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The identification of embryo-specific genes would provide insights into early embryonic development. However, the current methods employed to identify the genes that are expressed at a specific developmental stage are labor intensive and suffer from high rates of false positives. Here we employed a new and accurate reverse transcription-polymerase chain reaction (RT-PCR) method that involves annealing control primers (ACPs) to identify the genes that are specifically or prominently expressed in mouse blastocysts compared to 4-cell stage embryos. Using 120 ACPs, we identified and sequenced 74 of these differentially expressed genes (DEGs). Basic Local Alignment Search Tool (BLAST) searches revealed that 53 were known genes, 9 encoded ribosomal proteins, and 12 were unknown genes. Of the known genes, 14 were selected and further characterized using real-time quantitative PCR to assess their stage-specific expression in mouse embryos. This analysis suggests that the ACP system is a very good method for the identification of stage-specific genes in small numbers of mouse embryos. Further analysis of the differentially expressed blastocyst genes we have identified will provide insights into the molecular basis of preimplantation development., (Copyright 2005 Wiley-Liss, Inc.)

Being an essential mineral nutrient, potassium ([K.sup.+]) plays numerous important roles in plant growth and development and determines the yield and quality of crop products. The cellular level of [K.sup.+] is controlled to a large extent by the [K.sup.+] transporter, which belongs to the KT/HAK/KUP (HAK) family. However, little is known about these genes in tobacco. In this study, we surveyed the tobacco genome and identified 41 putative NtHAK genes (NtHAKS1-NtHAKS21 and NtHAKT1-NtHAKT20). Investigation of the cis-elements in upstream regions of these NtHAK genes suggests that members of this family respond to environmental cues and phytohormones. Expression data mining reveals that NtHAK genes showed clear sub-genome dominance. In all, these results will provide molecular insights into [K.sup.+] transporter research in tobacco. Key words: tobacco, potassium, HAK, gene family, asymmetrical evolution. En tant qu'element mineral nutritif essentiel, le potassium ([K.sup.+]) joue de nombreux roles importants dans la croissance et le developpement des plantes et il determine le rendement et la qualite de certains produits vegetaux. Le niveau cellulaire de [K.sup.+] est controle en grande partie par les transporteurs de [K.sup.+] qui appartiennent a la famille KT/HAK/KUP (HAK). Cependant, peu de choses sont connues au sujet de ces genes chez le tabac. Dans ce travail, les auteurs ont inspecte le genome du tabac et identifie 41 genes putatifs NtHAK (NtHAKS1-NtHAKS21 et NtHAKT1-NtHAKT20). L'etude des elements cis situes en amont de ces genes suggere que les membres de cette famille repondent a des signaux environnementaux et hormonaux. L'examen des donnees transcriptomiques revele que les genes NtHAK presentent clairement une dominance sub-genomique. Globalement, ces resultats fourniront un eclairage moleculaire sur les transporteurs de [K.sup.+] chez le tabac. [Traduit par la Redaction] Mots-cles : tabac, potassium, HAK, famille de genes, evolution asymetrique., Introduction Potassium ([K.sup.+]) is an essential nutrient in plants and can compose up to 10% of the total plant dry weight (Very and Sentenac 2003). It plays a major role [...]

Background: Peripheral blood carries a reservoir of mRNAs that regulate cardiac structure and function potential. Although it is well recognized that the typical symptoms of Myxomatous Mitral Valve Disease (MMVD) stage B2 are long-standing hemodynamic disorder and cardiac structure remodeling caused by mitral regurgitation, the transcriptomic alterations in blood from such dogs are not understood. Results: In the present study, comparative high-throughput transcriptomic profiling of blood was performed from normal control (NC) and naturally-occurring MMVD stage B2 (MMVD) dogs. Using Weighted Gene Co-expression Network Analyses (WGCNA), Gene Ontology (GO), and Kyoto Encyclopedia of Gene and Genomes (KEGG), we identified that the turquoise module was the most highly correlated with echocardiographic features and found 64 differentially expressed genes (DEGs) that were significantly enriched in platelet activation related pathways. Therefore, from the turquoise module, we selected five DEGs (MDM2, ROCK1, RIPK1, SNAP23, and ARHGAP35) that, according to real-time qPCR, exhibited significant enrichment in platelet activation related pathways for validation. The results showed that the blood transcriptional abundance of MDM2, ROCK1, RIPK1, and SNAP23 differed significantly (P < 0.01) between NC and MMVD dogs. On the other hand, Correlation Analysis revealed that MDM2, ROCK1, RIPK1, and SNAP23 genes negatively regulated the heart structure parameters, and followed the same trend as observed in WGCNA. Conclusion: We screened four platelet activation related genes, MDM2, ROCK1, RIPK1, and SNAP23, which may be considered as the candidate biomarkers for the diagnosis of MMVD stage B2. These findings provided new insights into MMVD pathogenesis. [ABSTRACT FROM AUTHOR]

In recent years, the application of single cell RNA-seq (scRNA-seq) has become more and more popular in fields such as biology and medical research. Analyzing scRNA-seq data can discover complex cell populations and infer single-cell trajectories in cell development. Clustering is one of the most important methods to analyze scRNA-seq data. In this paper, we focus on improving scRNA-seq clustering through gene selection, which also reduces the dimensionality of scRNA-seq data. Studies have shown that gene selection for scRNA-seq data can improve clustering accuracy. Therefore, it is important to select genes with cell type specificity. Gene selection not only helps to reduce the dimensionality of scRNA-seq data, but also can improve cell type identification in combination with clustering methods. Here, we proposed RFCell, a supervised gene selection method, which is based on permutation and random forest classification. We first use RFCell and three existing gene selection methods to select gene sets on 10 scRNA-seq data sets. Then, three classical clustering algorithms are used to cluster the cells obtained by these gene selection methods. We found that the gene selection performance of RFCell was better than other gene selection methods. [ABSTRACT FROM AUTHOR]

Motivation Alzheimer's disease (AD) is a complex brain disorder with risk genes incompletely identified. The candidate genes are dominantly obtained by computational approaches. In order to obtain biological insights of candidate genes or screen genes for experimental testing, it is essential to assess their relevance to AD. A platform that integrates different types of omics data and approaches would facilitate the analysis of candidate genes and is in great need. Results We report AlzCode, a platform for multiview analysis of genes related to AD. First, this platform integrates a rich collection of functional genomic data, including expression data of AD samples (gene expression, single-cell RNA-seq data and protein expression), AD-specific biological networks (co-expression networks and functional gene networks), neuropathological and clinical traits (CERAD score, Braak staging score, Clinical Dementia Rating, cognitive function and clinical severity) and general data such as protein–protein interaction, regulatory networks, sequence similarity and miRNA-target interactions. These data provide basis for analyzing genes from different views. Second, the platform integrates multiple approaches designed for the various types of data. We implement functions to analyze both individual genes and gene sets. We also compare AlzCode with two existing platforms for AD analysis, which are Agora and AD Atlas. We pinpoint the features of each platform and highlight their differences. This platform would be valuable to the understanding of AD genetics and pathological mechanisms. Availability and implementation AlzCode is freely available at: http://www.alzcode.xyz. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Key message: RgC4H promotes phenolic accumulation inR. glutinosa, activating the molecular networks of its antioxidant systems, and enhancing the tolerance to oxidative stresses exposed to drought, salinity and H2O2 conditions. Rehmannia glutinosa is of great economic importance in China and increasing R. glutinosa productivity relies, in part, on understanding its tolerance to oxidative stress. Oxidative stress is a key influencing factor for crop productivity in plants exposed to harsh conditions. In the defense mechanisms of plants against stress, phenolics serve an important antioxidant function. Cinnamate 4-hydroxylase (C4H) is the first hydroxylase in the plant phenolics biosynthesis pathway, and elucidating the molecular characteristics of this gene in R. glutinosa is essential for understanding the effect of tolerance to oxidative stress tolerance on improving yield. Using in vitro and in silico methods, a C4H gene, RgC4H, from R. glutinosa was isolated and characterized. RgC4H has 86.34–93.89% amino acid sequence identity with the equivalent protein in other plants and localized to the endoplasmic reticulum. An association between the RgC4H expression and total phenolics content observed in non-transgenic and transgenic R. glutinosa plants suggests that this gene is involved in the process of phenolics biosynthesis. Furthermore, the tolerance of R. glutinosa to drought, salinity and H2O2 stresses was positively or negatively altered in plants with the overexpression or knockdown of RgC4H, respectively, as indicated by the analysis in some antioxidant physiological and molecular indices. Our study highlights the important role of RgC4H in the phenolics/phenylpropanoid pathway and reveals the involvement of phenolic-mediated regulation in oxidative stress tolerance in R. glutinosa. [ABSTRACT FROM AUTHOR]

Starch biosynthesis, a very critical event during pollen development, is not well understood in terms of gene regulation and intracellular controls. Using the rice HL-type cytoplasmic male sterile (HL-CMS) line with starch deficiency in pollen and two related male-fertile lines ( Oryza sativa L.), we have studied two specific developmental stages: ‘early’, that is, before or during pollen mitosis I, without starch accumulation, and ‘late’, the actively starch-filling postpollen mitosis I phase. Real-time reverse transcription-PCR analysis showed temporal changes in the expression patterns of six metabolic genes involved in the sucrose–starch pathway, i.e. sucrose synthase (EC 2.4.1.13), Rsus3; acid invertase (EC 3.2.1.26), OSINV2; phosphoglucomutase (EC 5.4.2.2), OsPGM; uridine diphosphate-glucose pyrophosphorylase (EC 2.7.7.9), OsUGP; a subunit of adenosine diphosphate-glucose pyrophosphorylase (AGPase) (EC 2.2.7.2), OsAGPL3; soluble starch synthase (EC 2.4.1.21), OsSSI and three transporter genes [sucrose transporter, OsSUT3; hexose transporter, OSMST7 and plasma membrane H+-adenosine triphosphatase (ATPase) (EC 3.6.1.35), OSA2]. Regarding metabolic enzyme activities, lower activity of sucrose synthase was detected at ‘late’ compared with ‘early’ stage in the three rice lines; invertase and other downstream enzymes had higher activities at ‘late’ stage in male-fertile but not male-sterile lines. Meanwhile, significantly reduced sugars and ATP levels were detected at ‘early’ and ‘late’ stages in male-sterile compared with male-fertile tissues. Furthermore, transgenic data showed that AGPase gene can stimulate starch accumulation in pollen of male-sterile host lines, showing the importance of AGPase in the metabolic pathway. Taken together, these data suggest that the combined effects of the reduced energy supply and sugar levels in starch biosynthesis may lead to the observed temporal changes in gene expression, and eventually to pollen sterility. [ABSTRACT FROM AUTHOR]