, TNFRSF11B, IMPG2, WNT9A , and FOXF1 , played pivotal roles in the immune response during Eimeria maxima infection of chicken jejunum. In addition, the potential detection of FSTL3, RBP7, CCL20, DPP4, PRKG2, TFPI2 , and CDKN1A in the cecum during the host immune response against Eimeria maxima infection is particularly noteworthy. Furthermore, our functional enrichment analysis revealed the primary involvement of DEmRNAs in small molecule metabolic process, immune response function, inflammatory response, and toll-like receptor 10 signaling pathway in the jejunum at 4 and 7 days postinfection. Similarly, in the cecum, DEmRNAs at 4 and 7 days postinfection were enriched in processes related to oxidative stress response and immune responses. Our findings provide new insights and contribute significantly to the field of poultry production and parasitology. [ABSTRACT FROM AUTHOR]

[Display omitted] • Upregulation of SORT1 gene expression and increased sortilin concentration in CAD patients. • SORT1 gene expression varies in patients with different CAD syndromes (CSA, ACS, MI). • Positive correlation between gene expression and the severity of coronary artery stenosis, the number of diseased vessels. • ROC curve analysis shows strong discrimination for SORT1 gene expression and sortilin concentration in diagnosing CAD. Genome-wide association studies identify SORT1 gene associated with risk of coronary artery disease (CAD). Sortilin protein enhances LDL absorption, form cell development, and atherosclerosis in macrophages. We therefore explored SORT1 expression in CAD patients and its gene expression's predictive usefulness for the severity of the disease. This is a case control study and Quantitative real-time PCR; Sandwich ELISA and western blotting were used to determine the expression of SORT1 gene at the mRNA and protein level in two hundred healthy controls and two hundred patients with various CAD syndromes. CAD patients exhibit higher SORT1 gene expression in CAD patients, a higher concentration of sortilin in their plasma, and distinct expression patterns in various CAD syndromes. The study reveals a positive correlation between gene expression and the severity of coronary artery stenosis, the number of diseased vessels, and the presence of diabetes. ROC curve analysis of SORT1 gene expression both at mRNA and protein level showed strong discrimination between significant CAD and control subjects. Therefore, elevated SORT1 gene expression in various CAD syndromes may be a potential biomarker for the disease. [ABSTRACT FROM AUTHOR]

This paper is concerned with higher odd-order boundary value problems. We first prove that the operators associated with the problems are symmetric and the corresponding eigenvalues are real, and we give the resolvent operators related to the differential operators. Then we obtain that the eigenvalues are not only continuously but also smoothly dependent on the parameters of the problem. Moreover, the differential expressions of the eigenvalues as regards these parameters are given. In particular, we give the Frechet derivatives of the eigenvalues for the leading coefficient function q 0 and coefficient functions q 1 , ⋯ , q n. • This paper is concerned with dependence of eigenvalues of higher odd-order boundary value problems. • We give a brief overview of the studies related to the problems, and show that the eigenvalues of the problem depend not only continuously but also smoothly on all parameters of the problem. • By some derivation methods and techniques, we give the differential expressions of the eigenvalues with respect to the coefficient functions q 0 , q 1 , ⋯ , q n , which are some interesting and concise results. And these results have not been done by the predecessors. [ABSTRACT FROM AUTHOR]

Previous studies have indicated that noncoding RNAs are important factors in gene functions. To explore the mechanism of male sterility of YS3038, the sterile genes were mapped, and based on previous work, the expression of long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and their target genes was studied. Weighted gene coexpression network analysis (WGCNA) and competitive endogenous RNA (ceRNA) analysis were further performed for differentially expressed noncoding RNAs and target genes. At last, the candidate genes were silenced by barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) to prove their function. The sterile genes were mapped on chromosomes 1B and 6B based on chip mix pool analysis, and one major effect QTL (27.3190% variation) was found based on SSR primers. The WGCNA analysis revealed that the dark turquoise and steel blue modules were highly correlated with anther development and fertility conversion, respectively. The ceRNA analysis showed that a total of 184 RNAs interacted with each other, including 115 mRNAs, 55 microRNAs (miRNAs), eight circRNAs, and six lncRNAs. Finally, the seed setting rate of the plant was significantly decreased after fatty acyl-CoA reductase 5 silencing. This study provides breeders with a new option for the development of thermosensitive cytoplasmic male-sterile (TCMS) wheat lines, which will favor the sustainable development of two-line hybrid wheat. Image 1 • The sterile genes of YS3038 were mapped on 1B chromosome (81–91 Mb). • The "steel blue" module was highly correlated with fertility conversion in YS3038. • A total of 184 differentially expressed RNAs interacted with each other in YS3038. • The fatty acyl-CoA reductase 5 was involved in the fertility conversion of YS3038. [ABSTRACT FROM AUTHOR]

The levels of tau phosphorylation differ between sexes in Alzheimer's disease (AD). Transcriptome-wide associations of sex by disease interaction could indicate whether specific genes underlie sex differences in tau pathology; however, no such study has been reported yet. We report the first analysis of the effect of the interaction between disease status and sex on differential gene expression, meta-analyzing transcriptomic data from the 3 largest publicly available case-control studies (N = 785) in the brain to date. A total of 128 genes, significantly associated with sex-AD interactions, were enriched in phosphoproteins (false discovery rate (FDR) = 0.001). High and consistent associations were found for the overexpressions of NCL (FDR = 0.002), whose phosphorylated protein generates an epitope against neurofibrillary tangles and KIF2A (FDR = 0.005), a microtubule-associated motor protein gene. Transcriptome-wide interaction analyses suggest sex-modulated tau phosphorylation, at sites like Thr231, Ser199, or Ser202 that could increase the risk of women to AD and indicate sex-specific strategies for intervention and prevention. [ABSTRACT FROM AUTHOR]

• Tuberculous pleurisy is common, but difficult to diagnose. • Little is known about its proteome in patients. • 5101 proteins were quantified, where 903 were differentially expressed between patient and control samples. • Protein expression was mostly down, with the minority overly expressed in patient samples. • 19 proteins were validated as potential diagnostic markers. Tuberculous pleurisy is a common type of tuberculosis (TB), but its diagnosis is challenging. This study aimed to profile the protein expression of this disease and identify new diagnostic makers. Biopsy tissues from patients with tuberculous pleurisy and controls were taken through thoracoscopy, and proteins were extracted for Tandem Mass Tag Mass Spectrometry. Differential protein expression was performed between patients and controls, and the identified proteins were analyzed for pathway enrichment. Selected proteins were further validated in another set of samples using a more quantitative method. A total of 5101 proteins were detected and quantified in a discovery set of patients and controls. Overall protein expression was quite different between patients and controls. Most proteins were down-expressed, while a minority were overly expressed in the patient samples. At p value < 0.05 and absolute fold change >2, 295 proteins were found to be up-expressed and 608 down-expressed. The top enriched pathways included ECM-receptor interaction, complement and coagulation cascades and focal adhesion. All 19 selected candidates were validated in an independent set of patient and control samples. This unbiased proteomics approach not only provided unique insights into protein expression and pathways, but also discovered potential diagnostic markers for tuberculous pleurisy. [ABSTRACT FROM AUTHOR]

Oxidative stress reflects an imbalance between the systemic manifestation of reactive oxygen species (ROS) and a biological system's ability to readily detoxify the reactive intermediates or to repair the resulting damage. Glutaredoxins (GRXs) are ubiquitous oxidoreductase enzymes involved in diverse cellular processes and play a key role in oxidative stress responsive mechanisms. This study was aimed to explore the structure–function relationship and to provide a framework for functional validation and biochemical characterization of various GRX members. In this study, our analysis revealed the presence of 127 genes encoding GRX proteins in G. hirsutum. A total of 758 genes from two typical monocot and nine dicot species were naturally divided into four classes based on phylogenetic analysis. The classification was supported with organization of conserved protein motifs and sequence logos comparison between cotton, rice and Arabidopsis. Cotton GRX gene family has underwent strong purifying selection with limited functional divergence. A good collinearity was observed in the synteny analysis of four Gossypium species. Majority of cotton GRX s were influenced by various phytohormones and abiotic stress conditions during expression analysis, suggesting an important role of GRX proteins in response to oxidative stress. Cis -regulatory elements, gene enrichments and co-expression network analysis also support their predicted role against various abiotic stresses. Whole genome and segmental duplication were determined to be the two major impetuses for the expansion of gene numbers during the evolution. The identification of GRX genes showing differential expression in specific tissues or in response to environmental stimuli provides a new avenue for in-depth characterization of selected genes of importance. This study will further broaden our insights into the evolution and functional elucidation of GRX gene family in cotton. [ABSTRACT FROM AUTHOR]

[Display omitted] • Transcription factors and miRNA co-regulate gene expression in reproductive tissues. • Transcription factors and miRNA have a predicted influence over spermatogenesis and male fertility. • Genes involved in contrary regulations were associated with spermatogenesis, sexual reproduction and sperm motility. Spermatogenesis is highly conserved among mammalians, but its gene expression and regulatory profile are not entirely known. As transcription factors (TFs) and miRNAs are crucial for gene expression regulation, identifying genes negatively regulated by miRNAs and positively regulated by TFs in the testis and epididymis can provide a deeper understanding of gene expression and regulatory patterns. To do this, we used expression data coming from RNA-Seq and miRNA-Seq experiments made with biopsies from testicular parenchyma, head of the epididymis, and tail of the epididymis of four Brahman bulls. We identified miRNA differentially expressed (DE) by comparing the three distinct tissues. A co-expression analysis combined with a regulatory impact factor approach identified miRNAs and TFs with regulatory impact over gene expression regulation in the Bos indicus tissues studied. We identified 116 DE miRNAs, 206 miRNAs and 237 TFs with a significant regulatory impact on mRNA patterns in the tissues' comparisons. bta-miR-196b was the only DE miRNA for all tissue comparisons and it may be a regulator of spermatogenesis through its links with adipogenesis and insulin biosynthesis. DE genes and TFs involved in contrary regulations between the epididymis head and testis parenchyma were associated with spermatogenesis, sexual reproduction, and sperm motility. Our results provide possible mechanisms, governed by the contrary effect of miRNA and TF, leading to the differential expression between the studied tissues. We have demonstrated that our predictions of miRNAs and TFs co-regulations over target DE genes can retrieve known regulatory mechanisms and predict new ones that merit further validation. [ABSTRACT FROM AUTHOR]

Confirmatory diagnosis of celiac disease (CD) include histopathology of duodenal biopsy and tissue trans-glutaminase-IgA. Identification of tissue-specific histological markers is warranted to improve the diagnosis. A genetic study in CD identified the association of ankyrin-G that connects E-cadherin with β2-spectrin in epithelial cells of the duodenal tissue. We attempted to investigate the differential expression of ankyrin-G, E-cadherin and β2-spectrin in duodenal biopsy of CD subjects compared to non-CD controls. Duodenal tissue was collected from 83 study participants, of which 50 were CD, and 33 were non-CD controls. Whole RNA was isolated from 32 CD and 23 non-CD controls from available tissues, and differential mRNA expression was measured using real-time PCR. Tissue sections from 18 CD cases and 10 non-CD controls were immunostained using monoclonal antibodies. Tissue immunohistochemistry were evaluated for differential expression and pattern of expression. RT-PCR revealed significantly reduced expression of ankyrin-G (fold change=0.63; p =0.03) and E-cadherin (fold change=0.50; p =0.02) among CD subjects compared to non-CD controls. Tissue immunohistochemistry confirmed the reduced expression of ankyrin-G and E-cadherin in CD. Differential expression is grossly limited within the outer columnar epithelial cell layer. Expression fold change of E-cadherin was seen to partially correlate with the serum tTG level (r=0.4; p =0.04). In CD, reduced expression of two key cytoskeletal proteins (ankyrin-G and E-cadherin) in duodenum mucosa was observed, which indicates its implication in disease biology and could be tested as a tissue-specific biomarker for CD. Functional studies may unravel the specific contribution of these proteins in CD pathophysiology. [ABSTRACT FROM AUTHOR]

• A total of 28 RsZIP genes were identified and classified into 18 subgroups. • Four tandem and six WGD/segmental duplication events exist in radish genome. • Four RsZIP genes were induced at 2 h under Pb and Cd treatment. • RsIRT1d and RsIRT1e confer yeast Pb but no Cd tolerance. Radish is an important root vegetable crop susceptible to heavy metal (HM) stresses. Zinc- and iron-regulated transporter-like proteins play vital roles in transporting metal ion to enhance HM tolerance or decrease detoxification in plants. In this study, 27 out of 28 RsZIP genes were unevenly located on eight chromosomes with exception of chromosome 3 (Chr.3). The evolutionary pattern divided the whole RsZIP proteins into 18 subgroups. Furthermore, four tandem and six WGD/segmental duplication events were identified, while 24 pairs containing 16 RsZIP and 13 AtZIP genes were orthologous. Moreover, the expression levels of 17 RsZIP genes including RsZIP10b,c and RsIRT1a,b were significantly decreased under 200 mg/L CdCl 2 and 1000 mg/L Pb(NO 3) 2 treatment. RT-qPCR analysis indicated that four RsZIP genes (RsIRT1d, RsIRT1e, RsIAR1 and RsZIP10d) were rapidly induced at 2 h under Pb and Cd treatment, while both RsZIP1 and RsZIP10b were downregulated. The results of yeast functional complementation indicated that RsIRT1d and RsIRT1e confer yeast Pb but no Cd tolerance, suggesting that they might play an important role in the transport of metal ions. These results could provide valuable insights into the characteristics of ZIP family genes and facilitate further exploring the molecular mechanism underlying HM stress responses in radish and other root vegetable crops. [ABSTRACT FROM AUTHOR]

Carboxylesterase (CXE) is a class of hydrolases that contain an α/β folding domain, which plays critical roles in plant growth, development, and stress responses. Based on the genomic and transcriptomic data of Salvia miltiorrhiza , the SmCXE family was systematically analyzed using bioinformatics. The results revealed 34 SmCXE family members in S. miltiorrhiza , and the SmCXE family could be divided into five groups (Group I, Group II, Group III, Group IV, and Group V). Cis -regulatory elements indicated that the SmCXE promoter region contained tissue-specific and development-related, hormone-related, stress-related, and photoresponsive elements. Transcriptome analysis revealed that the expression levels of SmCXE2 were highest in roots and flowers (SmCXE8 was highest in stems and SmCXE19 was highest in leaves). Further, two GA receptors SmCXE1 (SmGID1A) and SmCXE2 (SmGID1B) were isolated from the SmCXE family, which are homologous to other plants. SmGID1A and SmGID1B have conserved HGGSF motifs and active amino acid sites (Ser-Asp-Val/IIe), which are required to maintain their GA-binding activities. SmGID1A and SmGID1B were significantly responsive to gibberellic acid (GA 3) and methyl jasmonate (MeJA) treatment. A subcellular assay revealed that SmCXE1 and SmCXE2 resided within the nucleus. SmGID1B can interact with SmDELLAs regardless of whether GA 3 exists, whereas SmGID1A can only interact with SmDELLAs in the presence of GA 3. A Further assay showed that the GRAS domain mediated the interactions between SmGID1s and SmDELLAs. This study lays a foundation for further elucidating the role of SmCXE in the growth and development of S. miltiorrhiza. • The SmCXE family was analyzed by bioinformatics. • Screening two gibberellin receptors SmGID1A and SmGID1B from SmCXE family. • The concentration of gibberellin can determine whether SmDELLAs and SmGID1s interact. • The GRAS domain dominates the interactions between SmDELLAs and SmGID1s. [ABSTRACT FROM AUTHOR]

N-glycosylation is one of the most frequently occurring protein post-translational modifications (PTMs) with broad cellular, physiological and pathological relevance. Mass spectrometry-based N-glycomics has become the state-of-the-art instrumental analytical pipeline for sensitive, high-throughput and comprehensive characterization of N-glycans and N-glycomes. Improvement and new development of methods in N-glycan release, enrichment, derivatization, isotopic labeling, separation, ionization, MS, tandem MS and informatics accompany side-by-side wider and deeper application. This review provides a comprehensive update of mass spectrometry-based qualitative and quantitative N-glycomics in the years of 2017–2018. Image 1 • MS-based N-glycomics is the best tool for high-throughput profiling of N-glycans. • Qualitative information of N-glycans at multi-level are readily available. • Updated progresses in frontier methods and applications in 2017–2018 are reviewed. [ABSTRACT FROM AUTHOR]

Microbial community function in freshwater sediments is influenced by the presence and persistence of anthropogenic pollutants, yet simultaneously imposes significant control on their transformation. Thus, microbes provide valuable ecosystem services in terms of biodegradation and bioindicators of compromised habitats. From a remediation perspective it is valuable to leverage the suite of microbial genes at the transcriptional level that are active in either natural versus stressed environments to provide insight into the cycling and fate of contaminants. Metatranscriptomic analysis of total bacterial and archaeal messenger RNA (mRNA) is a useful tool in this facet and was applied to sediments sampled from the Detroit River; a binational Area of Concern (AOC) in the Great Lakes. Previously established sediment surveys and modelling delineated the river into contaminant gradients based on concentrations of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and metals. Differential expression analysis through DESeq2 revealed that microbial transcripts associated with nitrate reduction, methanogenesis, and beta-oxidation were significant in legacy polluted sediments and linked with energetic pathways key in the generation of cellular currencies (acetyl-CoA, succinyl-CoA). Gluconeogenesis and polyester synthesis also showed high abundance in contaminated regions, along with increased expression of stress response genes and transposons, despite decreases in community α-diversity. Aromatic cleavage genes were detected, but in low abundance across the contaminant gradient. These results suggest that microbial communities within the Detroit River exploit unique anabolic and catabolic pathways to derive and store energy from legacy organic contaminants while simultaneously recruiting stress-response and gene transfer mechanisms to cope with xenobiotic pressures. By coupling well-resolved chemical datasets with metatranscriptomics, this study adds to the spatial understanding of in-situ microbial activities in pristine and perturbed freshwater sediments. Unlabelled Image • Geospatial model confirmed contaminant gradient in selected Detroit River sediments. • Microbial diversity decreased with increasing metals, PAHs, and PCBs. • Metatranscriptomics revealed linked microbial contaminant degradation pathways. • Nitrate reduction and methanogenesis are key processes in community energetics. • Microbial transposons showed significant increased abundance in polluted sediments. [ABSTRACT FROM AUTHOR]

• Sequence polymorphism can counfound RNAseq analysis in genetically diverse organisms due to read mapping biases. • Optimising read mapping and excluding highly polymorphic genes reduces differential gene expression analysis biases. • Genetically divergent strains of Haemonchus contortus have very high levels of inter-strain transcriptional diversity. • Analyses of inter-strain differential expression must consider sequence polymorphism and overall transcriptional diversity. Differential expression analysis between parasitic nematode strains is commonly used to implicate candidate genes in anthelmintic resistance or other biological functions. We have tested the hypothesis that the high genetic diversity of an organism such as Haemonchus contortus could complicate such analyses. First, we investigated the extent to which sequence polymorphism affects the reliability of differential expression analysis between the genetically divergent H. contortus strains MHco3(ISE), MHco4(WRS) and MHco10(CAVR). Using triplicates of 20 adult female worms from each population isolated under parallel experimental conditions, we found that high rates of sequence polymorphism in RNAseq reads were associated with lower efficiency read mapping to gene models under default TopHat2 parameters, leading to biased estimates of inter-strain differential expression. We then showed it is possible to largely compensate for this bias by optimising the read mapping single nucleotide polymorphism (SNP) allowance and filtering out genes with particularly high single nucleotide polymorphism rates. Once the sequence polymorphism biases were removed, we then assessed the genuine transcriptional diversity between the strains, finding ≥824 differentially expressed genes across all three pairwise strain comparisons. This high level of inter-strain transcriptional diversity not only suggests substantive inter-strain phenotypic variation but also highlights the difficulty in reliably associating differential expression of specific genes with phenotypic differences. To provide a practical example, we analysed two gene families of potential relevance to ivermectin drug resistance; the ABC transporters and the ligand-gated ion channels (LGICs). Over half of genes identified as differentially expressed using default TopHat2 parameters were shown to be an artifact of sequence polymorphism differences. This work illustrates the need to account for sequence polymorphism in differential expression analysis. It also demonstrates that a large number of genuine transcriptional differences can occur between H. contortus strains and these must be considered before associating the differential expression of specific genes with phenotypic differences between strains. [ABSTRACT FROM AUTHOR]

We evaluated microsatellite instability (MSI) in selected mismatch repair (MMR) and tumor suppressor (TS) genes with a view to exploring genetic changes associated with the occurrence of gastric cancer (GC). Moreover, expression of MSI positive genes was measured to get insights into molecular events operating in the tumor microenvironment. We anticipated discovering new molecular targets with potential as molecular biomarkers of gastric cancer. Of the 13 genes screened, we observed 15% to 52.5% MSI at eight microsatellite loci located in 3′ UTR and coding regions of six genes (TGFBR2 , PDCD4 , MLH3 , DLC1 , MSH6 , and MSH3). The union probability of different combinations of unstable microsatellite loci unveiled a set of four MSI markers from TGFBR2 , PDCD4 , MLH3 , and MSH3 genes that allows detection of up to 85% incidences of GC. Significant downregulation of MLH3 , PDCD4 , TGFBR2 , and DLC1 genes was observed in tumor tissues. Protein structure analyses of two unexplored targets, MSH3 (TG 4) and MSH6 (A 7), with MSI in the coding region, exhibited the loss of essential domains in the encoded aberrant protein hampering its function in the MMR machinery. The molecular markers thus identified could potentially be used as MSI biomarkers for the diagnosis of gastric tumorigenesis after further validation. • Microsatellite instability (MSI) was studied in 26 motifs in 7 MMR and 6 TS genes associated with gastric cancer (GC). • Microsatellite markers showing potential as GC biomarkers were identified. • Four of the six MSI positive genes showed significant down regulation in GC. • Microsatellite instability was corroborated with the structural variations in the encoded proteins. [ABSTRACT FROM AUTHOR]

Busseola fusca (Fuller) (Lepidoptera: Noctuidae), a major insect pest of maize in sub-Saharan Africa, has developed high levels of non-recessive resistance to Cry1Ab toxin expressed in genetically modified Bt maize. Multiple resistance mechanisms to various Cry toxins have been identified in Lepidoptera, but no study has yet been done to determine the mechanism of Cry1Ab resistance in B. fusca. Therefore, the larval transcriptome of B. fusca was sequenced, de novo assembled and characterized. Differential expression analysis was performed to compare gene expression profiles of Cry toxin challenged and unchallenged neonate larvae to assess the molecular basis of the defence mechanism employed by this insect. Several genes associated with Cry toxin resistance in other lepidopteran pests were detected in B. fusca. Results suggest that differential expression of metabolic and immune-related genes might explain Cry1Ab toxin defence in this pest (supplemental file). Transcript expression profiles of neonates demonstrated that 33.59% and 60.31% of the 131 differentially expressed genes were upregulated and downregulated in the toxin-challenged neonate larvae, respectively. Transcripts were grouped into two subclusters according to the similarity of their expression patterns. Transcripts in subcluster 1 were moderately upregulated in the toxin-challenged neonate larvae, and, conversely, downregulated in the unchallenged neonate larvae. The solute carrier organic anion transporter, which is involved in insecticide detoxification, was upregulated in the toxin-challenged neonate larvae. Conversely, most of the transcripts in subcluster 2 were moderately downregulated in the toxin-challenged neonate larvae, and upregulated for neonates feeding on non-challenged maize. Four unidentified transcripts were extremely down-regulated in the toxin-challenged neonate larvae, and upregulated in the unchallenged neonate larvae. Further studies are recommended to establish if there is a direct correlation between these differentially expressed genes and the observed resistance. Elucidation of such defence mechanisms is crucial for developing insect resistance management strategies to ensure sustainable use of genetically modified maize in Africa. Nevertheless, this is the first study on gene expression profiles of B. fusca strains challenged with Cry toxin. The transcriptome characterized in this study provides a significant resource base for future studies on B. fusca and contributes to understanding some of the gene regulation and signalling networks involved in the defence of B. fusca against Cry1Ab toxin. • First whole transcriptome analysis of Busseola fusca • Busseola fusca defence against Cry1Ab toxin. • Differential expression of immune genes in response to toxin challenge. • Identification of potential Bt resistance genes • Signal transduction and immune system pathways identified for Busseola fusca. [ABSTRACT FROM AUTHOR]

• The miRNA expression profiles in blood between MZ individuals were compared. • 545 differentially expressed miRNAs were found in seven pairs of MZ twins. • 29 differentially expressed miRNAs were shared across ≥ 4 pairs of MZ twins. • The results of microarray analysis were similar to those of qRT-PCR. • Putative targets of 29 differentially expressed miRNAs were predicted. • Pathway enrichment of the predicted target genes were also depicted. Monozygotic (MZ) twins are widely regarded as genetically identical, and traditional DNA typing methods are insufficient in identifying MZ twins. So the discrimination of MZ twins become a forensic problem. MicroRNAs (miRNAs) are a class of small, endogenous, non-protein-coding RNA molecules of approximately 22 nucleotides in length, and exist extensively in a variety of eukaryotic cells. MiRNAs regulate gene expression and play fundamental roles in multiple biological processes, including cell differentiation, proliferation and apoptosis as well as aging and disease processes. The goal of this study is to explore the differential expression of miRNAs within MZ twin pairs, and aimed to find new biomarkers for distinguishing MZ twins. Thus, the miRNA expression profiles of seven pairs of healthy MZ twins of different sex and age were analyzed by miRNA microarray. A total of 545 miRNAs were found to be differentially expressed in these MZ twin pairs, and 2, 5, 22, 53 and 132 differentially expressed miRNAs were shared across six, five, four, three and two pairs of MZ twins respectively. These findings had been confirmed by real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assays on select miRNAs, including miR-151a-3p, miR-3653-3p, miR-142-3p, miR-4325, miR-16-5p, let-7i-5p, miR-222-3p, miR-550 b- 3p, miR-4791 and miR-27a-3p. The results demonstrated that there are differences in the expression of miRNAs within MZ twin pairs, suggesting a role of miRNAs in identifying MZ twins. [ABSTRACT FROM AUTHOR]

The present study reports the isolation and analysis of two novel GH1 β-glucosidases from the alkalophilic fungus Stachybotrys microspora , using PCR and Nested-PCR. Three major gene fragments were obtained by PCR: the first two are very similar and constitute a novel gene, which was named Smbgl1A , and the third PCR fragment is part of a different gene, named Smbgl1B. The truncated gene sequences were completely filled using the recent partial whole genome sequencing data of S. microspora (data not yet published). Moreover, we investigated the relative effects of glucose in comparison to cellulose rather than evaluate their absolute effects. In fact, RT-PCR analysis showed that while Smbgl1A was expressed when the fungus was grown in the presence of cellulose but not when grown with glucose, Smbgl1B was equally expressed under both conditions. The putative catalytic residues and the conserved glycone binding sites were identified. Zymogram analysis showed the intracellular production of β-glucosidases in S. microspora. The predicted secondary structure exhibited a classical (β/α)8 barrel fold, showing that both SmBGL1A and SmBGL1B belong to the GH1 family. Phylogenetic studies showed that SmBGL1A and SmBGL1B belong to the same branch as β-glucosidases from Stachybotrys chlorohalonata and Stachybotrys chartarum. However, SmBGL1A and SmBGL1B form two distinct clades. • Isolation of two novel GH 1 β-glucosidases from Stachybotrys microspora • Investigation of the relative effects of glucose in comparison to cellulose • Zymogram analysis has shown the intracellular production of GH1 β-glucosidases. • Prediction of the secondary structure with the presence of a classical (β/α) 8 barrel [ABSTRACT FROM AUTHOR]

Abstract To adapt to xeric environments, microorganisms have evolved with the capability of the superior desiccation tolerance and rapid resuscitation after rehydration. Nostoc flagelliforme, a representative terrestrial cyanobacterium that is distributed in west and west-northern parts of China, serves as an ideal model for gaining insight in the physiological recovery mechanism. In this study, LC-MS/MS combined with isobaric chemical labeling technique (iTRAQ) was used to quantify dynamic changes of proteins in N. flagelliforme during the rehydration processes. Approximately 113 proteins were identified to be differentially expressed, with function mainly related to photosynthesis, defense response, biosynthesis, antioxidant system, and energy and carbohydrate metabolism. Among them, protective proteins including high light inducible proteins and antioxidants showed a down regulation trend during the rehydration process, while proteins involved in photosynthesis, biosynthesis and signaling pathways and regulation of gene expression tend to be up-regulated. These results might shed light on molecular mechanism for the N.flagelliforme response to hydration. Significance In this work, iTRAQ-based proteome expression profiling provides a holistic proteomic insight for N. flagelliforme in response to rehydration processes. Proteins involved in defense system could help to limit the damage to a repairable level and maintain cellular physiological integrity in the dried state. In addition, results in this work suggest that changes in expression of light-harvesting complexes phycobilisome is closely related to the switch of photosynthesis apparatus, while only a few proteins in PSI and PSI I present significant expression change, which may indicate the integrity of PSI and PSI I photosynthetic system. Graphical abstract Unlabelled Image Highlights • A comprehensive proteomic analysis of differentially expressed proteins during rehydration process of N. flagelliforme using iTRAQ. • 113 proteins were found differently expressed, including 65 up-regulated proteins and 48 down-regulated proteins. • The robust defense system and integrity of PSI and PSI I photosynthetic system promote resuscitation of N. flagelliforme. [ABSTRACT FROM AUTHOR]

Abstract Habitat salinity is a major abiotic factor governing the activity, physiology, biology and distribution of aquatic animals. Salinity changes cause salt stress, affecting crustaceans reared in aquaculture both on an ecological and economic level. Current salt stress research in aquatic animals is mainly focused on salt stress in the gills at relatively low salinity ranges. Knowledge about whole-body salinity response in crustaceans and other organisms is lacking, especially in hypersaline conditions. Artemia franciscana is a small halophilic model crustacean able to withstand high salinities up to 300 g/l and strong osmotic shocks thanks to its mitigating strategies for fluctuating salinity levels, such as its unique larval salt gland and osmoregulatory capacity. This study aims to identify the genes responsible for Artemia 's unique hypersalinity tolerance by differential expression analysis. First, the full transcriptome of A. franciscana in different metabolic and life cycle stages was assembled de novo (assembly statistics: N50 = 1,430; GC content = 35.63%; transcript number = 64,972) and functionally annotated (annotated transcripts = 36%). Then, naupliar RNA-Seq reads generated under respectively hypersaline and marine conditions were pseudo-aligned to the A. franciscana transcriptome. Expression levels in both conditions were finally compared and 177 differentially expressed, functionally annotated transcripts were identified, of which 113 transcripts with GO annotations. Signalling genes, such as EIF and several genes from the glutathione and the chitin metabolic pathways were induced in Artemia under hypersaline conditions. Hypersalinity also activated gene regulation mechanisms (expression, transcription and post transcription) in the nucleus for DNA repair, ubiquitination, and also for cell cycle arrest through La-related protein. Several lipid metabolic genes and lipid transporters were upregulated, potentially to provide energy for ion balance and to maintain membrane structure integrity. Transport of metal ions and other ions was upregulated as well to maintain ion homeostasis. Lastly, known crustacean stress response genes such as Heat shock 70 kDa protein cognate were upregulated. This work shows that salt stress in Artemia nauplii, through signal transduction, gene regulation, lipid metabolism, transport and stress response genes, has an important influence on known and novel homeostasis-repairing mechanisms in Artemia. Highlights • Salt stress impacts crustacean aquaculture. Artemia , a model crustacean used as live food is uniquely able to withstand high salinities. • Differential expression analysis on Artemia identified salt stress response genes, involved in homeostasis repair. • These results support crustacean omics projects and can help improve the Artemia and crustacean production chains. [ABSTRACT FROM AUTHOR]

• In all, 39 RsNRT genes are systematically identified at genome-wide level in radish. • A range of RsNRTs exhibit significant differential expression under abiotic stresses. • RsNRT1.1a may play a critical role in root NO 3 − uptake under low-nitrogen condition. Radish is an important economical vegetable crop that requires adequate nitrogen supply for taproot formation and enlargement. Nitrate transporter (NRT) family represents a key gatekeeper in modulating nitrogen uptake and utilization in plants. However, the comprehensive characterization of the NRT gene family remains largely unexplored in radish. Herein, a total of 39 RsNRT genes were identified from the radish genome, which were unevenly distributed onto eight chromosomes except Chr3. Phylogenetic analysis indicated that the NRT1 and NRT2 subfamily members from radish, Arabidopsis and Brassica rapa were classified into Cluster I and Cluster II, indicating that the NRT proteins were relatively conserved in the Brassicaceae family. A range of cis -regulatory elements (e.g. AuxRE, ABRE and LTR) in the promoter of RsNRTs were involved in phytohormone and abiotic stress response. Transcriptome-based expression analysis indicated that several RsNRTs showed differential expression under heat, salt or heavy metal stresses. RT-qPCR analysis revealed that six RsNRT genes, including RsNRT1.1a, RsNRT1.2a, RsNRT1.5a, RsNRT2.1b, RsNRT2.2a and RsNRT2.3b , exhibited significantly up-regulated expression under NO 3 − deficiency condition. Notably, the expression of RsNRT1.1a was significantly increased in both the 'NAU-WXQ' (low-N-sensitive) and 'NAU-ZYQ' (low-N-tolerant) genotypes under 5 mM NO 3 − treatment, indicating that it might act as a critical participator in root NO 3 − uptake under low-N supply condition. These results would provide fundamental basis to decipher the molecular mechanisms underlying RsNRT -mediated N absorption and translocation in radish. [ABSTRACT FROM AUTHOR]

[Display omitted] • Discovery of three miRNAs specific to mollusks, exhibiting significant expression levels in Small RNA-seq analysis. • MIR-1984 displayed higher expression levels in the resistant population compared to the susceptible population at the 4-h time after infection. • No miRNAs were differentially expressed in the comprehensive model, suggesting that the resistance of the Taim is inherent and constitutive. Schistosomiasis is a neglected tropical disease caused by Schistosoma and affects over 240 million people worldwide. One of the most prominent causative agents is Schistosoma mansoni , which develops inside the intermediate host. Biomphalaria tenagophila is the second most important vector of schistosomiasis in Brazil and the Taim population is completely resistant to infection by S. mansoni. This study aims to identify and characterize B. tenagophila microRNAs (miRNAs) and evaluate their differential expression in S. mansoni -susceptible and - resistant populations of B. tenagophila. Two populations of B. tenagophila snails, susceptible and resistant to S. mansoni infection, were used to investigate the small RNA response of these snails after being infected with the parasite. Small RNA sequencing and quantitative real-time PCR were employed to identify and validate differentially expressed miRNAs. Bioinformatics analysis were performed to identify miRNA precursors and mature and evaluate their differential expression. The study predicted 173 mature miRNAs and 123 precursors. Among them were six Lophotrochozoa-specific miRNAs, three mollusk-specific miRNAs, and six pre-miRNAs in a cluster. The small RNA sequencing and RT-PCR of B. tenagophila samples allowed assessing the expression patterns of miRNAs. The results obtained may support future studies in Biomphalaria spp., generating a global impact on disease control. [ABSTRACT FROM AUTHOR]

Abstract Objective To screen for circular RNAs (circRNAs) that are associated with the activation of hepatic stellate cell (HSC) by monitoring changes in liver circRNA expression in a model of liver fibrosis. Methods The classic mouse model of CCl 4 -induced liver fibrosis was established and validated by histopathological examination. JS1 cells were activated by TGF-β1 to model HSC activation in vitro. Differentially expressed circRNAs in the fibrotic liver tissues and JS1 cells were determined using circRNA microarray, and some of those circRNAs were verified by RT-qPCR. The target genes of the above circRNAs were then predicted by bioinformatics analysis and summarized into a "circRNA-miRNA-mRNA" network diagram. Constructed plasmid mmu_circ_34116 siRNA was transfected to JS1 cells by Lipo2000, then we detected the expression changes of α-SMA. Results A total of 10,389 circRNAs were identified by microarray screening, and 69 differentially expressed circRNAs were detected in the fibrotic liver tissues with >2-fold difference in expression level relative to normal liver tissues (P < 0.05); 14 circRNAs were up-regulated and 55 were down-regulated. Five differentially expressed circRNAs in fibrotic liver and JS1 cells were verified by RT-qPCR, while all five showed similar trends with the microarray results in the liver, only 3 circRNAs in the JS1 activation model were consistent with the microarray results while one showed no significant change and one circRNA was not detected. Bioinformatics analysis predicted that the "mmu_circ_34116/miR-22-3P/BMP7" signal axis might be involved in the activation of HSC. Transfection experiment confirmed that the expression of α-SMA is significantly elevated as a result of inhibitory expression of mmu_circ_34116. Conclusion The circRNAs expression profile of liver tissue had changed in fibrosis mouse model, and some of these circRNAs may be associated with HSC activation. For instance, mmu_circ_34116 would inhibit HSC activation. Highlights • circRNAs associated with liver fibrosis and the activation of hepatic stellate cell [ABSTRACT FROM AUTHOR]

Background Although intracranial and spinal ependymomas are histopathologically similar, the molecular landscape is heterogeneous. An urgent need exists to identify differences in the genomic profiles to tailor treatment strategies. In the present study, we delineated differential gene expression patterns between intracranial and spinal ependymomas. Methods We searched the Gene Expression Omnibus database using the term "ependymoma" and analyzed the raw gene expression profiles of 292 ependymomas (31 spinal and 261 intracranial). The gene expression data were analyzed to find differentially expressed genes (DEGs) between 2 regions. The fold change (FC) and false discovery rate (FDR) were used to assess DEGs after gene integration (|log 2 FC|>2; FDR P < 0.01). Enrichment and pathway analysis was also performed. Results A total of 201 genes (105 upregulated and 96 downregulated) were significant DEGs in the data sets. The underexpression of NF2 in spinal ependymomas was statistically significant (FDR P = 7.91 × 10−9). However, the FC of NF2 did not exceed the cutoff value (log 2 FC, −1.2). The top 5 ranked upregulated genes were ARX , HOXC6 , HOXA9 , HOXA5 , and HOXA3 , which indicated that spinal ependymomas frequently demonstrate overexpression of HOX family genes, which play fundamental roles in specifying anterior/posterior body patterning. Moreover, the gene ontology enrichment analysis specified "anterior/posterior pattern specification" and "neuron migration" in spinal and intracranial ependymomas, respectively. Conclusions The most substantial magnitude of DEGs in ependymoma might be HOX genes. However, whether the differential expression of these genes is the cause or consequence of the disease remains to be elucidated in a larger prospective study. Highlights • Differential expression of whole exome was evaluated between intracranial and spinal ependymoma using public datasets. • Although NF2 was known to a representative DEG, the magnitude of difference was relatively low (FC, −1.2; FDR P = 7.91×10−9). • Four of top 5 DEGs were HOX family genes among 201 DEGs with statistical significance (|log2FC| >2; FDR P < 0.01). • HOX family genes might have a key role in the clinical differences between intracranial and spinal ependymomas. [ABSTRACT FROM AUTHOR]

The orphan histidine kinase (HK) from Streptomyces peucetius ATCC 27952 ( ohkAsp ) was found to be implicated in the regulation of doxorubicin (DOX)/daunorubicin (DNR) biosynthesis, self-defense and developmental attributes. OhkAsp is a homolog of OhkA from Streptomyces coelicolor and Streptomyces avermitilis (with 73 and 75% identity). As in its homologs, S. peucetius mutant with deletion of ohkAsp was found to enhance metabolite biosynthesis and impaired the morphological differentiation. But, unlike its homologs from Streptomyces coelicolor and Streptomyces avermitilis, differential enhancement in level of secondary metabolite production was found in overexpression mutants apart from deletion mutant. The deflection in characteristics of OhkA in its homologue from S. peucetius ATCC 27952, and its imminent implications was monitered by making various mutants with differential expression level of ohkAsp . The variations were observed in the morphology of mutants, transcriptional level of effectors and regulators of DOX/DNR biosynthesis pathway, DOX/DNR precursor pool and biomass accumulation. Based on comparisons of domain arrangements among its homologs, Low Complexity Region (LCR) present on the OhkAsp was the only domain that stood out. Further, the LCR on OhkAsp was found to be overlapping with a putative receiver domain responsible for interaction with response regulator. The imminent implications of differential expression level of ohkAsp on: regulation and biosynthesis of DOX/DNR, morphological differentiation, DOX/DNR precursor pool and biomass accumulation were explored in this study. [ABSTRACT FROM AUTHOR]

Serine/threonine kinase 11 (STK11) is a protein kinase that is encoded by Stk11 gene located on chromosome 19 and 10 in humans and mouse respectively. It acts as a master kinase of adenine monophosphate-activated protein kinase (AMPK) pathway that coordinates the regulation of cellular energy metabolism and cell division. STK11 exerts effect by activating more than 14 kinases including AMPK and AMPK-related kinases. It is also known to regulate cell polarity and acts as tumor suppressor. Alternative splicing of pre-mRNA is a mechanism which results in multiple transcript variants of a single gene. In human, two STK11 isoforms have been reported, an alternatively spliced isoform which has variation at its C-terminal and mostly expressed in testis (LKB1 S ). Another isoform exhibiting oncogenic properties lacks few residues at its N-terminal (ΔN-LKB1). In the present study, we report the identification of a new transcript variant Stk11N which is generated through alternative splicing. The new variant was found to have differential and tissue specific expression at Postnatal-7 and adult stages of mouse. As compared to the known variant Stk11C, the conceptually translated amino acid sequences of the new variant differ from exon-E2 onwards. In silico post translational studies of the new and published variant show similarity in some of the properties while differ in properties like nuclear export signals, phosphorylation, glycosylation, etc. Thus, alternative splicing of Stk11 gene generating new variant with heterogeneous properties suggests for complex regulation of these variants in controlling the AMPK pathway and other functions. [ABSTRACT FROM AUTHOR]

Peroxisome proliferator-activated receptor gamma (PPARγ) is a key regulator of adipogenesis. It is also a central player in energy metabolism, inflammation and immunity. As an important nuclear transcription factor, PPARγ can regulate the expression and function of genes or biological processes directly or indirectly via association with other factors and thus modulate their activities. To better understand the impact of PPARγ on the global gene expression profile, we evaluated the bioinformatic data, which revealed the changes that occurred in genes and their pathways in the absence of PPARγ. In brief, we performed RNA deep sequencing (RNA-Seq) analysis using RNA samples isolated from multipotent mesenchymal stromal cells (MSCs) of PPARγ knockout and wild type control mice. The RNA-Seq data sets were then subjected to bioinformatic analyses from various angles to better reveal the breadth of PPARγ function in different biological processes. Our results reveal novel genes and networks modulated by PPARγ and provides new insights into our understanding of the physiologic and pathophysiologic role this nuclear receptor plays in health and disease. [ABSTRACT FROM AUTHOR]

Peripheral diabetic neuropathy (DN) manifests in nearly 60% of diabetic patients, being pain its most debilitating symptom. Although electrophysiological and morphological aspects are well described, little is known about its development and progression, undermining effective therapies. Hyperglycemia and insulin signaling impairment are considered the triggering events of oxidative stress observed in the dying nerves, however there are still many gaps in the knowledge of intracellular plastic changes it generates. Aims In this study we aimed to evaluate the early transcriptome changes in DN when the first symptoms of the disease start to appear. Main methods Next-Generation Sequencing of messenger RNA (RNA-Seq) of L4 and L5 dorsal root ganglia (DRG) four weeks post-diabetes induction in a rat model for type 1 diabetes. Key findings RNA sequencing found 66 transcripts differentially expressed between diabetic and control groups, related mainly to the following biological processes: inflammation, hyperalgesia/analgesia, cell growth and cell survival. Given their roles, the differentially expressed genes suggest an attempt to switch to a survival/regenerative program. Significance Our results show that changes in the transcriptome profile start to appear early in the course of DN and might be related to secure cell homeostasis. Hence, the present data may indicate how DRG cells are responding to hyperglycemia in its early stages and which mechanisms first fail to respond, further leading to cell damage and cell death. Early screening of cell alterations in DN might lead to more concrete targets for pharmaceutical interventions, which could more efficiently delay cell damage. [ABSTRACT FROM AUTHOR]

The development of circular RNA (circRNA) microarrays has facilitated studies on the role of circRNAs in regulating gene expression through a circRNA-miRNA-mRNA network. In our study, a microarray was used to detect the expression profiles of circRNAs in mouse bone marrow stromal cell (MSCs) after total body irradiation (TBI) in an X-ray field. Forty mice were randomly distributed into two groups, the control group and the TBI group, with 20 mice in each. Using circRNA microarray data, we compared the circRNA expression profiles in the MSCs between the two groups. Randomly chosen differentially expressed circRNAs were validated as potential TBI biomarkers. Overall, 148 circRNAs were significantly upregulated while the other 133 were downregulated between the TBI group and the sham group. Among them, two upregulated circRNAs (mmu_circRNA_011235 and mmu_circRNA_016901) and three downregulated circRNAs (mmu_circRNA_008488, mmu_circRNA_000551 and mmu_circRNA_005365) exhibited trends comparable to microarray data in the validation experiments. The miRNA support vector regression method was used to predict potential target miRNAs for the circRNAs while ClueGO was used for functional analysis of predicted miRNA target genes. This is the first study to investigate the differential circRNA expression profile in TBI and the associated functions. Significantly upregulated or downregulated circRNAs may represent novel biomarkers and novel therapeutic targets for the clinical management of radiation injury with TBI. [ABSTRACT FROM AUTHOR]

Glutathione peroxidases (GPXs) are redox sensor proteins that maintain a steady-state of H 2 O 2 in plant cells. They exhibit distinct sub-cellular localization and have diverse functionality in response to different stimuli. In this study, a total of 14 TaGPX genes and three splice variants were identified in the genome of Triticum aestivum and evaluated for various physicochemical properties. The TaGPX genes were scattered on the various chromosomes of the A, B, and D sub-genomes and clustered into five homeologous groups based on high sequence homology. The majority of genes were derived from the B sub-genome and localized on chromosome 2. The intron-exon organization, motif and domain architecture, and phylogenetic analyses revealed the conserved nature of TaGPXs. The occurrence of both development-related and stress-responsive cis -acting elements in the promoter region, the differential expression of these genes during various developmental stages, and the modulation of expression in the presence of biotic and abiotic stresses suggested their diverse role in T. aestivum . The majority of TaGPX genes showed higher expression in various leaf developmental stages. However, TaGPX1-A1 was upregulated in the presence of each abiotic stress treatment. A co-expression analysis revealed the interaction of TaGPXs with numerous development and stress-related genes, which indicated their vital role in numerous biological processes. Our study revealed the opportunities for further characterization of individual TaGPX proteins, which might be useful in designing future crop improvement strategies. [ABSTRACT FROM AUTHOR]

Study on kiwifruit ( Actinidia chinensis and A. deliciosa ) color mainly concentrated in green and yellow-fleshed cultivars, less about molecular mechanism of red-fleshed trait formation, rarely in all red-fleshed fruit. Using ‘Tianyuanhong’ and ‘Yongfengyihao’ (‘TY’, a kind of all red-fleshed cultivar, from Actinidia arguta ; ‘YF’, a kind of all green-fleshed cultivar, also from Actinidia arguta ) as experimental material, we performed RNA-seq to obtain 202,742 unigenes with an average length of 603 bp and N50 of 873 bp via transcriptome data analysis. Of these unigenes, 72,508 (35.76%) were annotated and 997 were assigned to secondary metabolic pathways, of which 104 unigenes were involved in flavonoid and anthocyanin biosynthesis. According to the parameter log2fold-change and p-adjusted, 12 differentially expressed structural genes were selected for performing expression profiles and cluster analysis. Physiological traits including color ration, hue angle, and anthocyanin content were also investigated. From the results, we concluded Aa LDOX (genes encoding leucoanthocyanidin dioxygenase) maybe the key gene controlling anthocyanin biosynthesis in flesh of ‘TY’ kiwifruit, which promoted accumulation of anthocyanin, finally leading to the red flesh coloration. [ABSTRACT FROM AUTHOR]

Cardiac hypertrophy is one of the initial symptoms of many heart diseases. We found that miR-672-5p may participate in the regulation of heart disease development in mouse, but the association between miR-672-5p and cardiac hypertrophy remains unclear. In the present study, we found that the abundance of miR-672-5p decreased in hypertrophic cardiomyocytes induced by phenylephrine, angiotensin II (Ang II) and insulin-like growth factor 1. Putative target genes of miR-672-5p were identified using four pipelines, miRWalk, miRanda, RNA22 and Targetscan, and a total of 834 genes were predicted by all four pipelines. Among these target genes, 98 were associated with the development of heart disease. PPI networks showed that the Jun proto-oncogene product (JUN), a subunit of the AP-1 transcription factor, had the highest node degree, and it was defined as the hub gene of the PPI networks. Luciferase assays showed that miR-672-5p bound to the 3′ UTR of the JUN gene and decreased luciferase activity, indicating that JUN is a target of miR-672-5p. Finally, we found that increasing the abundance of miR-672-5p in cardiomyocytes controlled the relative cell area in Ang II-stimulated hypertrophic cardiomyocytes. Correspondingly, the abundance of JUN, a target of miR-672-5p, was decreased in hypertrophic cardiomyocytes on both mRNA and protein levels, implying that miR-672-5p had suppressive effects on cardiac hypertrophy through regulating the expression of Jun in cardiomyocytes. [ABSTRACT FROM AUTHOR]

A total of 114 microRNAs (miRNAs) were identified for Coptotermes formosanus workers, while a total of 97 miRNAs were identified for Reticulitermes speratus workers, of which 91 were common in C. formosanus and R. speratus . While the relationship between miRNA expression levels in C. formosanus and R. speratus workers had a strong positive correlation, considerable difference in miRNA expressions between C. formosanus and R. speratus was observed. Among the miRNAs up-regulated in C. formosanus workers, miR-11-3p showed the highest expression increase of 2.30 fold, while miR-13b-3p showed the highest expression increase of 5.16 fold among the up-regulated miRNAs in R. speratus workers. Workers of C. formosanus and R. speratus seem to use different miRNAs, miR-11-3p in C. formosanus or miR-13b-3p in R. speratus , to regulate homeodomain transcription factor genes, araucan , caupolican , and nubbin , basic helix-loop-helix (bHLH) transcription factor genes, spineless and E(spl)m3-HLH , and zinc finger transcription factor gene, castor . [ABSTRACT FROM AUTHOR]

Silkworms (Bombyx mori) are lepidopterans of economic importance for global silk production. However, factors that directly affect the yield and quality of silkworm cocoon production, such as diseases and temperature fluctuations, cause great economic losses. Knowing how they respond to rearing temperature during the most critical stage of their life cycle (i.e., fifth instar) could provide information on their adaptation and improve silk production. In the current work, we analyzed transcriptional data from two groups of B. mori that were reared at 26 °C and 34 °C throughout the fifth instar. The silkworms and cocoons were weighed. In total, 3115 transcripts were differentially expressed (DE; including 1696 down-regulated and 1419 up-regulated) among the 29,157 sequences found by transcriptome assembly. We emphasize the genes associated with immunological response, transcription factors, silk biosynthesis, and heat shock proteins, among the DE transcripts in response to the temperature conditions. Silkworms reared at 34 °C presented a reduced mean body weight (−0.944 g in comparison to the 26 °C group), which had a direct impact on the weight of cocoons formed and the silk conversion rate. These changes were statistically significant when compared to silkworms reared at 26 °C. Mortality rates (6 and 9 %, at 26 °C and 34 °C, respectively) were similar to those obtained in breeding fields. The findings provide information on the biological processes involved in the temperature response mechanism of silkworms, as well as information that may be used in future climatization processes at rearing facilities and in breeding for improved thermotolerance. [Display omitted] [ABSTRACT FROM AUTHOR]

• Human peripheral blood circRNA profile changes in response to exercise. • Distinct circRNA expression profile found in ME/CFS patients. • CircLINS1 was differentially expressed on multiple days of exercise study. • CircNUP98 , circNPAT , circCSF3R and circLIN54 may serve as potential biomarkers. Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating disease with obscure aetiology. The underdiagnosis rate of ME/CFS is high due to the lack of diagnostic criteria based on objective markers. In recent years, circRNAs have emerged as potential genetic biomarkers for neurological diseases, including Parkinson's disease and Alzheimer's disease, making them likely to have the same prospect of being biomarkers in ME/CFS. However, despite the extensive amount of research that has been performed on the transcriptomes of ME/CFS patients, all of them are solely focused on linear RNAs, and the profiling of circRNAs in ME/CFS has been completely omitted. In this study, we investigated the expression profiles of circRNAs, comparing ME/CFS patients and controls before and after two sessions of cardiopulmonary exercise longitudinally. In patients with ME/CFS, the number of detected circRNAs was higher compared to healthy controls, indicating potential differences in circRNA expression associated with the disease. Additionally, healthy controls showed an increase in the number of circRNAs following exercise testing, while no similar pattern was evident in ME/CFS patients, further highlighting physiological differences between the two groups. A lack of correlation was observed between differentially expressed circRNAs and their corresponding coding genes in terms of expression and function, suggesting the potential of circRNAs as independent biomarkers in ME/CFS. Specifically, 14 circRNAs were highly expressed in ME/CFS patients but absent in controls throughout the exercise study, indicating a unique molecular signature specific to ME/CFS patients and providing potential diagnostic biomarkers for the disease. Significant enrichment of protein and gene regulative pathways were detected in relation to five of these 14 circRNAs based on their predicted miRNA target genes. Overall, this is the first study to describe the circRNA expression profile in peripheral blood of ME/CFS patients, providing valuable insights into the molecular mechanisms underlying the disease. [ABSTRACT FROM AUTHOR]

The ixodid tick Dermacentor nuttalli is distributed from southern Siberia to North China and is a vector of many pathogens. This species can have severe impacts on animal husbandry and human health. To date, the control of D. nuttalli is limited to the use of acaricides such as organophosphorus, synthetic pyrethroids and amidine pesticides. There are no environmentally friendly or reliable prevention and control measures, and little is known regarding key antigens involved in blood feeding. Salivary glands are major tissues involved in the blood feeding and pathogen transmission of ticks. Therefore, this study focused on salivary glands tissue to identify the dominant antigens of D. nuttalli involved in tick feeding. For this, high-throughput RNA sequencing (RNA-seq) was used for analysis. The transcriptome of female D. nuttalli ticks was assembled and characterized, and differentially expressed genes (DEGs) were identified in the salivary glands of ticks that had not fed (0 h) and of ticks after 24, 48, 72 and 96 h of feeding. There were 22,802,784, 22,275,013, 26,629,453, 24,982,389, and 22,596,230 high-quality clean reads obtained from salivary glands tissues at the five different blood feeding time points. The total number of annotated unigenes was 100,347. The differences in gene expression between different time points were compared, and functional enrichment was performed. Quantitative reverse transcription PCR (RT‒qPCR) was used to validate the RNA-seq results, the results of which showed that the differences in expressed transcripts presented similar trends. Among the identified DEGs, the most numerous were those with catalytic and binding activities and those involved in diverse metabolic pathways and cellular processes. The expression patterns of homologous and family-member proteins throughout the blood feeding period exhibited significant differences, strongly suggesting that the transcriptome composition is highly dynamic and likely subjected to important variation throughout the life cycle. Studies of gene sequences in D. nuttalli will greatly increase the information on tick protective antigens, which could potentially function as effective vaccine candidates or drug targets for the development of environmentally friendly acaricides. [ABSTRACT FROM AUTHOR]

Bivalve molluscs are filter feeding species that can accumulate biotoxins in their body tissues during harmful algal blooms. Amnesic Shellfish Poisoning (ASP) is caused by species of the diatom genus Pseudo-nitzschia , which produces the toxin domoic acid. The Mytilus galloprovincialis digestive gland transcriptome was de novo assembled based on the sequencing of 12 cDNA libraries, six obtained from control mussels and six from mussels naturally exposed to domoic acid-producing diatom Pseudo-nitzschia australis . After de novo assembly 94,727 transcripts were obtained, with an average length of 1015 bp and a N50 length of 761 bp. The assembled transcripts were clustered (homology > 90%) into 69,294 unigenes. Differential gene expression analysis was performed (DESeq2 algorithm) in the digestive gland following exposure to the toxic algae. A total of 1158 differentially expressed unigenes (absolute fold change > 1.5 and p-value < 0.05) were detected: 686 up-regulated and 472 down-regulated. Several membrane transporters belonging to the family of the SLC (solute carriers) were over-expressed in exposed mussels. Functional enrichment was performed using Pfam annotations obtained from the genes differentially expressed, 37 Pfam families were found to be significantly (FDR adjusted p-value < 0.1) enriched. Some of these families (sulfotransferases, aldo/keto reductases, carboxylesterases, C1q domain and fibrinogen C-terminal globular domain) could be putatively involved in detoxification processes, in the response against of the oxidative stress and in immunological processes. Protein network analysis with STRING algorithm found alteration of the Notch signaling pathway under the action of domoic acid-producing Pseudo-nitzschia . In conclusion, this study provides a high quality reference transcriptome of M. galloprovincialis digestive gland and identifies potential genes involved in the response to domoic acid. [ABSTRACT FROM AUTHOR]

Utilization of laccases in biotechnology and bioremediation has created a strong demand for the characterization of new enzymes and an increase in production of known laccases. Thus, additional research into these enzymes is critically needed. In this study, we report a comparative study of the biochemical and transcriptional properties of two different laccase isozymes from Trametes hirsuta 072 – the constitutive and inducible forms. A recombinant LacC enzyme was expressed in Penicillium canescens to characterize its properties. LacC is single-purpose enzyme, unlike LacA, which can operate efficiently under a wide range of temperatures and pHs (55–70 °C and pH 3–5, respectively). LacC has a lower RedOx potential than LacA and does not oxidize substrates containing amine groups. Expression of the lacC gene was selective compared to that of the lacA gene and increased significantly in the presence of complex synthetic compounds such as dyes and xenobiotics. This study shows that laccases from the multigene families of basidiomycetes differ significantly in their properties, thus providing a complementary effect during lignin degradation. [ABSTRACT FROM AUTHOR]

Objective To compare the expression patterns of two multiple transcripts derived from DSP-PP gene during tooth development. One is DSP-only transcript (i.e. does not encode PP) and the other is DSP-PP 523 transcript, a main DSP-PP transcript . Design Unique antisense and sense riboprobes were generated from DSP-only and DSPPP 523 cDNAs for in situ studies to examine DSP-only and DSP-PP 523 transcript expression in developing molars. Paraffin-embedded sections (5–7 μ m) from embryonic 20 day, postnatal 2, 3 and 6 days were deparaffined and hydrated. Tissues were prehybridized, then hybridized with DSP-only and DSP-PP 523 anti-sense (AS) or sense (S) Digoxigenin labeled-riboprobes overnight, and washed. Anti-Digoxigenin antibodies conjugated to alkaline phosphatase were used to detect the presence of bound riboprobes by color reaction with NBT/BCIP. Stro-1 antibody was used for immunohistochemical analysis of Stro-1 protein expression in rat molars. Results We found that unlike the DSP-PP 523 transcript, the DSP-only transcript does not express in the entire polarized mature odontoblasts but is expressed in the areas subjacent to the mature odontoblast layer. In addition, DSP-only transcript is expressed in the dental pulp. Interestingly, Stro-1 protein, a stem cell marker, was also identified in the areas subjacentto odontoblasts and in dental pulp. Conclusion Differential expression of DSP-only and DSP-PP 523 transcripts suggest that these two kinds of transcripts may play different roles during dentinogenesis. DSP-PP 523 transcript is expressed in mature odontoblasts, which actively participates in dentin formation. DSP-only transcript might have a different function. [ABSTRACT FROM AUTHOR]

GAEC1 (Gene amplified in esophageal cancer 1 ) alterations have oncogenic properties in oesophageal squamous cell carcinomas and frequent amplifications of the gene were noted in colorectal adenocarcinomas. However, the subcellular localization and expression of GAEC1 at the protein level have never been reported in human cancer cells. The present study aimed to investigate whether GAEC1 is differentially expressed in different stages of colon cancer and to elucidate its underlying cellular and molecular mechanism in colon cancer progression. We found differential expression of GAEC1 protein and mRNA in different pathological stages of colon cancer cells (SW480-Stage II, SW48-Stage III and HCT116-Stage IV) when compared to non-neoplastic colon cells (FHC cells) by immunocytochemistry, immunofluorescence, western blot analysis and real-time polymerase chain reaction. GAEC1 protein was predominantly expressed in the cytoplasm of colon cancer cells (SW480, SW48, and HCT116) and in the nucleus of non-neoplastic colon epithelial cells (FHC cells). The transient knockdown of GAEC1 using siRNA induced apoptosis in SW480 and SW48 cells, which was associated with G2/M phase arrest and decreased expression of bcl-2 and K-ras proteins and increased expression of p53. In addition, down-regulation of GAEC1 significantly inhibited (p < 0.05) cell proliferation, reduced migration capacity and decreased clonogenic potentiality of colon cancer cells (SW480 and SW48 cells). Furthermore, a xenotransplantation model showed that stable knockdown of GAEC1 using shRNA constructs in colon cancer cells fully suppressed xenograft tumour growth in mice. Collectively, the expression analysis, in vitro and in vivo data indicated that GAEC1 is differentially expressed in cancer cells and act as an oncogene in colon cancer progression. [ABSTRACT FROM AUTHOR]