Obvious Differential Expression Research Articles

Comprehensive transcriptome, physiological and biochemical analyses reveal that key role of transcription factor WRKY and plant hormone in responding cadmium stress

Cadmium (Cd) is readily absorbed by tobacco and accumulates in the human body through smoke inhalation, posing threat to human health. While there have been many studies on the negative impact of cadmium in tobacco on human health, the specific adaptive mechanism of tobacco roots to cadmium stress is not well understood. In order to comprehensively investigate the effects of Cd stress on the root system of tobacco, the combination of transcriptomic, biochemical, and physiological methods was utilized. In this study, tobacco growth was significantly inhibited by 50 μM of Cd, which was mainly attributed to the destruction of root cellular structure. By comparing the transcriptome between CK and Cd treatment, there were 3232 up-regulated deferentially expressed genes (DEGs) and 3278 down-regulated DEGs. The obvious differential expression of genes related to the nitrogen metabolism, metal transporters and the transcription factors families. In order to mitigate the harmful effects of Cd, the root system enhances Cd accumulation in the cell wall, thereby reducing the Cd content in the cytoplasm. This result may be mediated by plant hormones and transcription factor (TF). Correlational statistical analysis revealed significant negative correlations between IAA and GA with cadmium accumulation, indicated by correlation coefficients of −0.91 and −0.93, respectively. Conversely, ABA exhibited a positive correlation with a coefficient of 0.96. In addition, it was anticipated that 3 WRKY TFs would lead to a reduction in Cd accumulation. Our research provides a theoretical basis for the systematic study of the specific physiological processes of plant roots under Cd stress.

Single-cell RNA sequencing reveals roles of unique retinal microglia types in early diabetic retinopathy

BackgroundThe pathophysiological mechanisms of diabetic retinopathy (DR), a blinding disease, are intricate. DR was thought to be a microvascular disease previously. However, growing studies have indicated that the retinal microglia-induced inflammation precedes microangiopathy. The binary concept of microglial M1/M2 polarization paradigms during inflammatory activation has been debated. In this study, we confirmed microglia had the most significant changes in early DR using single-cell RNA sequencing.MethodsA total of five retinal specimens were collected from donor SD rats. Changes in various cells of the retina at the early stage of DR were analyzed using single-cell sequencing technology.ResultsWe defined three new microglial subtypes at cellular level, including two M1 types (Egr2+ M1 and Egr2− M1) and one M2 type. We also revealed the anatomical location between these subtypes, the dynamic changes of polarization phenotypes, and the possible activation sequence and mutual activation regulatory mechanism of different cells. Furthermore, we constructed an inflammatory network involving microglia, blood-derived macrophages and other retinal nonneuronal cells. The targeted study of new disease-specific microglial subtypes can shorten the time for drug screening and clinical application, which provided insight for the early control and reversal of DR.ConclusionsWe found that microglia show the most obvious differential expression changes in early DR and reveal the changes in microglia in a high-glucose microenvironment at the single-cell level. Our comprehensive analysis will help achieve early reversal and control the occurrence and progression of DR.

MiR-30b-3p Inhibits the Proliferation and Invasion of Lung Adenocarcinoma by Targeting COX6B1

背景与目的肺腺癌（lung adenocarcinoma, LUAD）是当前最常见的肺癌亚型，微小RNA（microRNAs, miRNAs）是一类非编码小RNA，在细胞活动中发挥核心作用。miR-30b-3p在许多类型的癌症中均起到了关键作用，但关于其在肺腺癌中如何发挥作用的研究仍然很少。本研究通过探索miR-30b-3p在肺腺癌增殖和侵袭中的作用和机制，以期为临床上抑制肺腺癌的增殖和侵袭拓展新的方向。方法利用NCBI生物数据库查找肺腺癌中差异表达明显的miRNA，并查询其差异表达及生存曲线；采用实时荧光定量聚合酶链反应（real-time fluorescence quantitative polymerase chain reaction, qRT-PCR）检测miR-30b-3p在各肺腺癌细胞系中的表达；5-乙炔基-2’脱氧尿嘧啶核苷（5-ethynyl-2'-deoxyuridine, EdU）细胞增殖实验和Transwell实验检测各组A549细胞增殖和侵袭能力的变化；使用在线预测数据网站确定miR-30b-3p的靶蛋白；Western blot验证COX6B1在不同组肺腺癌细胞中的表达情况；双荧光素酶实验证实miR-30b-3p与COX6B1是否存在结合位点。结果miR-30b-3p在肺腺癌组织和细胞中表达下调（P<0.05），低表达水平的miR-30b-3p与肺腺癌患者的不良预后有关（P=0.005,8）；过表达miR-30b-3p能够抑制肺腺癌细胞的增殖与侵袭能力（P<0.05）；双荧光素酶实验证明miR-30b-3p和COX6B1存在结合位点（P<0.05）；Western blot实验表明在肺腺癌细胞A549中，过表达miR-30b-3p能够下调COX6B1的表达（P<0.05）；EdU细胞增殖实验和Transwell侵袭实验表明，miR-30b-3p的过表达能够逆转上调COX6B1对肺腺癌细胞增殖和侵袭能力的促进作用（P<0.05）。结论miR-30b-3p在肺腺癌中起到了抑癌基因的作用，并能够通过调控COX6B1的表达来抑制肺腺癌的增殖和侵袭。

Comparative Analysis of Salt Responsive MicroRNAs in Two Sweetpotato [Ipomoea batatas (L.) Lam.] Cultivars With Different Salt Stress Resistance.

Sweetpotato [Ipomoea batatas (L.) Lam.] is an important food, vegetable and economic crop, but its productivity is remarkably affected by soil salinity. MiRNAs are a class of endogenous non-coding small RNAs that play an important role in plant resistance to salt stress. However, the function of miRNAs still remains largely unknown in sweetpotato under salt stress. Previously, we identified salt-responsive miRNAs in one salt-sensitive sweetpotato cultivar “Xushu 32.” In this study, we identified miRNAs in another salt-tolerant cultivar “Xushu 22” by high-throughput deep sequencing and compared the salt-responsive miRNAs between these two cultivars with different salt sensitivity. We identified 687 miRNAs in “Xushu 22,” including 514 known miRNAs and 173 novel miRNAs. Among the 759 miRNAs from the two cultivars, 72 and 109 miRNAs were specifically expressed in “Xushu 32” and “Xushu 22,” respectively, and 578 miRNAs were co-expressed. The comparison of “Xushu 32” and “Xushu 22” genotypes showed a total of 235 miRNAs with obvious differential expression and 177 salt-responsive miRNAs that were obviously differently expressed between “Xushu 32” and “Xushu 22” under salt stress. The target genes of the miRNAs were predicted and identified using the Target Finder tool and degradome sequencing. The results showed that most of the targets were transcription factors and proteins related to metabolism and stress response. Gene Ontology analysis revealed that these target genes are involved in key pathways related to salt stress response and secondary redox metabolism. The comparative analysis of salt-responsive miRNAs in sweetpotato cultivars with different salt sensitivity is helpful for understanding the regulatory pattern of miRNA in different sweetpotato genotypes and improving the agronomic traits of sweetpotato by miRNA manipulation in the future.

A study of the differential expression profiles of Keshan disease lncRNA/mRNA genes based on RNA-seq.

This study aims to analyze the differential expression profiles of lncRNA in Keshan disease (KSD) and to explore the molecular mechanism of the disease occurrence and development. RNA-seq technology was used to construct the lncRNA/mRNA expression library of a KSD group (n=10) and a control group (n=10), and then Cuffdiff software was used to obtain the gene lncRNA/mRNA FPKM value as the expression profile of lncRNA/mRNA. The fold changes between the two sets of samples were calculated to obtain differential lncRNA/mRNA expression profiles, and a bioinformatics analysis of differentially expressed genes was performed. A total of 89,905 lncRNAs and 20,315 mRNAs were detected. Statistical analysis revealed that 921 lncRNAs had obvious differential expression, among which 36 were up-regulated and 885 were down-regulated; 2,771 mRNAs presented with obvious differential expression, among which 253 were up-regulated and 2,518 were down-regulated, and cluster analysis indicated that the gene expression trends among the sample groups were consistent. The differentially expressed lncRNAs were tested for target genes, and 117 genes were found to be regulated by differential lncRNAs, which were concentrated in six signaling pathways, among which the apoptosis FoxO signaling pathway ranked first, so the target genes IGF1R and TGFB2 were screened out. In this study, RNA-seq technology was used to obtain the differential gene expression profiles of KSD, and bioinformatics analysis was performed to screen out target genes, pointing out the direction for further research into the etiology, pathogenesis and drug treatment targets of KSD.

Genome wide identification and expression pattern analysis of the GRAS family in quinoa.

GRAS, a key transcription factor in plant growth and development, has not yet been reported in quinoa. Therefore, this study used the latest quinoa genomic data to identify and analyse GRAS genes in quinoa: 52 GRAS genes were identified in quinoa, these being unevenly distributed on 19 chromosomes. Fragment duplication and tandem duplication events were the main reasons for the expansion of the GRAS gene family in quinoa. Protein sequence analysis showed that there were some differences in amino acid numbers and isoelectric points amongst different subfamilies, and the main secondary structures were α-helix and random coil. The CqGRAS gene was divided into 14 subfamilies based on results from phylogenetic analysis. The genes located in the same subfamily had similar gene structures, conserved motifs, and three-level models. Promoter region analysis showed that the GRAS family genes contained multiple homeostasis elements that responded to hormones and adversity. GO enrichment indicated that CqGRAS genes were involved in biological processes, cell components, and molecular functions. By analysing the expression of CqGRAS genes in different tissues and different treatments, it was found that GRAS genes had obvious differential expression in different tissues and stress, which indicates that GRAS genes had tissue or organ expression specificity and thus might play an important role in response to stress. These results laid a foundation for further functional research on the GRAS gene family in quinoa.

Bioinformatic evaluation of the potential animal models for studying SARS-Cov-2

Recently, the severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2), a novel coronavirus, which results in corona virus disease 2019 (COVID-19), has caused over 40 millions of people infected and over 1 million fatalities, challenging the public health. The recognition of its functional receptor, angiotensin converting enzyme 2 (ACE2), have facilitated the antivirus drugs testing and vaccines development. Due to the natural resistance of mouse model to SARS-Cov-2, there is an urgent need to find out the alternative animal model. Considering the crucial role of ACE2 in the host cell entry, we analyzed the phylogeny and expression pattern of ACE2 from various mammals. Firstly, crab-eating macaque possesses all of the 5 identical hotspot residues with human, suggesting high likelihood of interaction between ACE2 and spike protein of SARS-CoV-2 to occur. Cattle and pig show 4 identical sites. Ferret, cat and dog possess 3 identical sites. Bat and mouse only share 2 same amino acids with human. Secondly, in humans, ACE2 is widely present, with particularly high expression in adipose, thyroid, lung and colon tissues. In crab-eating macaque, liver, lung, thyroid and colon showed high expression level of ACE2. For dog, ACE2 is most highly expressed in colon with obvious differential expression level between female and male group. The results would provide clues for establishing the appropriate animal model in the research and clinical cure of COVID-19.

Up-Regulation of circRNA hsa_circ_0003074 Expression is a Reliable Diagnostic and Prognostic Biomarker in Patients with Osteosarcoma.

ObjectiveThe purpose of this study was to detect the expression level of circRNA hsa_circ_0003074 in the tissues and peripheral blood of patients with osteosarcoma, and to explore its value in diagnosis and predicting prognosis of patients with osteosarcoma.Materials and MethodsTissue samples of osteosarcoma patients for chip sequencing were collected and circRNA hsa_circ_0003074, which was associated with the most obvious differential expression, was selected for qRT-PCR analysis. At the same time, the expression levels of hsa_circ_0003074 in different osteosarcoma cell lines, and in the peripheral blood of osteosarcoma patients before and after chemotherapy or surgery, as well as those in healthy volunteers matched by age and sex were also tested. This study aimed to explore the relationship between hsa_circ_0003074 and clinical characteristics of patients with osteosarcoma and analyzed its impact on patient survival.ResultsHigh expression of hsa_circ_0003074 was detected in osteosarcoma tissues, peripheral blood and osteosarcoma cell lines, and the expression level of hsa_circ_0003074 in the peripheral blood of patients with osteosarcoma decreased significantly after chemotherapy or surgery. In addition, hsa_circ_0003074 was closely related to clinical characteristics, such as tumor size, lung metastasis, enneking stage, and chemotherapy resistance. The ROC curve showed that hsa_circ_0003074 was a good diagnostic indicator for osteosarcoma, and survival analysis results revealed that high expression of hsa_circ_0003074 affected the survival of patients.Conclusionhsa_circ_0003074 is not only highly expressed in the tissues and peripheral blood of osteosarcoma patients but also a reliable diagnostic and prognostic biomarker for osteosarcoma patients.

Differential expression of miR-30a-5p in post stroke depression and bioinformatics analysis of the possible mechanism

To investigate the differential expression of miR-30a-5p in patients with poststroke depression and explore the possible mechanism. We obtained the target microRNAs through searching PubMed using the online software VENNY2.1. We collected the baseline demographic, clinical and radiographic data from consecutive patients with first-ever acute ischemic stroke on admission in our department from October, 2018 to March, 2019. From each patient, 5 mL peripheral venous blood was collected upon admission. Hamilton Depression Scale (HAMD-17) was used to evaluate the degree of depression at the end of the 3-month follow-up. The patients with a HAMD-17 score≥7 were diagnosed to have depression according to the diagnostic criteria of the Fourth Edition of the Diagnostic and Statistical Manual of Mental Disorders of the American Psychiatric Association (DSM-IV). The patients were divided into post-stroke depression group (PSD group, n=11) and non-post-stroke depression group (non-PSD group, n=25), and their plasma levels of miR-30a-5p were detected using qPCR. The STARBASE Database ENCORI miRNA-mRNA module and Comparative Toxicogenomics Database were used to predict and screen the possible target genes related to miR-30a-5p, and the possible mechanism of the target genes was further analyzed through bioinformatics. miR-30a-5p was identified by cross-screening as the target miRNA associated with stroke and depression and showed obvious differential expression between PSD and non-PSD patients (2.462±0.326 vs 1±0.126, P &lt; 0.0001). ROC curve analysis showed that the AUC of miR-30a-5p for predicting PSD was 0.869 (95%CI: 0.745-0.993, P=0.0005) at the cutoff value of 1.597, with a sensitivity and specificity of 0.727 and 0.840, respectively. The target proteins of miR-30a-5p involved a wide range of biological processes, including signal transduction, intercellular communication, regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism. KEGG pathway enrichment analysis showed that the target proteins affected mainly the neural nutrient signaling pathway, axon guidance signaling pathway and insulin signaling system. We also identified the top 20 HUB genes that might be associated with post-stroke depression. Plasma miR-30a-5p is differentially expressed in PSD and can serve as a new blood marker for diagnosis and also a therapeutic target of PSD.

Regulatory effect of miR-30b on migration and invasion of pancreatic cancer stem cells

Objective: To detect the expression of micro RNA(miRNA, miR)-30bin pancreatic cancer stem cells (PCSCs) and to observe the regulatory effect of miR-30b on epithelial-mesenchymal transformation (EMT) process, migration and invasion of PCSCs. Methods: CD24, CD44 and EpCAM triple-positive PCSCs in pancreatic ductal adenocarcinoma(PDAC) cell line PANC-1 were sorted out by flow cytometry and the expression of Nanog and Oct4 were evaluated. The expression profile of miR-30 family in PCSCs and common cancer cells was analyzed, and the memberwith the most obvious differential expression was selected.miR-30b mimic was transfected into PCSCs and then RT-qPCR or Western Blot were performed to investigate the expression of EMT markers. The effect of miR-30b on the migration and invasion ability of PCSCs was detected by Transwell assay. Then, miR-30b agomir was transfected into PCSCs and inoculated in nude mice to study the effect of mir-30b on the tumorigenic ability. Results: PCSCs accounted for 4.52-8.09% of the total. The mRNA and protein levels of Oct4 and Nanog of PCSCswere significantly higher than those of PANC-1(P<0.001). The expression levels of miR-30b, c and d were significantly down-regulated, among which miR-30b was the most significant. After miR-30b overexpression in PCSCs, E-cadherin was significantly up-regulated (P<0.001), N-cadherin (P<0.001) and transcription factor Snail (P<0.001) were significantly down-regulated, while vimentin expression was not significantly changed. Transwell assay showed that both migration and invasiveness of PCSCs were significantly decreased after transfection (P<0.001). In vivo experiments, the tumor volume and weight of the nude mice injected with PCSCs overexpressing miR-30b were also significantly lower than those of the control group (P<0.01). Conclusions: CD24, CD44 and EpCAMtriple positive PCSCs in pancreatic cancer cells showed obvious stemness characteristics. miR-30b can reverse the EMT process of PCSCs, reduce their migration and invasion, and inhibit the tumorigenicity of PCSCs.

Overexpression of BcbZIP134 negatively regulates the biosynthesis of saikosaponins

Chaihu, the dried roots of several Bupleurum species, are widely used as herbal drugs. Triterpene saponins, as saikosaponins (SSs) in Chaihu, exhibit a wide range of pharmacological actions, including significant anti-inflammatory, immunomodulatory, hepatoprotective, antioxidant, anti-tumor and antiviral activities. To explore the regulatory biosynthesis of SS in Bupleurum chinense roots, we screened putative transcription factor (TF) genes from transcriptome data. Here, we report one of the bZIP TF genes, named BcbZIP134, which belongs to bZIP G subfamily. The expression of BcbZIP134 was elevated in MeJA-treated adventitious roots of B. chinense. No obvious differential expression of BcbZIP134 was detected in tissues (root, stem, leaf, flower and fruit) of B. chinense. Overexpressing BcbZIP134 in B. chinense hairy roots revealed that the content of the main SS monomers a, c and d were decreased compared to control hairy roots. Furthermore, the contents of a few other minor SS monomers were also affected when compared to the controls. The results indicate that BcbZIP134 may play a negative regulatory role in SS biosynthesis.

Genes Expression in the Early Stage of Acute Renal Ischemia-reperfusion Injury in Rats

To study the differential genes expression in the early stage of acute renal ischemia-reperfusion injury and explore potential molecular mechanisms. The ischemia-reperfusion model was made via clamping renal artery of rat. The microarray detection and bioinformatics analyzing of the genes expression were performed. Differentially expressed genes were screened and related cellular activities and signaling pathways were analyzed in early stage of acute kidney injury. Meanwhile, molecules closely relative to acute kidney injury were explored by establishing a biological network of the differentially expressed genes, and the results were verified by real-time PCR. A total of 151 genes showed differential expression in this study, including 132 up-regulated and 19 down-regulated genes. Cell proliferation, cytokines mediated signaling transduction and immune responses were greatly enriched by GO and KEGG analysis. The results of real-time PCR showed that compared with control groups, three selected genes （ANXA1, PHLDA1 and KLF6） which related to the acute kidney injury had an obvious differential expression in the early stage of disease. The multiple of increase was essentially the same as the multiple detected by microarray. This study shows differential gene expression profile, related biological processes and signaling pathways involved in the early stage of acute kidney injury. ANXA1, PHLDA1 and KLF6 may play a role in the pathogenesis of acute kidney injury.

Differential expression of miR-672-5p and miR-146a-5p in osteoblasts in rats after steroid intervention

BackgroundApoptosis of osteoblasts and osteocytes is one cause of steroid-induced osteonecrosis of the femoral head; however, the molecular mechanism of steroid affecting osteoblasts at the genetic level is unclear. The aim of the present work is to examine differential expression of osteoblasts in rats after steroid intervention and to verify expression by real-time polymerase chain reaction (RT-PCR). MethodsPrimary culture, passaging and identification of osteoblasts of SD neonatal rats were conducted; osteoblasts were divided into two groups, the control group, and the steroid group. Total RNA was extracted separately, and quality control was performed; by means of RNA labeling and microarray hybridization, data were collected and then standardized to ascertain differences in miRNA expression between the two groups. The gene expression spectrum was analyzed. Obvious differential expression of miR-672-5p and miR-146a-5p was verified by RT-PCR. Miranda, microcosm and mirdb bioinformatics software were used to predict target genes. ResultsCompared with the control group, morphologically, the osteoblasts in the steroid group were more irregular and showed various shapes. The number of miRNAs (fold change >2) in the steroid group was six. Four miRNAs were upregulated and two miRNAs were downregulated. In particular, upregulated miR-672-5p expression and downregulated miR-146a-5p expression were significant. RT-PCR results showed that the 2−△△ CT value of miR-672-5p in the steroid group was 3.743-fold of that in the control group, and the 2−△△ CT value of miR-146a-5p in the steroid group was 0.322-fold of that in the control group. Angptl4, Ccdc51, Ssbp3 and RGD1306991 were predicted as the target gene of miR-672-5p, while Hrp12 was that of miR-146a-5p. ConclusionExpression profiles of miR-672-5p and miR-146a-5p had the most significant changes in the osteoblasts of rats with steroid intervention, which may provide a new viewpoint to pathogenesis of osteonecrosis of the femoral head.

Differential proteomics analysis on fluoride-resistant Streptococcus mutans by label-free quantitation

To figure out the changed biological characteristics of a fluoride-resistant strain compared with those of the parent sensitive strain of Streptococcus mutans(S. mutans) with the help of differential proteomics analysis, sixty-seven proteins with obvious differential expression were identified in fluoride-resistant strain. Among them are the important virulence factors causing caries, including glucosyltransferase-S, glucosyltransferase-I, glucosyltransferase-Si, major cell-surface adhesin Pac, F-ATPase β-subunit, Ffh, molecular chaperone DnaK, chaperonin GroEL, and the lactate dehydrogenase. We obtained the differential proteomics expression profiles of the fluoride-resistant strain(UA159-FR) and its parental strain(UA159) of S. mutans. Several important virulence factors bringing about caries were identified to have differential expressions, among which the expression of lactate dehydrogenase in fluoride-resistant strain was enhanced compared to that in its parent strain. The results could provide the basis for analysing the functions of proteins encoded by caries-related genes from the fluoride-resistant S. mutans strain.

Background‐Independent Quantitative Trait Loci for Drought Tolerance Identified Using Advanced Backcross Introgression Lines in Rice

ABSTRACTDrought is one of the major abiotic stresses limiting rice (Oryza sativa L.) production. Quantitative trait loci (QTL) for drought tolerance (DT) at the reproductive stage were identified with two sets of advanced backcross introgression lines (ILs) using a common donor Tarom Molaei introgressed separately into two recipients used as female parents, Teqing and IR64. A total of 24 and 22 QTL were identified in the IR64 and Teqing backgrounds, respectively, during the reproductive stage under drought and irrigated conditions for thousand‐grain weight, panicle number per plant, filled grains per panicle, seed fertility, and grain yield per plant. Most of these QTL showed obvious differential expression in response to drought stress. In addition, another 12 QTL were detected by the ratio of trait values under drought stress relative to the normal irrigation condition in the two backgrounds. The Tarom Molaei alleles at 8 of 12 loci with increased trait values could improve tolerance under drought stress. Only three (18.8%) DT QTL (QTgw7, QSf7, and QFgp11) were in common in the two backgrounds, clearly suggesting overwhelming genetic background effects on QTL detection for DT. Eight of the DT QTL identified were found to share the same genomic regions with previously reported DT‐related genes. Introgressing and pyramiding of favorable alleles from Tarom Molaei into Teqing and IR64 backgrounds may facilitate development of superior ILs with greater DT levels.

Identification of Genetic Overlaps for Salt and Drought Tolerance Using Simple Sequence Repeat Markers on an Advanced Backcross Population in Rice

ABSTRACTSalinity and drought are two of the major abiotic stresses that affect rice (Oryza sativa L.) production especially in Asia. Quantitative trait loci (QTL) for salt tolerance (ST) at seedling stage and drought tolerance (DT) at reproductive stage were identified using 77 BC2F8 advanced backcross introgression lines (ILs) derived from a cross of Teqing × Binam in Teqing background. Ten ST QTL were identified governing days to seedlings survival (DSS), score on salt toxicity symptoms on leaves (SST), shoot K+ concentration (SKC), and shoot Na+ concentration (SNC) at seedling stage, and 23 QTL were identified under reproductive stage drought and irrigated conditions for panicle number per plant (PN), thousand grain weight (TGW), seed fertility (SF), plant height (PH), and grain yield per plant (GYP). Most QTL detected at reproductive stage showed obvious differential expression to drought stress. In addition, another eight QTL were detected by trait ratio of the stress to the irrigation; the alleles at all loci except QSf3 showed increasing trait values to be associated with Binam, indicating Binam alleles at these loci could improve DT under drought stress. Upon comparison of identified ST and DT QTL we found 14 QTL shared the same genome regions with similar gene actions, clearly suggesting that genetic overlap existed between the two abiotic stress tolerances. Pyramiding of favorable alleles from Binam into Teqing background should allow us to develop superior ILs with higher levels of ST and DT.

Dissection of genetic overlap of salt tolerance QTLs at the seedling and tillering stages using backcross introgression lines in rice

QTLs for salt-tolerance (ST) related traits at the seedling and tillering stages were identified using 99 BC(2)F(8) introgression lines (IL) derived from a cross between IR64 (indica) as a recurrent parent and Binam (japonica) from Iran as the donor parent. Thirteen QTLs affecting survival days of seedlings (SDS), score of salt toxicity of leaves (SST), shoot K(+) concentration (SKC) and shoot Na(+) concentration (SNC) at the seedling stage and 22 QTLs underlying fresh weight of shoots (FW), tiller number per plant (TN) and plant height (PH) at the tillering stage were identified. Most QTLs detected at the tillering stage showed obvious differential expression to salt stress and were classified into three types based on their differential behaviors. Type I included 11 QTLs which were expressed only under the non-stress condition. Type II included five QTLs expressed in the control and the salt stress conditions, and three of them (QPh5, QPh8 and QTn9) had similar quantity and the same direction of gene effect, suggesting their expression was less influenced by salt stress. Type III included six QTLs which were detectable only under salt stress, suggesting that these QTLs were apparently induced by the stress. Thirteen QTLs affecting trait difference or trait stability of ILs between the stress and non-stress conditions were identified and the Binam alleles at all loci except QPh4, QTn2 and QFw2a decreased trait difference. The three QTLs less influenced by the stress and 13 QTLs affecting trait stability were considered as ST QTLs which contributed to ST. Comparing the distribution of QTLs detected at the seedling and tillering stages, most (69%) of them were genetically independent. Only four were the same or adjacent regions on chromosomes 1, 2, 8 and 11 harboring ST QTLs detected at the two stages, suggesting that partial genetic overlap of ST across the two stages occurs. It is likely, therefore, to develop ST rice variety for both stages by pyramiding of ST QTLs of different stages or selection against the overlapping QTLs between the two stages via marker-assisted selection (MAS).

In situ hybridization study of PSP94 (prostatic secretory protein of 94 amino acids) expression in human prostates.

The prostatic secretory protein of 94 amino acids (PSP94), also named beta-microseminoprotein, is one of the major proteins secreted by the human prostate. However, its value as a prognostic marker for prostate cancers is still under debate. The aim of the present study was to examine the expression pattern of this protein in fetal, pubertal, and aged human prostates. Nonisotopic in situ hybridization using a digoxigenin-labeled riboprobe for PSP94 and immunohistochemistry were used to demonstrate the expression of PSP94 in different regions or zones of fetal, pubertal, and adult human prostates. Its localization pattern was also compared with those of two other major secretory proteins, prostate-specific antigen (PSA) and prostatic acid phosphatase (PAP), by immunohistochemistry. PSP94 mRNA and its protein were localized to the secretory epithelium of normal pubertal and adult human prostates. No hybridization signal and immunoreactivity of PSP94 were seen in fetal prostates at 6-7 months of gestation, whereas some glandular cells were positive to PSA and PAP immunostainings. In the adult prostates, PSP94 expression was intense in the acini in the peripheral zone, less intense in the transition zone, and variable in the central zone. Such a zonal expression pattern was more apparent in the pubertal prostates. However, no obvious differential expression pattern was observed in the immunohistochemistry of PAP and PSA, which showed a uniform staining of the secretory epithelia of the acini in all anatomic zones. The hybridization signals and immunoreactivity of PSP94 became reduced or lost in premalignant prostatic intraepithelial neoplastic lesions and different grades of prostatic carcinomas. Fetal prostates at 6-7 months of gestation already synthesize PSA and PAP but not PSP94. The delayed expression of PSP94 appears to correlate with the development of the prostate gland. A differential expression pattern of PSP94 is demonstrated in different anatomical zones, showing that this protein is more expressed and synthesized in the acini in the peripheral zone than in the central and transition zones. However, such a zonal pattern is not seen in the immunohistochemistry of PSA and PAP. The present study also shows that PSP94 is downregulated in different grades of prostate cancers.

In situ hybridization study of PSP94 (prostatic secretory protein of 94 amino acids) expression in human prostates

BACKGROUND The prostatic secretory protein of 94 amino acids (PSP94), also named β-microseminoprotein, is one of the major proteins secreted by the human prostate. However, its value as a prognostic marker for prostate cancers is still under debate. The aim of the present study was to examine the expression pattern of this protein in fetal, pubertal, and aged human prostates. METHODS Nonisotopic in situ hybridization using a digoxigenin-labeled riboprobe for PSP94 and immunohistochemistry were used to demonstrate the expression of PSP94 in different regions or zones of fetal, pubertal, and adult human prostates. Its localization pattern was also compared with those of two other major secretory proteins, prostate-specific antigen (PSA) and prostatic acid phosphatase (PAP), by immunohistochemistry. RESULTS PSP94 mRNA and its protein were localized to the secretory epithelium of normal pubertal and adult human prostates. No hybridization signal and immunoreactivity of PSP94 were seen in fetal prostates at 6–7 months of gestation, whereas some glandular cells were positive to PSA and PAP immunostainings. In the adult prostates, PSP94 expression was intense in the acini in the peripheral zone, less intense in the transition zone, and variable in the central zone. Such a zonal expression pattern was more apparent in the pubertal prostates. However, no obvious differential expression pattern was observed in the immunohistochemistry of PAP and PSA, which showed a uniform staining of the secretory epithelia of the acini in all anatomic zones. The hybridization signals and immunoreactivity of PSP94 became reduced or lost in premalignant prostatic intraepithelial neoplastic lesions and different grades of prostatic carcinomas. CONCLUSIONS Fetal prostates at 6–7 months of gestation already synthesize PSA and PAP but not PSP94. The delayed expression of PSP94 appears to correlate with the development of the prostate gland. A differential expression pattern of PSP94 is demonstrated in different anatomical zones, showing that this protein is more expressed and synthesized in the acini in the peripheral zone than in the central and transition zones. However, such a zonal pattern is not seen in the immunohistochemistry of PSA and PAP. The present study also shows that PSP94 is downregulated in different grades of prostate cancers. Prostate 41:99–109, 1999. © 1999 Wiley-Liss, Inc.