Temporal Gene Expression Profiles Research Articles

Functional regression clustering with multiple functional gene expressions.

Gene expression data is often collected in time series experiments, under different experimental conditions. There may be genes that have very different gene expression profiles over time, but that adjust their gene expression patterns in the same way under experimental conditions. Our aim is to develop a method that finds clusters of genes in which the relationship between these temporal gene expression profiles are similar to one another, even if the individual temporal gene expression profiles differ. We propose a K-means-type algorithm in which each cluster is defined by a function-on-function regression model, which, inter alia, allows for multiple functional explanatory variables. We validate this novel approach through extensive simulations and then apply it to identify groups of genes whose diurnal expression pattern is perturbed by the season in a similar way. Our clusters are enriched for genes with similar biological functions, including one cluster enriched in both photosynthesis-related functions and polysomal ribosomes, which shows that our method provides useful and novel biological insights.

Temporal Gene Expression Profiles From Pollination to Seed Maturity in Sorghum Provide Core Candidates for Engineering Seed Traits.

Sorghum (Sorghum bicolor (L.) Moench) is a highly nutritional multipurpose millet crop. However, the genetic and molecular regulatory mechanisms governing sorghum grain development and the associated agronomic traits remain unexplored. In this study, we performed a comprehensive transcriptomic analysis of pistils collected 1-2 days before pollination, and developing seeds collected -2, 10, 20 and 30 days after pollination of S. bicolor variety M35-1. Out of 31 337 genes expressed in these stages, 12 804 were differentially expressed in the consecutive stages of seed development. These exhibited 10 dominant expression patterns correlated with the distinct pathways and gene functions. Functional analysis, based on the pathway mapping, transcription factor enrichment and orthology, delineated the key patterns associated with pollination, fertilization, early seed development, grain filling and seed maturation. Furthermore, colocalization with previously reported quantitative trait loci (QTLs) for grain weight/size revealed 48 differentially expressed genes mapping to these QTL regions. Comprehensive literature mining integrated with QTL mapping and expression data shortlisted 25, 17 and 8 core candidates for engineering grain size, starch and protein content, respectively.

Metabolic role of the amino acids in the adaptation of Holstein dairy cows to two contrasting challenging situations

This thesis investigated the role of the amino acids (AA) during the transition period and lactation under grazing conditions, and heat stress (HS) as two contrasting challenging situations for the dairy cow. In the experiment 1, the branched-chain AA (BCAA) metabolism was studied in North American (NAH) vs. New Zealand (NZH) Holstein cows between -45 and 180 days in milk (DIM). Higher plasma concentrations of BCAA were confirmed in NAH vs. NZH in early lactation. The temporal profile of hepatic gene expression of specific BCAA transporters, especially LAT1 and Eeg1, differed between the genetic strains in association with the level of somatotropic axis uncoupling and insulin resistance in the liver. In the experiments 2 and 3, we studied the role of the metabolism of the AA against HS and its amelioration through nutritional strategies under controlled conditions. The plasma and milk metabolomics indicated that the HS triggered skeletal muscle mobilization and enhanced AA catabolism. Dietary supply of vitamin E and Se above requirements seemed to have modulated the skeletal muscle mobilization, while D3 and Ca did not show significant effects (experiment 2). The results of experiment 3 suggested that the partial amelioration of HS effects on productive and physiological parameters through high dietary supply of Met (+70 %), Lys (+65 %) and His (+21 %) were mediated by a recovery of phosphatidylcholines and decreased oxidation of Val, Trp and Leu due to enhanced one-carbon metabolism and Lys oxidation, respectively.

Molecular Basis of Cerebral Vasospasm: What Can We Learn from Transcriptome and Temporal Gene Expression Profiling in Intracranial Aneurysm?

Cerebral vasospasm (CV) is a significant complication following aneurysmal subarachnoid hemorrhage (aSAH), and lacks a comprehensive molecular understanding. Given the temporal trajectory of intracranial aneurysm (IA) formation, its rupture, and development of CV, altered gene expression might be a molecular substrate that runs through these clinical events, influencing both disease inception and progression. Utilizing RNA-Seq, we analyzed tissue samples from ruptured IAs with and without vasospasm to identify the dysregulated genes. In addition, temporal gene expression analysis was conducted. We identified seven dysregulated genes in patients with ruptured IA with vasospasm when compared with those without vasospasm. We found 192 common genes when the samples of each clinical subset of patients with IA, that is, unruptured aneurysm, ruptured aneurysm without vasospasm, and ruptured aneurysm with vasospasm, were compared with control samples. Among these common genes, TNFSF13B, PLAUR, OSM, and LAMB3 displayed temporal expression (progressive increase) with the pathological progression of disease that is formation of aneurysm, its rupture, and consequently the development of vasospasm. We validated the temporal gene expression pattern of OSM at both the transcript and protein levels and OSM emerges as a crucial gene implicated in the pathological progression of disease. In addition, RSAD2 and ATP1A2 appear to be pivotal genes for CV development. To the best of our knowledge, this is the first study to compare the transcriptome of aneurysmal tissue samples of aSAH patients with and without CV. The findings collectively provide new insights on the molecular basis of IA and CV and new leads for translational research.

Influence of metallic particles and TNF on the transcriptional regulation of NLRP3 inflammasome-associated genes in human osteoblasts.

The release of mature interleukin (IL-) 1β from osteoblasts in response to danger signals is tightly regulated by the nucleotide-binding oligomerization domain leucine-rich repeat and pyrin-containing protein 3 (NLRP3) inflammasome. These danger signals include wear products resulting from aseptic loosening of joint arthroplasty. However, inflammasome activation requires two different signals: a nuclear factor-kappa B (NF-κB)-activating priming signal and an actual inflammasome-activating signal. Since human osteoblasts react to wear particles via Toll-like receptors (TLR), particles may represent an inflammasome activator that can induce both signals. Temporal gene expression profiles of TLRs and associated intracellular signaling pathways were determined to investigate the period when human osteoblasts take up metallic wear particles after initial contact and initiate a molecular response. For this purpose, human osteoblasts were treated with metallic particles derived from cobalt-chromium alloy (CoCr), lipopolysaccharides (LPS), and tumor necrosis factor-alpha (TNF) alone or in combination for incubation times ranging from one hour to three days. Shortly after adding the particles, their uptake was observed by the change in cell morphology and spectral data. Exposure of osteoblasts to particles alone increased NLRP3 inflammasome-associated genes. The response was not significantly enhanced when cells were treated with CoCr + LPS or CoCr + TNF, whereas inflammation markers were induced. Despite an increase in genes related to the NLRP3 inflammasome, the release of IL-1β was unaffected after contact with CoCr particles. Although CoCr particles affect the expression of NLRP3 inflammasome-associated genes, a single stimulus was not sufficient to prime and activate the inflammasome. TNF was able to prime the NLRP3 inflammasome of human osteoblasts.

Single dose human perinatal stem cells accelerate healing of cold-induced rat burn wound.

Temporal phases of wound healing and their corresponding healing factors are essential in wound regeneration. Mesenchymal stem cells (MSCs)accelerate wound healing via their paracrine secretions by enhancing cell migration, angiogenesis, and reducing inflammation. This study evaluated the local therapeutic effect of human umbilical cord MSCs (hUCMSCs)in the healing of cold-induced burn wounds. An in vitro wound (scratch) was developed in rat skin fibroblasts. The culture was maintained in the conditioned medium (CM)which was prepared by inducing an artificial wound in hUCMSCs in a separate experiment. Treated fibroblasts were analyzed for the gene expression profile of healing mediators involved in wound closure. Findings revealed enhanced cell migration and increased levels of healing mediators in the treated fibroblasts relative to the untreated group. Cold-induced burn wounds were developed in Wistar rats, followed by a single injection of hUCMSCs. Wound healing pattern was examined based on the healing phases: hemostasis/inflammation (Days 1, 3), cell proliferation (Day 7), and remodeling (Day 14). Findings exhibited enhanced wound closure in the treated wound. Gene expression, histological, and immunohistochemical analyses further confirmed enhanced wound regeneration after hUCMSC transplantation. Temporal gene expression profile revealed that the level of corresponding cytokines was substantially increased in the treated wound as compared with the control, indicating improvement in the processes of angiogenesis and remodeling, and a substantial reduction in inflammation. Histology revealed significant collagen formation along with regenerated skin layers and appendages, whereas immunohistochemistry exhibited increased neovascularization during remodeling. Leukocyte infiltration was also suppressed in the treated group. Overall findings demonstrate that a single dose of hUCMSCs enhances wound healing in vivo, and their secreted growth factors accelerate cell migration in vitro.

Temporal gene expression profiling during early-stage traumatic temporomandibular joint bony ankylosis in a sheep model

BackgroundInvestigating the molecular biology underpinning the early-stage of traumatic temporomandibular joint (TMJ) ankylosis is crucial for discovering new ways to prevent the disease. This study aimed to explore the dynamic changes of transcriptome from the intra-articular hematoma or the newly generated ankylosed callus during the onset and early progression of TMJ ankylosis.MethodsBased on a well-established sheep model of TMJ bony ankylosis, the genome-wide microarray data were obtained from samples at postoperative Days 1, 4, 7, 9, 11, 14 and 28, with intra-articular hematoma at Day 1 serving as controls. Fold changes in gene expression values were measured, and genes were identified via clustering based on time series analysis and further categorised into three major temporal classes: increased, variable and decreased expression groups. The genes in these three temporal groups were further analysed to reveal pathways and establish their biological significance.ResultsOsteoblastic and angiogenetic genes were found to be significantly expressed in the increased expression group. Genes linked to inflammation and osteoclasts were found in the decreased expression group. The various biological processes and pathways related to each temporal expression group were identified, and the increased expression group comprised genes exclusively involved in the following pathways: Hippo signaling pathway, Wnt signaling pathway and Rap 1 signaling pathway. The decreased expression group comprised genes exclusively involved in immune-related pathways and osteoclast differentiation. The variable expression group consisted of genes associated with DNA replication, DNA repair and DNA recombination. Significant biological pathways and transcription factors expressed at each time point postoperatively were also identified.ConclusionsThese data, for the first time, presented the temporal gene expression profiling and reveal the important process of molecular biology in the early-stage of traumatic TMJ bony ankylosis. The findings might contributed to identifying potential targets for the treatment of TMJ ankylosis.

Convergent and divergent genes expression profiles associated with brain-wide functional connectome dysfunction in deficit and non-deficit schizophrenia.

Deficit schizophrenia (DS) is a subtype of schizophrenia characterized by the primary and persistent negative symptoms. Previous studies have identified differences in brain functions between DS and non-deficit schizophrenia (NDS) patients. However, the genetic regulation features underlying these abnormal changes are still unknown. This study aimed to detect the altered patterns of functional connectivity (FC) in DS and NDS and investigate the gene expression profiles underlying these abnormal FC. The study recruited 82 DS patients, 96 NDS patients, and 124 healthy controls (CN). Voxel-based unbiased brain-wide association study was performed to reveal altered patterns of FC in DS and NDS patients. Machine learning techniques were used to access the utility of altered FC for diseases diagnosis. Weighted gene co-expression network analysis (WGCNA) was employed to explore the associations between altered FC and gene expression of 6 donated brains. Enrichment analysis was conducted to identify the genetic profiles, and the spatio-temporal expression patterns of the key genes were further explored. Comparing to CN, 23 and 20 brain regions with altered FC were identified in DS and NDS patients. The altered FC among these regions showed significant correlations with the SDS scores and exhibited high efficiency in disease classification. WGCNA revealed associations between DS/NDS-related gene expression and altered FC. Additionally, 22 overlapped genes, including 12 positive regulation genes and 10 negative regulation genes, were found between NDS and DS. Enrichment analyses demonstrated relationships between identified genes and significant pathways related to cellular response, neuro regulation, receptor binding, and channel activity. Spatial and temporal gene expression profiles of SCN1B showed the lowest expression at the initiation of embryonic development, while DPYSL3 exhibited rapid increased in the fetal. The present study revealed different altered patterns of FC in DS and NDS patients and highlighted the potential value of FC in disease classification. The associations between gene expression and neuroimaging provided insights into specific and common genetic regulation underlying these brain functional changes in DS and NDS, suggesting a potential genetic-imaging pathogenesis of schizophrenia.

Circadian Clock Genes Are Regulated by Rhythmic Corticosterone at Physiological Levels in the Rat Hippocampus

Plain Language SummaryAll mammals, including humans, have an internal 24 h biological clock enabling us to synchronize and optimize our physiology to daily life. The 24 h circadian clock of body is localized in neurons of the suprachiasmatic nucleus (SCN) located in the hypothalamus of the brain and is characterized by rhythmic activity of special clock genes. Circadian 24 h rhythms are present throughout the brain, including the hippocampus, where clock genes seem to be important for memory and mood. However, the signaling mechanism controlling circadian clock gene rhythms in the hippocampus is unknown. We hypothesized that oscillations of clock genes in the hippocampus could be driven by a well-established SCN-controlled circadian rhythm in glucocorticoid hormones from the adrenal glands, known as stress hormone or cortisol in humans and corticosterone in rodents. To test this hypothesis, we generated a rat surgical animal model, in which the SCN and adrenal glands were removed and a 24 h exogenous corticosterone rhythm at normal physiological levels was reestablished by use of an implanted programmable infusion pump. Removal of the SCN efficiently abolished clock gene rhythms in the hippocampus; however, reintroducing the natural glucocorticoid rhythm led to reestablishment of 24 h activity rhythms in hippocampal clock genes. Thus, our data suggest that rhythmic hormone release from the adrenal glands drives hippocampal clock gene rhythms and therefore provides a dynamic 24 h hormonal link between the circadian clock of the SCN and circadian function of the hippocampus.

Integrated whole-genome gene expression analysis reveals an atlas of dynamic immune landscapes after myocardial infarction.

Myocardial infarction (MI) is a deadly medical condition leading to irreversible damage to the inflicted cardiac tissue. Elevated inflammatory response marks the severity of MI and is associated with the development of heart failure (HF), a long-term adverse outcome of MI. However, the efficacy of anti-inflammatory therapies for MI remains controversial. Deciphering the dynamic transcriptional signatures in peripheral blood mononuclear cells (PBMCs) is a viable and translatable route to better understand post-MI inflammation, which may help guide post-MI anti-inflammatory treatments. In this work, integrated whole-genome gene expression analysis was performed to explore dynamic immune landscapes associated with MI. GSEA and GSVA showed that pathways involved in the inflammatory response and metabolic reprogramming were significantly enriched in PBMCs from MI patients. Based on leukocyte profiles generated by xCell algorithm, the relative abundance of monocytes and neutrophils was significantly increased in PBMCs from MI patients and had positive correlations with typical inflammation-associated transcripts. Mfuzz clustering revealed temporal gene expression profiles of PBMCs during the 6-month post-MI follow-up. Analysis of DEGs and gene sets indicated that PBMCs from HF group were characterized by elevated and lasting expression of genes implicated in inflammation and coagulation. Consensus clustering generated 4 metabolic subtypes of PBMCs with molecular heterogeneity in HF patients. In summary, integrated whole-genome gene expression analysis here outlines a transcriptomic framework that may improve the understanding of dynamic signatures present in PBMCs, as well as the heterogeneity of PBMCs in MI patients with or without long-term clinical outcome of HF. Moreover, the work here uncovers the diversity and heterogeneity of PBMCs from HF patients, providing novel bioinformatic evidence supporting the mechanistic implications of metabolic reprogramming and mitochondrial dysfunction in the post-MI inflammation and HF. Therefore, our work here supports the notion that individualized anti-inflammatory therapies are needed to improve the clinical management of post-MI patients.

Temporal and Spatial Gene Expression Profile of Stroke Recovery Genes in Mice.

Stroke patients show some degree of spontaneous functional recovery, but this is not sufficient to prevent long-term disability. One promising approach is to characterize the dynamics of stroke recovery genes in the lesion and distant areas. We induced sensorimotor cortex lesions in adult C57BL/6J mice using photothrombosis and performed qPCR on selected brain areas at 14, 28, and 56 days post-stroke (P14-56). Based on the grid walk and rotating beam test, the mice were classified into two groups. The expression of cAMP pathway genes Adora2a, Pde10a, and Drd2, was higher in poor- compared to well-recovered mice in contralesional primary motor cortex (cl-MOp) at P14&56 and cl-thalamus (cl-TH), but lower in cl-striatum (cl-Str) at P14 and cl-primary somatosensory cortex (cl-SSp) at P28. Plasticity and axonal sprouting genes, Lingo1 and BDNF, were decreased in cl-MOp at P14 and cl-Str at P28 and increased in cl-SSp at P28 and cl-Str at P14, respectively. In the cl-TH, Lingo1 was increased, and BDNF decreased at P14. Atrx, also involved in axonal sprouting, was only increased in poor-recovered mice in cl-MOp at P28. The results underline the gene expression dynamics and spatial variability and challenge existing theories of restricted neural plasticity.

Identification of novel anti-ZIKV drugs from viral-infection temporal gene expression profiles

ABSTRACT Zika virus (ZIKV) infections are typically asymptomatic but cause severe neurological complications (e.g. Guillain–Barré syndrome in adults, and microcephaly in newborns). There are currently no specific therapy or vaccine options available to prevent ZIKV infections. Temporal gene expression profiles of ZIKV-infected human brain microvascular endothelial cells (HBMECs) were used in this study to identify genes essential for viral replication. These genes were then used to identify novel anti-ZIKV agents and validated in publicly available data and functional wet-lab experiments. Here, we found that ZIKV effectively evaded activation of immune response-related genes and completely reprogrammed cellular transcriptional architectures. Knockdown of genes, which gradually upregulated during viral infection but showed distinct expression patterns between ZIKV- and mock infection, discovered novel proviral and antiviral factors. One-third of the 74 drugs found through signature-based drug repositioning and cross-reference with the Drug Gene Interaction Database (DGIdb) were known anti-ZIKV agents. In cellular assays, two promising antiviral candidates (Luminespib/NVP-AUY922, L-161982) were found to reduce viral replication without causing cell toxicity. Overall, our time-series transcriptome-based methods offer a novel and feasible strategy for antiviral drug discovery. Our strategies, which combine conventional and data-driven analysis, can be extended for other pathogens causing pandemics in the future.

Genome-wide association study of 23 flowering phenology traits and 4 floral agronomic traits in tree peony (Paeonia section Moutan DC.) reveals five genes known to regulate flowering time.

Tree peony is a unique traditional flower in China, with large, fragrant, and colorful flowers. However, a relatively short and concentrated flowering period limits the applications and production of tree peony. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of flowering phenology traits and ornamental phenotypes in tree peony. A diverse panel of 451 tree peony accessions was phenotyped for 23 flowering phenology traits and 4 floral agronomic traits over 3 years. Genotyping by sequencing (GBS) was used to obtain a large number of genome-wide single-nucleotide polymorphisms (SNPs) (107 050) for the panel genotypes, and 1047 candidate genes were identified by association mapping. Eighty-two related genes were observed during at least 2 years for flowering, and seven SNPs repeatedly identified for multiple flowering phenology traits over multiple years were highly significantly associated with five genes known to regulate flowering time. We validated the temporal expression profiles of these candidate genes and highlighted their possible roles in the regulation of flower bud differentiation and flowering time in tree peony. This study shows that GWAS based on GBS can be used to identify the genetic determinants of complex traits in tree peony. The results expand our understanding of flowering time control in perennial woody plants. Identification of markers closely related to these flowering phenology traits can be used in tree peony breeding programs for important agronomic traits.

TEDD: a database of temporal gene expression patterns during multiple developmental periods in human and model organisms.

Characterization of the specific expression and chromatin profiles of genes enables understanding how they contribute to tissue/organ development and the mechanisms leading to diseases. Whilst the number of single-cell sequencing studies is increasing dramatically; however, data mining and reanalysis remains challenging. Herein, we systematically curated the up-to-date and most comprehensive datasets of sequencing data originating from 2760 bulk samples and over 5.1 million single-cells from multiple developmental periods from humans and multiple model organisms. With unified and systematic analysis, we profiled the gene expression and chromatin accessibility among 481 cell-types, 79 tissue-types and 92 timepoints, and pinpointed cells with the co-expression of target genes. We also enabled the detection of gene(s) with a temporal and cell-type specific expression profile that is similar to or distinct from that of a target gene. Additionally, we illustrated the potential upstream and downstream gene-gene regulation interactions, particularly under the same biological process(es) or KEGG pathway(s). Thus, TEDD (Temporal Expression during Development Database), a value-added database with a user-friendly interface, not only enables researchers to identify cell-type/tissue-type specific and temporal gene expression and chromatin profiles but also facilitates the association of genes with undefined biological functions in development and diseases. The database URL is https://TEDD.obg.cuhk.edu.hk/.

Acute hypoxia changes the gene expression profiles and alternative splicing landscape in gills of spotted sea bass (Lateolabrax maculatus)

Hypoxia is one of the most important environmental stressors in aquatic ecosystems. To deal with the hypoxia environment, fishes exhibit a series of physiological and molecular responses to maintain homeostasis and organism functions. In the present study, hypoxia-induced changes in gene expression profiles and alternative splicing (AS) events in spotted sea bass (Lateolabrax maculatus), a promising marine-culture fish species in China, were thoroughly investigated by RNA-Seq analysis. A total of 1,242, 1,487 and 1,762 differentially expressed genes (DEGs) were identified at 3 h, 6 h and 12 h in gills after hypoxia stress. Functional enrichment analysis by KEGG and GSEA demonstrated that HIF signal network system was significantly activated and cell cycle process was remarkably suppressed in response to hypoxia. According to the temporal gene expression profiles, six clusters were generated and protein-protein interaction (PPI) networks were constructed for the two clusters that enriched with hypoxia-induced (cluster 2) or -suppressed genes (cluster 5), respectively. Results showed that HIF signaling related genes including vegfa, igf1, edn1, cox2b, cxcr4b, ctnnb1, and slc2a1a, were recognized as hubs in cluster 2, while mcm2, chek1, pole, mcm5, pola1, and rfc4, that tightly related to cell cycle, were down-regulated and considered as hubs in cluster 5. Furthermore, a total of 410 differential alternative splicing (DAS) genes were identified after hypoxia, which were closely associated with spliceosome. Of them, 63 DAS genes also showed differentially expressed levels after hypoxia, suggesting that their expression changes might be regulated by AS mechanism. This study revealed the key biological pathways and AS events affected by hypoxia, which would help us to better understand the molecular mechanisms of hypoxia response in spotted sea bass and other fish species.

Glucocorticoid Induces Atrial Arrhythmogenesis via Modification of Ion Channel Gene Expression in Rats.

Excess psychological stress is one of the precipitating factors for paroxysmal atrial fibrillation (AF), although the involved mechanisms are still uncertain. To test a hypothesis that one of the stress-induced hormones, glucocorticoid, is involved in the pathogenesis of stress-induced AF, we investigated whether the glucocorticoid could alter the temporal profile of cardiac ion channels gene expression, thereby leading to atrial arrhythmogenesis.Dexamethasone (DEX, 1.0 mg/kg) was injected subcutaneously in Sprague-Dawley rats. At predetermined times after DEX injection (0, 1, 3, 6, 12, and 24 hours), the mRNA levels of cardiac ion channel genes (erg, KvLQT1, Kv4.3, Kv4.2, Kv2.1, Kv1.5, Kv1.4, Kv1.2, SUR2A, Kir6.2, Kir3.4, Kir3.1 Kir2.2, Kir2.1, SCN5A, and α1C) were determined using RNase protection assay. DEX induced immediate and transient increase in the mRNA level of Kv1.5 and Kir2.2 with peaks at 6 (5.0 fold) and 3 hours (3.3 fold) after DEX injection, respectively. Patch-clamp studies revealed a significantly increased current density of the corresponding current, IKur and IK1 at 6 hours after DEX injection. Simultaneously, electrophysiological study in isolated perfused hearts showed significantly increased number of repetitive atrial responses induced by single atrial extrastimulus (3.2 ± 2.4 to 26.7 ± 16.4, P = 0.004) with shorting of the refractory period (36.4 ± 4.6 to 27.4 ± 5.5 ms, P = 0.049) after DEX injection.Glucocorticoid immediately modified Kv1.5 and Kir2.2 gene expression at pretranslational levels, thus leading to effective refractory period shortening that could be arrhythmogenic. These results implied that transient glucocorticoid-induced biochemical modification of cardiac ion channels might be one of the mechanisms underlying the stress-induced paroxysmal AF.

Influence of water hardness on zinc toxicity in Daphnia magna.

Zinc is an essential trace metal required for the maintenance of multiple physiological functions. Due to this, organisms can experience both zinc deficiency and toxicity. Hardness is recognized as one of the main modifying physiochemical factors regulating zinc bioavailability. Therefore, the present study analyzed the effect of hardness on zinc toxicity using Daphnia magna . Endpoint parameters were acute‐toxicity, development, reproduction, and expression data for genes involved in metal regulation and oxidative stress. In addition, the temporal expression profiles of genes during the initiation of reproduction and molting were investigated. Water hardness influenced the survival in response to exposures to zinc. A zinc concentration of 50 μg/l in soft water (50 mg CaCO3/L) caused 73% mortality after 96 h exposure, whereas the same zinc concentration in the hardest water did not cause any significant mortality. Moreover, increasing water hardness from 100 to 200 mg CaCO3/L resulted in a reduced number of offspring. Fecundity was higher at first brood for groups exposed to higher Zn concentrations. The survival data were used to assess the precision of the bioavailability models (Bio‐met) and the geochemical model (Visual MINTEQ). As the Bio‐met risk predictions overestimated the Zn toxicity, a competition‐based model to describe the effects of hardness on zinc toxicity is proposed. This approach can be used to minimize differences in setting environmental quality standards. Moreover, gene expression data showed that using the toxicogenomic approach was more sensitive than the physiological endpoints. Therefore, data presented in the study can be used to improve risk assessment for zinc toxicity.

An Optimal Boolean Approach for Computational Modeling of Gene Regulatory Networks from Temporal Gene Expression Profile

Deciphering the crucial interactions among genes is one of the key issues in understanding the fundamental molecular and intracellular mechanisms of cell. Computational modeling of gene regulatory networks can be used as a powerful tool in various fields of molecular biomedicine such as identification of metabolic, regulator, and signal transduction pathways, analysis of complex genetic diseases, and drug discovery. In this paper, an optimal Boolean approach was proposed for computational modeling of gene regulatory networks from temporal gene expression profile. In this method, the optimal values of the Boolean thresholds of gene expression signals and the parameters of the interaction patterns between target and regulator genes are all designed as a mixed-integer nonlinear programming solved by Genetic Algorithm. To evaluate the performance of the proposed scheme, it has been applied to a well-known time course microarray data and gene regulatory network of Saccharomyces cerevisiae from the literature. The reference network has 11 genes, 9 targets, and 61 regulatory interactions, and the original transcriptional dataset includes 18 time points for each gene expression signal. In this case study, the proposed computational model contains 142 unknown parameters that are optimally determined through optimization. The results demonstrate the efficiency of the proposed approach.

Radiochemical In Situ Hybridization in Developmental Studies of the Pineal Gland.

Radiochemical in situ hybridization enables detection of gene expression in small areas of the brain, such as the developing pineal gland in rodents. The method combines determination of spatial and temporal gene expression profiles with semiquantitative analyses. We here describe the procedure of radiochemical in situ hybridization on the developing rat pineal gland ranging from preparation of fetal tissue for in situ hybridization to principles of quantification.

Lignin biosynthesis and accumulation in response to abiotic stresses in woody plants.

Woody plants have to experience various abiotic stresses due to their immobility and perennial characteristics. However, woody plants have evolved a series of specific regulation pathways in physiological and molecular mechanisms to deal with adverse environments. Compared with herbaceous plants, perennial woody plants have the advantages of developed roots and hard stems, and increased secondary xylem, which can strengthen the vascular system of the plants. The lignification process involves the lignin deposition on the cell wall by oxidation and polymerization of lignin monomer, which plays an important role in abiotic stress tolerance. This review focuses on recent progress in the biosynthesis, content, and accumulation of lignin in response to various abiotic stresses in plants. The role of transcription factors is also discussed in regulating lignin biosynthesis to enhance abiotic stress tolerance via changing cell wall lignification. Although woody plants shared similar lignin biosynthesis mechanisms with herbaceous plants, the temporal and spatial expression and stress response profiles of lignin biosynthetic genes provide the basis for the differences in stress tolerance of various species. An in-depth understanding of the role of lignin in the abiotic stress tolerance of woody plants will lay the foundation for the next step in tree resistance breeding through genetic engineering.