Structural Molecule Activity Research Articles

Quantitative Proteomic Profiling of Renal Tissue in Human Chronic Rejection Biopsy Samples After Renal Transplantation

IntroductionChronic rejection (CR) is the leading cause of late renal transplant failure and is characterized by a relatively slow but progressive loss of renal function in combination with proteinuria and hypertension >3 months after transplantation. To identify and quantify the protein profiles in renal tissues of CR patients, we used isotope tagging for relative and absolute quantification (iTRAQ)-based proteomic technology to perform global protein expression analyses in CR patients and control subjects. Materials and MethodsAfter protein extraction, quantitation, and digestion, samples were labeled with iTRAQ reagents and then separated by strong cation exchange and high-performance liquid chromatography. The fractions were further analyzed by tandem mass spectrometry. ProteinPilot version 4.0 software and the Swiss-Prot human database were applied for statistical analysis and database searching, respectively. Differentially expressed proteins were subjected to bioinformatic analysis by using the Gene Ontology database and the Kyoto Encyclopedia of Genes and Genomes database to further characterize their potential functional roles and related pathways in CR. ResultsIn total, 1857 distinct proteins (confidence >95%, ρ < .05) were identified and quantified. Using a strict cutoff value of 1.5-fold for expressed variation, 87 proteins showed significant differences in expression between the CR and control groups; 53 were up-regulated and 34 were down-regulated. The differentially expressed proteins were mainly involved in protein binding, structural molecule activity, and extracellular matrix structural constituent. Several proteins, such as the alpha-1 chain of collagen type IV and integrin alpha-1, may play roles in the pathogenesis of CR and were implicated in the extracellular matrix–receptor interaction pathway. ConclusionsThis study is the first to focus on iTRAQ-based quantitative proteomic characterization of renal tissue in CR. These insights may broaden our understanding of the molecular mechanisms underlying CR and provide potential biomarker candidates for future diagnostics.

The regulatory network of ThbZIP1 in response to abscisic acid treatment.

Previously, a bZIP transcription factor from Tamarix hispida, ThbZIP1, was characterized: plants overexpressing ThbZIP1 displayed improved salt stress tolerance but were sensitive to abscisic acid (ABA). In the current study, we further characterized the regulatory network of ThbZIP1 and the mechanism of ABA sensitivity mediated by ThbZIP1. An ABF transcription factor from T. hispida, ThABF1, directly regulates the expression of ThbZIP1. Microarray analysis identified 1662 and 1609 genes that were respectively significantly upregulated or downregulated by ThbZIP1 when exposed to ABA. Gene ontology (GO) analysis showed that the processes including “response to stimulus,” “catalytic activity,” “binding function,” and “metabolic process” were highly altered in ThbZIP1 expressing plants exposed to ABA. The gene expression in ThbZIP1 transformed plants were compared between exposed to ABA and salt on the genome scale. Genes differentially regulated by both salt and ABA treatment only accounted for 9.75% of total differentially regulated genes. GO analysis showed that structural molecule activity, organelle part, membrane-enclosed lumen, reproduction, and reproductive process are enhanced by ABA but inhibited by salt stress. Conversely, immune system and multi-organism process were improved by salt but inhibited by ABA. Transcription regulator activity, enzyme regulator activity, and developmental process were significantly altered by ABA but were not affected by salt stress. Our study provides insights into how ThbZIP1 mediates ABA and salt stress response at the molecular level.

Gene profiling of bone around orthodontic mini-implants by RNA-sequencing analysis.

This study aimed to evaluate the genes that were expressed in the healing bones around SLA-treated titanium orthodontic mini-implants in a beagle at early (1-week) and late (4-week) stages with RNA-sequencing (RNA-Seq). Samples from sites of surgical defects were used as controls. Total RNA was extracted from the tissue around the implants, and an RNA-Seq analysis was performed with Illumina TruSeq. In the 1-week group, genes in the gene ontology (GO) categories of cell growth and the extracellular matrix (ECM) were upregulated, while genes in the categories of the oxidation-reduction process, intermediate filaments, and structural molecule activity were downregulated. In the 4-week group, the genes upregulated included ECM binding, stem cell fate specification, and intramembranous ossification, while genes in the oxidation-reduction process category were downregulated. GO analysis revealed an upregulation of genes that were related to significant mechanisms, including those with roles in cell proliferation, the ECM, growth factors, and osteogenic-related pathways, which are associated with bone formation. From these results, implant-induced bone formation progressed considerably during the times examined in this study. The upregulation or downregulation of selected genes was confirmed with real-time reverse transcription polymerase chain reaction. The RNA-Seq strategy was useful for defining the biological responses to orthodontic mini-implants and identifying the specific genetic networks for targeted evaluations of successful peri-implant bone remodeling.

Temporal transcriptome changes induced by methyl jasmonate in Salvia sclarea

Salvia sclarea is a traditional medicinal and aromatic plant that grows in Europe and produces various economically important compounds, including phenylpropanoid derivatives and terpenoids. Methyl jasmonate (MeJA) is commonly used to elicit plant stress responses. However, how MeJA enhances production of secondary metabolites in S. sclarea is not well understood. We performed a genome-wide analysis of temporal gene expression in S. sclarea leaves and roots. The transcriptome profiles 0, 10 and 26h after MeJA treatment were analyzed by Illumina RNA-Seq. A total of 16,142 isogenes (average length 866bp; N50 1035bp) were obtained by de novo assembly of 35,757,567 raw sequencing reads. When these sequencing reads were mapped onto the assembled Unigenes, 3236, 2792 and 798 Unigenes were found to be expressed differentially between 0 and 10h, 0 and 26h, and 10 and 26h, respectively. These included many secondary metabolite biosynthesis, stress and defense-related genes. A qRT-PCR analysis confirmed the expression profiles of selected differentially expressed genes (DEGs) revealed by RNA-Seq data, and also extended our analysis of differential gene expression to 73h. Our investigations revealed temporal differences in the responses of S. sclarea to MeJA treatment. MeJA treatment induced the expression of a large number of genes involved in phenylpropanoid biosynthesis, especially between 0 and 10h, and 0 and 26h. Additionally, many genes encoding transcription factors, cytochrome P450s, glycosyltransferases, methyltransferases and transporters were shown to respond to MeJA elicitation. DEGs related to structural molecule activity and cell death showed a significant temporal variation. A chromatographic analysis of metabolites at 26h, 73h and six days after MeJA treatment indicated that these transcriptomic changes precede MeJA-induced changes in secondary metabolite content. This study sheds light on the molecular mechanisms of MeJA elicitation and is helpful in understanding how exogenous MeJA treatment mediates extensive plant transcriptome reprogramming/remodeling. Our results can be utilized to characterize genes related to secondary metabolism and their regulation, and in breeding S. sclarea for desirable chemotypes.

Heterosis in early maize ear inflorescence development: a genome-wide transcription analysis for two maize inbred lines and their hybrid.

Heterosis, or hybrid vigor, contributes to superior agronomic performance of hybrids compared to their inbred parents. Despite its importance, little is known about the genetic and molecular basis of heterosis. Early maize ear inflorescences formation affects grain yield, and are thus an excellent model for molecular mechanisms involved in heterosis. To determine the parental contributions and their regulation during maize ear-development-genesis, we analyzed genome-wide digital gene expression profiles in two maize elite inbred lines (B73 and Mo17) and their F1 hybrid using deep sequencing technology. Our analysis revealed 17,128 genes expressed in these three genotypes and 22,789 genes expressed collectively in the present study. Approximately 38% of the genes were differentially expressed in early maize ear inflorescences from heterotic cross, including many transcription factor genes and some presence/absence variations (PAVs) genes, and exhibited multiple modes of gene action. These different genes showing differential expression patterns were mainly enriched in five cellular component categories (organelle, cell, cell part, organelle part and macromolecular complex), five molecular function categories (structural molecule activity, binding, transporter activity, nucleic acid binding transcription factor activity and catalytic activity), and eight biological process categories (cellular process, metabolic process, biological regulation, regulation of biological process, establishment of localization, cellular component organization or biogenesis, response to stimulus and localization). Additionally, a significant number of genes were expressed in only one inbred line or absent in both inbred lines. Comparison of the differences of modes of gene action between previous studies and the present study revealed only a small number of different genes had the same modes of gene action in both maize seedlings and ear inflorescences. This might be an indication that in different tissues or developmental stages, different global expression patterns prevail, which might nevertheless be related to heterosis. Our results support the hypotheses that multiple molecular mechanisms (dominance and overdominance modes) contribute to heterosis.

Aberrant Expression of Long Noncoding RNAs in Early Diabetic Retinopathy

Long noncoding RNAs (lncRNAs) are broadly classified as transcripts longer than 200 nucleotides. lncRNA-mediated biology has been implicated in a variety of cellular processes and human diseases. Diabetic retinopathy (DR) is one of the leading causes of blindness. However, little is known about the role of lncRNAs in DR The goal of this study aimed to identify lncRNAs involved in early DR and characterize their roles in DR pathogenesis. We established a mouse model of streptozotocin (STZ)-induced diabetes, and performed lncRNA expression profiling of retinas using microarray analysis. Based on the Pearson correlation analysis, an lncRNA/mRNA coexpression network was constructed. Gene ontology (GO) enrichment and KEGG analysis of lncRNAs-coexpressed mRNAs was conducted to identify the related biological modules and pathologic pathways. Real-time PCR was conducted to detect the expression pattern of lncRNA in the clinical samples and the RF/6A cell model of hyperglycemia. Approximately 303 lncRNAs were aberrantly expressed in the retinas of early DR, including 214 downregulated lncRNAs and 89 upregulated lncRNAs. GO analysis indicated that these lncRNAs-coexpressed mRNAs were targeted to eye development process (ontology: biological process), integral to membrane (ontology: cellular component), and structural molecule activity (ontology: molecular function). Pathway analysis indicated that lncRNAs-coexpressed mRNAs were mostly enriched in axon guidance signaling pathway. In addition, MALAT1, a conserved lncRNA, was significantly upregulated in an RF/6A cell model of hyperglycemia, in the aqueous humor samples, and in fibrovascular membranes of diabetic patients. lncRNAs are involved in the pathogenesis of DR through the modulation of multiple pathogenetic pathways. MALAT1, a conserved lncRNA, may become a potential therapeutic target for the prognosis, diagnosis, and treatment of DR.

Bioinformatics and functional analysis of proteins in serum of early pregnant buffaloes

Bioinformatics using different web based resources was done to classify 2–D gel resolved novel/ up- or down- regulated proteins (n=48) detected in serum of early pregnant buffaloes and find out interactions among them. Proteins were searched for their gene symbols on the ExPASy and the NCBI web portals and then PANTHER software was used to classify them. These proteins were primarily involved in regulatory, catalytic, immune regulation, cell differentiation and transporter functions. Among molecular functions, majority of proteins was involved in either catalytic or binding activities (29.5% each); receptor activity (13.6%), transporter activity (9.1%), enzyme regulator (6.8%) and structural molecule activity (6.8%) besides ion-channel and antioxidant activities. Based on biological functions, maximum (17.6%) proteins were found involved in metabolic function, followed by cellular processes (15.7%). Almost 10.8% proteins were involved in cell communications and 9.8% in transport functions, the rest were involved in immune and developmental processes. To these proteins 23 pathways were assigned, most predominantly Wnt signalling, inflammation - mediated by chemokine and cytokine signalling, and blood coagulation pathways. Other proteins were involved in as many as 20 pathways. A single layer extension to make connections for preparing protein-protein interaction map and network analysis of these bovine proteins, revealed that 9 of these proteins were interacting with each other in 6 different ways - interactions affecting molecular transportation, level of expression, regulation of expression, binding of proteins, interactions resulting in direct regulation and direct regulation inhibition and those leading to modification of the proteins. These findings suggested that the proteins identified with up-regulation, down-regulation or specific appearance at a particular stage during early buffalo pregnancy, primarily act interdependently in the functions involving cellular growth and differentiation.

Generation and Analysis of Expressed Sequence Tags (ESTs) from Muscle Full-Length cDNA Library of Wujin Pig

Porcine skeletal muscle genes play a major role in determining muscle growth and meat quality. Construction of a full-length cDNA library is an effective way to understand the expression of functional genes in muscle tissues. In addition, novel genes for further research could be identified in the library. In this study, we constructed a full-length cDNA library from porcine muscle tissue. The estimated average size of the cDNA inserts was 1 076 bp, and the cDNA fullness ratio was 86.2%. A total of 1 058 unique sequences with 342 contigs (32.3%) and 716 singleton (67.7%) expressed sequence tags (EST) were obtained by clustering and assembling. Meanwhile, 826 (78.1%) ESTs were categorized as known genes, and 232 (21.9%) ESTs were categorized as unknown genes. 65 novel porcine genes that exhibit no identity in the TIGR gene index of Sus scrofa and 124 full-length sequences with unknown functions were deposited in the dbEST division of GenBank (accession numbers: EU650784-EU650788, GE843306, GH228978-GH229100). The abundantly expressed genes in porcine muscle tissue were related to muscle fiber development, energy metabolism and protein synthesis. Gene ontology analysis showed that sequences expressed in porcine muscle tissue contained a high percentage of binding activity, catalytic activity, structural molecule activity and motor activity, which involved mainly in metabolic, cellular and developmental process, distributed mainly in intracellular region. The sequence data generated in this study would provide valuable information for identifying porcine genes expressed in muscle tissue and help to advance the study on the structure and function of genes in pigs.

Microarray gene expression analysis of Monochamus alternatus (Coleoptera: Cerambycidae) after treatment with a sublethal dose of chloramine phosphorus

Monochamus alternatus Hope (Coleoptera: cerambycidae), the Japanese pine sawyer beetle, is a serious pest management concern in pine stands. A new organophosphorus insecticide, chloramine phosphorus (CP), has been applied as an insecticide in China to control M. alternatus. In this study, we investigated gene expression changes in M. alternatus after 4 h of exposure to CP using a 60-mer oligonucleotide microarray. The results showed that 356 genes were differentially expressed, of which 76 were upregulated and 280 were downregulated. GO enrichment analysis of the differentially expressed genes indicated that those involved in structural molecule activity and transporter activity were among the most highly represented. Within the cellular component category of GO, cell and cell part were the most represented GO terms in upregulated genes. “Cellular process” was the most represented GO term in the biological process category among the downregulated genes. Molecular pathway analysis showed that a large portion of the differentially expressed genes were associated with metabolic pathways. This study sought to identify new biomarkers as nonacetylcholinesterase targets to assess the secondary effects of CP on M. alternatus and will provide a valuable resource for the scientific community to study the molecular toxicology of CP.

Proteomic remodeling of proteasome in right heart failure

The development of right heart failure (RHF) is characterized by alterations of right ventricle (RV) structure and function, but the mechanisms of RHF remain still unknown. Thus, understanding the RHF is essential for improved therapies. Therefore, identification by quantitative proteomics of targets specific to RHF may have therapeutic benefits to identify novel potential therapeutic targets. The objective of this study was to analyze the molecular mechanisms changing RV function in the diseased RHF and thus, to identify novel potential therapeutic targets. For this, we have performed differential proteomic analysis of whole RV proteins using two experimental rat models of RHF. Differential protein expression was observed for hundred twenty six RV proteins including proteins involved in structural constituent of cytoskeleton, motor activity, structural molecule activity, cytoskeleton protein binding and microtubule binding. Interestingly, further analysis of down-regulated proteins, reveals that both protein and gene expressions of proteasome subunits were drastically decreased in RHF, which was accompanied by an increase of ubiquitinated proteins. Interestingly, the proteasomal activities chymotrypsin and caspase-like were decreased whereas trypsin-like activity was maintained. In conclusion, this study revealed the involvement of ubiquitin–proteasome system (UPS) in RHF. Three deregulated mechanisms were discovered: (1) decreased gene and protein expressions of proteasome subunits, (2) decreased specific activity of proteasome; and (3) a specific accumulation of ubiquitinated proteins. This modulation of UPS of RV may provide a novel therapeutic avenue for restoration of cardiac function in the diseased RHF.

Proteomic Profiling of Rabbit Embryonic Stem Cells Derived from Parthenotes and Fertilized Embryos

Rabbit embryonic stem (rES) cells can be derived from various sources of embryos. However, understanding of the gene expression profile, which distincts embryonic stem (ES) cells from other cell types, is still extremely limited. In this study, we compared the protein profiles of three independent lines of rabbit cells, i.e., fibroblasts, fertilized embryo-derived stem (f-rES) cells, and parthenote-derived ES (p-rES) cells. Proteomic analyses were performed using two-dimensional gel electrophoresis (2-DE) and mass spectrometry. Collectively, the expression levels of 100 out of 284 protein spots differed significantly among these three cell types (p<0.05). Of those differentially expressed spots, 91% were identified in the protein database and represented 63 distinct proteins. Proteins with known identities are mainly localized in the cytoplasmic compartments (48%), nucleus (14%), and cytoskeletal machineries (13%). These proteins were majorly involved in biological functions of energy and metabolic pathways (25%), cell growth and maintenance (25%), signal transduction (14%), and protein metabolisms (10%). When protein expression levels among cell types were compared, six proteins associated with a variety of cellular activities, including structural constituents of the cytoskeleton (tubulins), structural molecule (KRT8), catalytic molecules (α-enolase), receptor complex scaffold (14-3-3 protein sigma), microfilament motor proteins (Myosin-9), and heat shock protein (HSP60), were found highly expressed in p-rES cells. Two proteins related to HSP activity and structural constituent of cytoskeleton in f-rES cells, and one structural molecule activity protein in fibroblasts showed significantly higher expression levels (p<0.05). Marker protein expressions in f-rES and p-rES cells were further confirmed by Western blotting and immunocytochemical staining. This study demonstrated unique proteomic profiles of the three rabbit cell types and revealed some novel proteins differentially expressed between f-rES and p-rES cells. These analyses provide insights into rES cell biology and would invite more in-depth studies toward rES cell applications.

The alteration of protein profile induced by cigarette smoking via oxidative stress in mice epididymis

Smoking is associated with a declining quality of semen. The aim of this study was to screen and investigate the differential expression of proteins extracted from the epididymis of mice exposed daily with cigarette smoke. Using MALDI-TOF–MS analysis, we found that the protein profile of the mouse epididymis was altered by cigarette smoking and identified 27 proteins from the most abundant and differentially expressed spots in the 2-DE gels of epididymal samples. These proteins were classified into groups according to their functions such as energy metabolism, reproduction and structural molecule activity. Through pathway analysis, these proteins were associated with the glutathione metabolism and protein processing in the endoplasmic reticulum. These results showed that the epididymis may experience oxidative stress following cigarette smoke exposure, which was confirmed using immunohistochemistry. We determine that cigarette smoking can induce oxidative stress in the mouse epididymis, which may cause protein profile altering, thereby impairing epididymis function, and leading to a decline in semen quality.

Global gene analysis of oocytes from early stages in human folliculogenesis shows high expression of novel genes in reproduction

The pool of primordial follicles in humans is laid down during embryonic development and follicles can remain dormant for prolonged intervals, often decades, until individual follicles resume growth. The mechanisms that induce growth and maturation of primordial follicles are poorly understood but follicles once activated either continue growth or undergo atresia. We have isolated pure populations of oocytes from human primordial, intermediate and primary follicles using laser capture micro-dissection microscopy and evaluated the global gene expression profiles by whole-genome microarray analysis. The array data were confirmed by qPCR for selected genes. A total of 6301 unique genes were identified as significantly expressed representing enriched specific functional categories such as 'RNA binding', 'translation initiation' and 'structural molecule activity'. Several genes, some not previously known to be associated with early oocyte development, were identified with exceptionally high expression levels, such as the anti-proliferative transmembrane protein with an epidermal growth factor-like and two follistatin-like domains (TMEFF2), the Rho-GTPase-activating protein oligophrenin 1 (OPHN1) and the mitochondrial-encoded ATPase6 (ATP6). Thus, the present study provides not only a technique to capture and perform transcriptome analysis of the sparse material of human oocytes from the earliest follicle stages but further includes a comprehensive basis for our understanding of the regulatory factors and pathways present during early human folliculogenesis.

Non-Biased Enrichment Does Not Improve Quantitative Proteomic Delineation of Reovirus T3D-Infected HeLa Cell Protein Alterations

Mass spectrometry-based methods have allowed elucidation of alterations in complex proteomes, such as eukaryotic cells. Such studies have identified and measured relative abundances of thousands of host proteins after cells are infected with a virus. One of the potential limitations in such studies is that generally only the most abundant proteins are identified, leaving the deep richness of the cellular proteome largely unexplored. We differentially labeled HeLa cells with light and heavy stable isotopic forms of lysine and arginine and infected cells with reovirus strain T3D. Cells were harvested at 24 h post-infection. Heavy-labeled infected and light-labeled mock-infected cells were mixed together 1:1. Cells were then divided into cytosol and nuclear fractions and each fraction analyzed, both by standard 2D-HPLC/MS, and also after each fraction had been reacted with a random hexapeptide library (Proteominer® beads) to attempt to enrich for low-abundance cellular proteins. A total of 2,736 proteins were identified by two or more peptides at >99% confidence, of which 66 were significantly up-regulated and 67 were significantly down-regulated. Up-regulated proteins included those involved in antimicrobial and antiviral responses, GTPase activity, nucleotide binding, interferon signaling, and enzymes associated with energy generation. Down-regulated proteins included those involved in cell and biological adhesion, regulation of cell proliferation, structural molecule activity, and numerous molecular binding activities. Comparisons of the r2 correlations, degree of dataset overlap, and numbers of peptides detected suggest that non-biased enrichment approaches may not provide additional data to allow deeper quantitative and comparative mining of complex proteomes.

147 HYDROSTATIC PRESSURE STRESS TREATMENT OF MOUSE OOCYTES INFLUENCES PROTEIN SYNTHESIS AT THE 4-CELL STAGE

Sublethal stress treatment [namely hydrostatic pressure (HP)] has been reported to improve the cryotolerance and developmental competence of mammalian gametes and embryos at cryopreservation, in vitro maturation, parthenogenetic activation and somatic cell NT (Pribenszky and Vajta 2011 Reprod. Fertil. Dev. 23, 48–55). In our previous study mouse oocytes were HP stress treated and then vitrified, warmed, fertilized by intracytoplasmic sperm injection (ICSI), cultured and transferred. Blastocyst rate, inner cell mass cell number and birth rate were significantly increased in the treated groups (Pribenszky et al. 2010 Fertil. Steril. 94, S32). In our present study we implemented gene expression microarray experiments to analyse the transcriptome of HP-treated eggs and 4-cell stage embryos developed from these oocytes. At first, 4 pools of 50 mouse oocytes were treated with 20 MPa for 60 min at 37°C in a programmable HP machine (Cryo-Innovation Inc., Budapest, Hungary). Second, mouse oocytes were treated with HP likewise, fertilized by ICSI and cultured to 4-cell stage. The controls were handled identically with no HP treatment. After ICSI, 78% of the treated and 82% of the control oocytes survived the procedure, of which 76 and 65% developed to 4-cell stage; furthermore 3–3 pools of 30 to 44 and 24 to 36 embryos were used for RNA isolation, respectively. The labelled cRNA target generated from 240 pg of total RNA was hybridized to 4 × 44 K whole mouse genome chips (Agilent Technologies, Palo Alto, CA, USA). All the microarray data have been deposited in the NCBI Gene Expression Omnibus database (accession GSE28443). The results were validated using RT-qPCR by analysing 9 genes per experiment. The GeneSpring GX 11 analysis of the normalized data showed no change in the global gene expression profile of the oocytes after the HP treatment; however, in the 4-cell embryo study, the analysis identified 676 significantly changed genes, confirmed by the similar expression of 8 genes by RT-qPCR. To characterise the affected pathways among these genes, we used the functional annotation tools of DAVID Bioinformatics Resources (Huang et al. 2009 Nat. Protoc. 4, 44–57). The cluster with the most outstanding gene ontology terms contained the ribosome, structural constituent of ribosome, ribonucleoprotein complex, translation and structural molecule activity (P &lt; 0.001). Among the 2 directly ribosome-related categories, there were 35 and 40 down-regulated genes along with only 2-2 up-regulated genes. These results showed that principally the protein synthesis machinery is affected by the HP stress, with a robust down-regulation. In conclusion, this study suggests that ribosomal processes play a central role in the HP-treated and fertilized oocytes during pre-implantation development. Stress effects in the transcriptional processes are visible after the embryonic genome activation showing down-regulation in the most energy-consuming processes. How these processes support higher blastocyst rate, cell number and birth rate needs further elucidation. Supported by OM-00069/2008, EGG_Care; EU FP7 (EpiHealth FP7-HEALTH-2011-278418).

Investigating the deep supercooling ability of an Alaskan beetle, Cucujus clavipes puniceus, via high throughput proteomics

Cucujus clavipes puniceus is a freeze avoiding beetle capable of surviving the long, extremely cold winters of the Interior of Alaska. Previous studies showed that some individuals typically supercool to mean values of approximately -40 °C, with some individuals supercooling to as low as -58 °C, but these non-deep supercooling (NDSC) individuals eventually freeze if temperatures drop below this. However, other larvae, especially if exposed to very cold temperatures, supercool even further. These deep supercooling (DSC) individuals do not freeze even if cooled to -100 °C. In addition, the body water of the DSC larvae vitrifies (turns to a glass) at glass transition temperatures of -58 to -70 °C. This study examines the proteomes of DSC and NDSC larvae to assess proteins that may contribute to or inhibit the DSC trait. Using high throughput proteomics, we identified 138 proteins and 513 Gene Ontology categories in the DSC group and 104 proteins and 573 GO categories in the NDSC group. GO categories enriched in DSC include alcohol metabolic process, cellular component morphogenesis, monosaccharide metabolic process, regulation of biological quality, extracellular region, structural molecule activity, and antioxidant activity. Proteins unique to DSC include alpha casein precursor, alpha-actinin, vimentin, tropomyosin, beta-lactoglobulin, immunoglobulins, tubulin, cuticle proteins and endothelins.

Large scale gene expression profiling during intestine and body wall regeneration in the sea cucumber Apostichopus japonicus

Sea cucumbers are fascinating invertebrate organisms because of their ability to rapidly regenerate many organs and appendages. In this study 454 cDNA sequencing method was used to characterize transcriptome in Apostichopus japonicus in order to investigate genes that are active in regeneration. Based on sequence similarity with known genes, our analysis identified 6590 genes expressed in the early stages of regeneration of the intestine and body wall. Assembled sequences were annotated with gene names and gene ontology terms. The transcription of genes associated with structural molecule activity was abundant during regeneration compared with the control sample (based on tissues from an uninjured animal). Many important genes involved in major intercellular signaling pathways associated with regeneration were identified, based on a KEGG database search. Our investigation also indicated the expression profiles of many genes associated with development, muscle dedifferentiation, ECM remolding and epigenetic reprogramming. During the early stages of regeneration we found that 324 genes were significantly up-regulated and 80 genes were significantly down-regulated. The top 25 genes that demonstrated the most significant differential expression during regeneration were verified using real-time PCR, which identified 90% consistency between these two approaches. The new candidate gene sequences, discovered for the first time in this study, will greatly enable future research – using the sea cucumber model – into the molecular mechanisms associated with intestine and body wall regeneration.

Study on pancreatic islet adaptation and gene expression during pregnancy in rats

During pregnancy, the pancreatic islets undergo major structural and functional changes in response to increased peripheral resistance to insulin. In this study, we investigated the adaptive changes of the pancreatic islet beta-cell mass during pregnancy in rats, and explored profiles of islet gene expression at various stages of pregnancy. Some differentially expressed genes were verified by RT-PCR and Real-time PCR. Our results showed that compared with the non-pregnant control group, insulin synthesis, glucose-stimulated insulin secretion, islet beta-cell proliferation, and islet size were all increased in pregnant rats. The study also demonstrated that expression of several-hundred islet genes were changed during pregnancy, especially at day 14.5. The differentially expressed genes identified were distributed into eight main categories according to their biological functions: (1) genes involved in apoptosis or tumor; (2) genes related to binding; (3) genes involved in metabolism; (4) genes related to cell cycle; (5) genes for signal transducer activity; (6) genes related to structural molecule activity; (7) genes involved in transcription regulator activity; (8) genes for transporter activity. Among these genes, regenerating islet-derived 3 alpha (Reg3a) was remarkably increased during pregnancy. We hypothesize that differentially expressed genes may play an important role in adaptation of pancreatic islets during pregnancy in rats. In addition, the markedly increased expression of gene Reg3a is probably related to islet regeneration.

Differential expression profiling of ovarian genes in prelaying and laying geese

The identification of the differential expression of genes in the ovaries of egg-laying and prelaying Zi geese is required to improve the laying performance of the geese. In the present study, suppression subtractive hybridization and reverse dot-blot were employed to identify such genes, using the ovary as a model. Furthermore, expression profiling of estrogen receptor 1, estrogen receptor 2, follicle stimulating hormone receptor, prolactin receptor, ferritin H chain, and ovary differentially expressed unknown gene 08 in ovaries from geese was performed by quantitative real-time PCR. Total RNA from the ovaries of laying and prelaying Zi geese was pooled and the mRNA was isolated. The cDNA that was reverse-transcribed from the ovarian mRNA of the prelaying geese was subtracted from the cDNA isolated from the laying geese. Four hundred sixty-five clones containing putative differentially expressed gene fragments were further identified by reverse dot-blot. Ninety-seven clones were subjected to sequencing and further analysis. Sequence analysis showed that the expression of 18 known (including a mitochondrial gene) and 8 unknown gene fragments was higher in the ovaries of laying geese compared with prelaying geese. Seventeen of the known genes encode proteins that belong to groups involved with binding, catalytic activity, enzyme regulatory activity, signal transducer activity, structural molecule, and transporter activity. The results of the quantitative real-time PCR showed that the expression of estrogen receptor 1, estrogen receptor 2, follicle stimulating hormone receptor, prolactin receptor, ferritin H chain, and ovary differentially expressed unknown gene 08 was higher in the ovaries of the laying geese than in those of the prelaying geese (P < 0.05). These differentially expressed genes may be relevant to the progression of prelaying geese to the egg-laying stage. Further study is required to elucidate the molecular mechanism that controls egg-laying in geese, to improve the productivity of laying geese.

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

The goal of this study was to assess the extent to which transposable elements (TEs) have contributed to protein-coding regions in Arabidopsis thaliana. To do this, we first characterized the extent of chimeric TE-gene constructs. We compared a genome-wide TE database to genomic sequences, annotated coding regions, and EST data. The comparison revealed that 7.8% of expressed genes contained a region with close similarity to a known TE sequence. Some groups of TEs, such as helitrons, were underrepresented in exons relative to their genome-wide distribution; in contrast, Copia-like and En/Spm-like sequences were overrepresented in exons. These 7.8% percent of genes were enriched for some GO-based functions, particularly kinase activity, and lacking in other functions, notably structural molecule activity. We also examined gene family evolution for these genes. Gene family information helped clarify whether the sequence similarity between TE and gene was due to a TE contributing to the gene or, instead, the TE co-opting a portion of the gene. Most (66%) of these genes were not easily assigned to a gene family, and for these we could not infer the direction of the relationship between TE and gene. For the remainder, where appropriate, we built phylogenetic trees to infer the direction of the TE-gene relationship by parsimony. By this method, we verified examples where TEs contributed to expressed proteins. Our results are undoubtedly conservative but suggest that TEs may have contributed small protein segments to as many as 1.2% of all expressed, annotated A. thaliana genes.