Evolutionarily distinct classes of S27 ribosomal proteins with differential mRNA expression in rat hypothalamus

Agromyces mariniharenae sp. nov., a novel indole-acetic acid producing actinobacterium isolated from marine sand

A Gram-positive, aerobic, heterotrophic, non-endospore-forming, rod-shaped and indole-acetic acid-producing strain, designated NEAU-184^T, was isolated from marine sand collected in Sanya, PR China, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence data indicated that strain NEAU-184^T should be assigned to the genus Agromyces and formed a distinct branch with its closest neighbour, Agromyces iriomotensis NBRC 106452^T (99.1 %). 2,4-Diaminobutyric acid, d-alanine, d-glutamic acid and glycine were detected in cell-wall hydrolysate and glucose, rhamnose and xylose were detected in whole-cell hydrolysate. The polar lipids were found to contain diphosphatidylglycerol, glycolipid, phosphatidylglycerol and two unidentified lipids. The major menaquinone was MK-12 and the minor menaquinones were MK-13 and MK-11. The predominant fatty acids were anteiso-C_17 : 0, anteiso-C_15 : 0 and iso-C_16 : 0. The DNA G+C content was 71.5 mol%. Furthermore, the strain could be clearly distinguished from its closely related type strains by the combination of DNA-DNA hybridization results and some phenotypic characteristics. Meanwhile, the strain has the ability to produce indole-acetic acid (0.334mg ml^-1). Therefore, strain NEAU-184^T represents a novel species of the genus Agromyces, for which the name Agromyces mariniharenae sp. nov. is proposed, with strain NEAU-184^T (=CGMCC 4.7505^T=JCM 32546^T) as the type strain.

Microbacterium helvum sp. nov., a novel actinobacterium isolated from cow dung

A Gram-positive, aerobic, non-motile, non-spore-forming, short rod-shaped strain, NEAU-LLC^T, was isolated from cow dung in Shangzhi City, Heilongjiang Province, Northeast China and identified by a polyphasic taxonomic study. Colonies was light yellow, round, with entire margin. Strain NEAU-LLC^T was grown at 15-45 ℃ and pH 6.0-10.0. NaCl concentration ranged from 0 to 5% (W/V). The 16S rRNA gene sequence of NEAU-LLC^T showed the high similarities with Microbacterium kyungheense JCM 18735^T (98.5%), Microbacterium trichothecenolyticum JCM 1358^T (98.3%) and Microbacterium jejuense JCM 18734^T (98.2%). The whole-cell sugars were glucose, rhamnose and ribose. The menaquinones contained MK-12 and MK-13. Ornithine, glutamic acid, lysine and a small amount of alanine and glycine were the amino acids in the hydrolyzed products of the cell wall. The major fatty acids were iso-C_16:0, iso-C_18:0, anteiso-C_15:0 and anteiso-C_17:0. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The genome of NEAU-LLC^T was 4,369,375 bp and G + C content is 70.28 mol%. A combination of DNA-DNA hybridization result and some phenotypic characteristics demonstrated that strain NEAU-LLC^T could be distinguished from its closely related strains. Therefore, the strain NEAU-LLC^T was considered to represent a novel species, which was named Microbacterium helvum sp. (Type strain NEAU-LLC^T = CCTCC AA 2018026^T = JCM 32661^T).

Micromonospora rubida sp. nov., a novel actinobacterium isolated from soil of Harbin

A novel actinobacterium, designated strain NEAU-HG-1^T, was isolated from soil collected from Harbin, Heilongjiang Province, Northeast China and characterised using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NEAU-HG-1^T belonged to the genus Micromonospora, and shared high sequence similarities with Micromonospora auratinigra DSM 44815^T (98.9%) and Micromonospora coerulea DSM 43143^T (98.7%). Morphological and chemotaxonomic characteristics of the strain also supported its assignment to the genus Micromonospora. Cell wall contained meso-diaminopimelic acid and the whole-cell sugars were arabinose and xylose. The polar lipid contained diphosphatidylglycerol, phosphatidylethanolamine, glycolipid and phosphatidylinositol. The predominant menaquinones were MK-10(H₂), MK-10(H₄) and MK-10(H₆). The major fatty acids were C_17:0 cycle, iso-C_15:0, and iso-C_16:0. Furthermore, strain NEAU-HG-1^T displayed a DNA-DNA relatedness of 33.8 ± 2.2% with M. coerulea DSM 43143^T. The level of digital DNA-DNA hybridization between strain NEAU-HG-1^T and M. auratinigra DSM 44815^T was 27.2% (24.8-29.7%). The value was well below the criteria for species delineation of 70% for dDDH. Whole-genome average nucleotide identity analyses result also indicated that the isolate should be assigned to a new species under the genus Micromonospora. Therefore, it is concluded that strain NEAU-HG-1^T represents a novel species of the genus Micromonospora, for which the name Micromonospora rubida sp. nov. is proposed, with NEAU-HG-1^T (= CGMCC 4.7479^T = JCM 32386^T) as the type strain.

Glycomyces albidus sp. nov., a novel actinobacterium isolated from rhizosphere soil of wheat (Triticum aestivum L.)

A novel actinobacterium, designated strain NEAU-7082^T, was isolated from rhizosphere soil of wheat (Triticum aestivum L.) and characterized by using a polyphasic approach. Morphological and chemotaxonomic characteristics confirmed the affiliation of strain NEAU-7082^T to the genus Glycomyces. 16S rRNA gene sequence analysis indicated that strain NEAU-7082^T belonged to the genus Glycomyces and was closely related to Glycomyces mayteni JCM 16217^T (99.0 % 16S rRNA gene sequence similarity), Glycomyces sambucus DSM 45047^T (98.4 %), Glycomyces scopariae DSM 44968^T (98.3 %), Glycomyces paridis DSM 102295^T (98.1 %), Glycomyces artemisiae NBRC 109773^T (98.0 %) and Glycomyces dulcitolivorans DSM 105121T (97.9 %). Phylogenetic analysis using the 16S rRNA gene sequence showed that the strain formed a stable clade with G. mayteni JCM 16217^T and clustered with G. sambucus DSM 45047^T, G. scopariae DSM 44968^T, G. artemisiae NBRC 109773^T and G. dulcitolivorans DSM 105121T in the genus Glycomyces. The cell wall contained meso-diaminopimelic acid and the whole-cell hydrolysates were glucose and xylose. The polar lipid profile consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), glycolipid (GL), phosphatidylinositol mannoside (PIM) and an unidentified lipid (UL). The menaquinones were MK-11(H₄), MK-11 and MK-10. Major fatty acids were anteiso-C_15 : 0, iso-C_16 : 0 and anteiso-C_17 : 0. These chemotaxonomic data substantiated the affiliation of strain NEAU-7082^T to the genus Glycomyces. The DNA G+C content was 71.3 mol%. A combination of DNA-DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-7082^T could be distinguished from its closest relatives. Therefore, strain NEAU-7082^T is considered to represent a novel species of the genus Glycomyces, for which the name Glycomyces albidus sp. nov. is proposed. The type strain is NEAU-7082^T (=CCTCC AA 2019045^T=JCM 33458^T).

Genome-Wide Identification, Evolution and Expression of the Complete Set of Cytoplasmic Ribosomal Protein Genes in Nile Tilapia

Ribosomal proteins (RPs) are indispensable in ribosome biogenesis and protein synthesis, and play a crucial role in diverse developmental processes. In the present study, we carried out a comprehensive analysis of RPs in chordates and examined the expression profiles of the complete set of 92 cytoplasmic RP genes in Nile tilapia. The RP genes were randomly distributed throughout the tilapia genome. Phylogenetic and syntenic analyses revealed the existence of duplicated RP genes from 2R (RPL3, RPL7, RPL22 and RPS27) and 3R (RPL5, RPL19, RPL22, RPL41, RPLP2, RPS17, RPS19 and RPS27) in tilapia and even more from 4R in common carp and Atlantic salmon. The RP genes were found to be expressed in all tissues examined, but their expression levels differed among different tissues. Gonadal transcriptome analysis revealed that almost all RP genes were highly expressed, and their expression levels were highly variable between ovaries and testes at different developmental stages in tilapia. No sex- and stage-specific RP genes were found. Eleven RP genes displayed sexually dimorphic expression with nine higher in XY gonad and two higher in XX gonad at all stages examined, which were proved to be phenotypic sex dependent. Quantitative real-time PCR and immunohistochemistry ofRPL5b and RPL24 were performed to validate the transcriptome data. The genomic resources and expression data obtained in this study will contribute to a better understanding of RPs evolution and functions in chordates.

Molecular cloning, expression and impact of ribosomal protein S-27 silencing in Haemaphysalis longicornis (Acari: Ixodidae)

Ticks, obligatory blood-feeding arthropods, are a major pathogen vector in humans and animals worldwide. Anti-tick vaccines are an exciting alternative to chemical acaricides for controlling these disease-transmitting vectors. However, identification of protective antigens for anti-tick vaccine development is challenging. Different ribosomal proteins play multifunctional roles in tick survival and feeding. Here, we first report the cloning and molecular characterization of ribosomal protein S27 (RPS-27) from the hard tick Haemaphysalis longicornis. We identified a complete open reading frame (ORF) of RPS-27: a 255-bp (base pair) cDNA encoding a mature protein of 84 amino-acid residues with a 9.4-kDa predicted molecular mass. Amino-acid sequence analysis revealed that RPS-27 was highly conserved among different tick and vertebrate animals with identity ranges of 97-98% and 60-85%, respectively. Phylogenetic tree analysis showed that RPS-27 from different tick species clustered together. Reverse transcription-polymerase chain reaction (RT-PCR) analysis showed that the RPS-27 mRNA transcript was expressed in all life stages. At the tissue level, it was more highly expressed in the salivary gland than in the midgut for both the fed and unfed conditions, which indicates a role for RPS-27 in tick feeding. In vitro analysis showed that recombinant RPS-27 (10-RPS-27) was successfully expressed in a pGEMEX-2 vector with an estimated 45-kDa molecular mass. The functional importance of RPS-27 was determined by gene silencing through RNA interference (RNAi). RPS-27 silencing showed a significant (P < 0.05) reduction of feeding abilityand engorgement weight after the blood meal in both nymph and adult female ticks and also significantly (P < 0.05) reduced molting rate in nymph. In addition, RPS-27 silencing in eggs led to abnormalities in shape and hatching. Taken together, our results suggest that RPS-27 is an important molecule that plays multiple roles in the tick life cycle including in both feeding and reproduction. Therefore, RPS-27 is an exciting target for future tick control strategies.

Kribbella jiaozuonensis sp. nov., a novel actinomycete isolated from soil

A novel actinobacterium, designated strain NEAU-THZ27^T, was isolated from soil collected from the Cornel peak in Jiaozuo, Henan Province, PR China and characterized using a polyphasic approach. Morphological and chemotaxonomic characteristics of the strain coincided with those of members of the genusKribbella. The results of 16S rRNA gene sequence analysis showed that strain NEAU-THZ27^T belongs to the genus Kribbella and was most closely related to Kribbella podocarpi YPL1^T (98.96 %), Kribbella karoonensis Q41^T (98.89 %), Kribbella aluminosa HKI 0478^T (98.86%) and Kribbella hippodromi S1.4^T (98.85 %), similarities to other type strains of species of the genus Kribbella were found to be less than 98.7 %. Phylogenetic analyses using the 16S rRNA gene sequence and multilocus sequence analysis using the concatenated gene sequences of the gyrB, rpoB, recA, relA and atpD genes all showed that the strain formed a separate branch in the genus Kribbella. The cell wall contained ll-diaminopimelic acid as the major diamino acid and the whole-cell hydrolysates were ribose and glucose. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinone was MK-9(H₄). Major fatty acids were iso-C_16 : 0, iso-C_14 : 0 and anteiso-C_15 : 0, these chemotaxonomic data supported the affiliation of strain NEAU-THZ27^T to the genus Kribbella. The DNA G+C content was 68.0 mol%. Furthermore, the strain could be clearly distinguished by concatenated gene genetic distances, the combination of DNA-DNA hybridization results and some phenotypic characteristics. Therefore, it is proposed that strain NEAU-THZ27^T represents a novel species of the genus Kribbella, for which the name Kribbella jiaozuonensis sp. nov. is proposed. The type strain is NEAU-THZ27^T (=CGMCC 4.7504^T=DSM 105535^T).

Agromyces tardus sp. nov., an actinobacterium isolated from the rhizosphere soil of wheat (Triticum aestivum L.)

A Gram-stain-positive, aerobic, heterotrophic, non-spore-forming and rod-shaped strain, designated SJ-23^T, was isolated from rhizosphere soil of wheat (Triticum aestivum L.) collected from Langfang, Hebei Province, central PR China and characterized using a polyphasic approach. Morphological and chemotaxonomic characteristics were consistent with those of members of the genus Agromyces. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, glycolipid and three unidentified lipids. The predominant menaquinones detected were MK-12, MK-11 and MK-10. Major fatty acids were identified as anteiso-C_17 : 0, anteiso-C_15 : 0 and iso-C_16 : 0. The 16S rRNA gene sequence analysis showed that strain SJ-23^T belongs to the genus Agromyces with high sequence similarities to Agromyces ramosus DSM 43045^T (99.2 %), Agromycescerinussubsp. cerinus DSM 8595^T (98.8 %) and Agromyces cerinussubsp. nitratus DSM 8596^T (98.6 %). Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain formed a separate branch in the genus Agromyces. Furthermore, the combination of DNA-DNA hybridization results and some phenotypic characteristics demonstrated that strain SJ-23^T could be distinguished from its closest relatives. Therefore, it is proposed that strain SJ-23^T represents a novel species of the genus Agromyces, for which the name Agromycestardus sp. nov. is proposed. The type strain is SJ-23^T (=CGMCC 4.7419^T=DSM 105049^T).

Kribbella monticola sp. nov., a novel actinomycete isolated from soil

A novel actinobacterium, designated strain NEAU-SW521^T, was isolated from soil collected from Xianglu Mountain, Heilongjiang province, north PR China. The results of analysis of the 16S rRNA gene indicated that NEAU-SW521^T represented a member of the genus Kribbella. The results of phylogenetic analyses using the 16S rRNA gene and multilocus sequence analysis using the concatenated gene sequences of the gyrB, rpoB, relA, recA and atpD genes all indicated that the strain formed a clade with Kribbella alba DSM 15500^T (99.16 %), Kribbella ginsengisoli JCM 16928^T (98.96 %), Kribbella catacumbae JCM 14968^T (98.82 %), Kribbella sancticallisti JCM 14969^T (98.62 %), Kribbella qitaiheensis NEAU-GQTH2-3^T (98.61 %) and Kribbella koreensis JCM 10977^T (98.47 %). The cell wall contained ll-diaminopimelic acid as the major diamino acid and the whole-cell hydrolysates were ribose, glucose and galactose. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid. The predominant menaquinone was MK-9(H4). Major fatty acids were iso-C16 : 0 and anteiso-C15 : 0. These chemotaxonomic data supported the affiliation of NEAU-SW521^T to the genus Kribbella. The DNA G+C content was 67.8 mol%. Furthermore, the strain could be clearly distinguished by concatenated gene genetic distances, the combination of DNA-DNA hybridization results and some phenotypic characteristics. Therefore, it is proposed that NEAU-SW521^T represents a novel species of the genus Kribbella, for which the name Kribbellamonticola sp. nov. is proposed. The type strain is NEAU-SW521^T (=CGMCC 4.7465^T=DSM 105770^T).

Lechevalieria rhizosphaerae sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.) and emended description of the genus Lechevalieria

A novel actinomycete, designated strain NEAU-A2^T, was isolated from rhizosphere soil of wheat (Triticum aestivum L.) and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-A2^T should be assigned to the genus Lechevalieria and forms a distinct branch with its closest neighbour Lechevalieria aerocolonigenes DSM 40034^T (99.0 %). Moreover, key morphological and chemotaxonomic properties also confirmed the affiliation of strain NEAU-A2^T to the genus Lechevalieria. The cell wall contained meso-diaminopimelic acid and the whole-cell hydrolysates were galactose, mannose, rhamnose, glucose and ribose. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositolmannoside and two glycolipids. The predominant menaquinones were MK-9(H4) and MK-9(H6). The major fatty acids were iso-C16 : 0, anteiso-C15 : 0, C16 : 1ω7c and anteiso-C17 : 0. The DNA G+C content was 68.2 mol%. The combination of the DNA-DNA hybridization result and some phenotypic characteristics demonstrated that strain NEAU-A2^T could be distinguished from its closest relative. Therefore, it is proposed that strain NEAU-A2^T represents a novel species of the genus Lechevalieria, for which the name Lechevalieriarhizosphaerae sp. nov. is proposed. The type strain is NEAU-A2^T (=CGMCC 4.7405^T=DSM 104541^T).

Ribosomal protein S27-like in colorectal cancer: a candidate for predicting prognoses

Background

The development and progression of colorectal cancer (CRC) involve a complex process of multiple genetic changes. Tumor suppressor p53 is capable of determining the fate of CRC cells. However, the role of a p53-inducible modulator, ribosomal protein S27-like (RPS27L), in CRC is unknown.

Methods

Here, the differential expression of RPS27L was examined in the feces and colonic tissues of CRC patients, to explore its possible correlation with patient survival and to investigate the cellular mechanisms underlying their clinical outcomes. Eighty intermediate-stage CRC patients (42 at stage II and 38 at stage III) were divided into two groups according to their fecal RPS27L mRNA levels. The survival probabilities of the groups were estimated using the Kaplan–Meier method. The RPS27L protein in the colonic tissues of stage III patients with different prognoses was further examined immunohistochemically. RPS27L expression in LoVo cells was manipulated to examine the possible cellular responses in vitro.

Results

Elevated RPS27L expression, in either feces or tissues, was related to a better prognosis. In vitro, RPS27L-expressing LoVo cells ceased DNA synthesis and apoptotic activity while the expression of their DNA repair molecules was upregulated.

Conclusions

Elevated RPS27L may improve the prognoses of certain CRC patients by enhancing the DNA repair capacity of their colonic cells, and can be determined in feces. By integrating clinical, molecular, and cellular data, our study demonstrates that fecal RPS27L may be a useful index for predicting prognoses and guiding personalized therapeutic strategies, especially in patients with intermediate-stage CRC.

Identification of TTP mRNA targets in human dendritic cells reveals TTP as a critical regulator of dendritic cell maturation

Dendritic cells provide a critical link between innate and adaptive immunity and are essential to prime a naive T-cell response. The transition from immature dendritic cells to mature dendritic cells involves numerous changes in gene expression; however, the role of post-transcriptional changes in this process has been largely ignored. Tristetraprolin is an AU-rich element mRNA-binding protein that has been shown to regulate the stability of a number of cytokines and chemokines of mRNAs. Using TTP immunoprecipitations and Affymetrix GeneChips, we identified 393 messages as putative TTP mRNA targets in human dendritic cells. Gene ontology analysis revealed that approximately 25% of the identified mRNAs are associated with protein synthesis. We also identified six MHC Class I alleles, five MHC Class II alleles, seven chemokine and chemokine receptor genes, indoleamine 2,3 dioxygenase, and CD86 as putative TTP ligands. Real-time PCR was used to validate the GeneChip data for 15 putative target genes and functional studies performed for six target genes. These data establish that TTP regulates the expression of DUSP1, IDO, SOD2, CD86, and MHC Class I-B and F via the 3'-untranslated region of each gene. A novel finding is the demonstration that TTP can interact with and regulate the expression of non-AU-rich element-containing messages. The data implicate TTP as having a broader role in regulating and limiting the immune response than previously suspected.

Translational machinery of the chaetognath Spadella cephaloptera: a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression

Background

Chaetognaths, or arrow worms, are small marine, bilaterally symmetrical metazoans. The objective of this study was to analyse ribosomal protein (RP) coding sequences from a published collection of expressed sequence tags (ESTs) from a chaetognath (Spadella cephaloptera) and to use them in phylogenetic studies.

Results

This analysis has allowed us to determine the complete primary structures of 23 out of 32 RPs from the small ribosomal subunit (SSU) and 32 out of 47 RPs from the large ribosomal subunit (LSU). Ten proteins are partially determined and 14 proteins are missing. Phylogenetic analyses of concatenated RPs from six animals (chaetognath, echinoderm, mammalian, insect, mollusc and sponge) and one fungal taxa do not resolve the chaetognath phylogenetic position, although each mega-sequence comprises approximately 5,000 amino acid residues. This is probably due to the extremely biased base composition and to the high evolutionary rates in chaetognaths. However, the analysis of chaetognath RP genes revealed three unique features in the animal Kingdom. First, whereas generally in animals one RP appeared to have a single type of mRNA, two or more genes are generally transcribed for one RP type in chaetognath. Second, cDNAs with complete 5'-ends encoding a given protein sequence can be divided in two sub-groups according to a short region in their 5'-ends: two novel and highly conserved elements have been identified (5'-TAATTGAGTAGTTT-3' and 5'-TATTAAGTACTAC-3') which could correspond to different transcription factor binding sites on paralog RP genes. And, third, the overall number of deduced paralogous RPs is very high compared to those published for other animals.

Conclusion

These results suggest that in chaetognaths the deleterious effects of the presence of paralogous RPs, such as apoptosis or cancer are avoided, and also that in each protein family, some of the members could have tissue-specific and extra-ribosomal functions. These results are congruent with the hypotheses of an allopolyploid origin of this phylum and of a ribosome heterogeneity.

Comparative sequence analysis of the complete set of 40S ribosomal proteins in the Senegalese sole (Solea senegalensis Kaup) and Atlantic halibut (Hippoglossus hippoglossus L.) (Teleostei: Pleuronectiformes): phylogeny and tissue- and development-specific expression

Background

Ribosomal proteins (RPs) are key components of ribosomes, the cellular organelle responsible for protein biosynthesis in cells. Their levels can vary as a function of organism growth and development; however, some RPs have been associated with other cellular processes or extraribosomal functions. Their high representation in cDNA libraries has resulted in the increase of RP sequences available from different organisms and their proposal as appropriate molecular markers for phylogenetic analysis.

Results

The development of large-scale genomics of Senegalese sole (Solea senegalensis) and Atlantic halibut (Hippoglossus hippoglossus), two commercially important flatfish species, has made possible the identification and systematic analysis of the complete set of RP sequences for the small (40S) ribosome subunit. Amino acid sequence comparisons showed a high similarity both between these two flatfish species and with respect to other fish and human. EST analysis revealed the existence of two and four RPS27 genes in Senegalese sole and Atlantic halibut, respectively. Phylogenetic analysis clustered RPS27 in two separate clades with their fish and mammalian counterparts. Steady-state transcript levels for eight RPs (RPS2, RPS3a, RPS15, RPS27-1, RPS27-2, RPS27a, RPS28, and RPS29) in sole were quantitated during larval development and in tissues, using a real-time PCR approach. All eight RPs exhibited different expression patterns in tissues with the lowest levels in brain. On the contrary, RP transcripts increased co-ordinately after first larval feeding reducing progressively during the metamorphic process.

Conclusion

The genomic resources and knowledge developed in this survey will provide new insights into the evolution of Pleuronectiformes. Expression data will contribute to a better understanding of RP functions in fish, especially the mechanisms that govern growth and development in larvae, with implications in aquaculture.

Transcriptional upregulation of genes related to virulence activation in Entamoeba histolytica

BACKGROUND

To understand the molecular basis of virulence variability in Entamoeba histolytica, this study presents results about differential gene expression induced by E. histolytica trophozoites in liver of hamsters in order to produce experimental amebic liver abscess (ALA) and consequently reactivate its virulence.

METHODS

Amebic cultures were studied before (BALA) and after (AALA) inoculation in hamster peritoneal cavity. Markers of pathogenicity such as the rate of erythrophagocytosis, hemolytic activity, and cytotoxic effects on MDCK cell monolayers were evaluated in order to correlate these phenotypic characteristics to differential gene expression between virulent and non-virulent strains. Genotypic variability was determined by genetic polymorphism using the random-amplified polymorphic DNA (RAPD) technique, which defines the parasite genomic plasticity. mRNA differential display was used in order to identify variable transcripts levels.

RESULTS

The rate of erythrophagocytosis and hemolytic activity were notably increased in AALA in comparison with BALA E. histolytica cultures, as well as the cytotoxic effect on MDCK cells. An increment in the transcription level of several mRNA was shown.

CONCLUSIONS

The RAPD technique allowed us to confirm differences in number and size of polymorphic markers bands between virulent and non-virulent stages, suggesting genomic adaptability in E. histolytica. Eight different genes (membrane-bound acid phosphatase, cysteine proteinase, two different ribosomal proteins, heat shock transcription factor, ribosomal RNA, aldehyde dehydrogenase-1 and patatin-like phospholipase) were sequenced and may be associated with a biological function related to the virulence of E. histolytica. Together these findings show genomic variability between virulent and non-virulent cultures of E. histolytica.

Composition and structure of the 80S ribosome from the green alga Chlamydomonas reinhardtii: 80S ribosomes are conserved in plants and animals

We have conducted a proteomic analysis of the 80S cytosolic ribosome from the eukaryotic green alga Chlamydomonas reinhardtii, and accompany this with a cryo-electron microscopy structure of the ribosome. Proteins homologous to all but one rat 40S subunit protein, including a homolog of RACK1, and all but three rat 60S subunit proteins were identified as components of the C. reinhardtii ribosome. Expressed Sequence Tag (EST) evidence and annotation of the completed C. reinhardtii genome identified genes for each of the four proteins not identified by proteomic analysis, showing that algae potentially have a complete set of orthologs to mammalian 80S ribosomal proteins. Presented at 25A, the algal 80S ribosome is very similar in structure to the yeast 80S ribosome, with only minor distinguishable differences. These data show that, although separated by billions of years of evolution, cytosolic ribosomes from photosynthetic organisms are highly conserved with their yeast and animal counterparts.

Gene expression profiling in fetal, aged, and Alzheimer hippocampus: a continuum of stress-related signaling

While specific components of normal brain aging and Alzheimer's disease (AD) appear to be genetically determined, it is not well understood whether AD is due to accelerated aging or if AD represents an independent disease entity superimposed upon senescence. Using gene expression profiling, significant alterations in brain-specific transcription patterns have been observed between AD and age-matched controls. In AD, although a general depression in brain genetic output has been reported, there are robust increases in the expression of potentially neuropathological genes. The data in this study show increases in the RNA abundance patterns for a stress-response, proinflammatory, apoptotic, and angiogenic gene family that occur during the transition from fetal to aged, and again during the transformation from aged to AD brain. Significantly up-regulated RNAs include those encoding stress-induced factors (HSP70), transcriptional repressors (DAXX), pentraxins (SAP), proapoptosis factors (FAS and DAXX), and several inflammatory markers (betaAPP, CEX1, NF-IL6, NF-kappaBp100, cyclooxygenase-2, IL-1alpha and IL-1beta precursors and cPLA2). These findings support the hypothesis that there is a continuum of stress-related gene expression as the brain ages and an advancement of inflammatory, apoptotic, and angiogenic gene signaling that correlates with the transition to AD.

Gene expression profiling of 12633 genes in Alzheimer hippocampal CA1: transcription and neurotrophic factor down-regulation and up-regulation of apoptotic and pro-inflammatory signaling

Alterations in transcription, RNA editing, translation, protein processing, and clearance are a consistent feature of Alzheimer's disease (AD) brain. To extend our initial study (Alzheimer Reports [2000] 3:161-167), RNA samples isolated from control and AD hippocampal cornu ammonis 1 (CA1) were analyzed for 12633 gene and expressed sequence tag (EST) expression levels using DNA microarrays (HG-U95Av2 Genechips; Affymetrix, Santa Clara, CA). Hippocampal CA1 tissues were carefully selected from several hundred potential specimens obtained from domestic and international brain banks. To minimize the effects of individual differences in gene expression, RNA of high spectral quality (A(260/280) > or= 1.9) was pooled from CA1 of six control or six AD subjects. Results were compared as a group; individual gene expression patterns for the most-changed RNA message levels were also profiled. There were no significant differences in age, postmortem interval (mean < or = 2.1 hr) nor tissue pH (range 6.6-6.9) between the two brain groups. AD tissues were derived from subjects clinically classified as CDR 2-3 (CERAD/NIA). Expression data were analyzed using GeneSpring (Silicon Genetics, Redwood City, CA) and Microarray Data Mining Tool (Affymetrix) software. Compared to controls and 354 background/alignment markers, AD brain showed a generalized depression in brain gene transcription, including decreases in RNA encoding transcription factors (TFs), neurotrophic factors, signaling elements involved in synaptic plasticity such as synaptophysin, metallothionein III, and metal regulatory factor-1. Three- or morefold increases in RNAs encoding DAXX, cPLA(2), CDP5, NF-kappaBp52/p100, FAS, betaAPP, DPP1, NFIL6, IL precursor, B94, HB15, COX-2, and CEX-1 signals were strikingly apparent. These data support the hypothesis of widespread transcriptional alterations, misregulation of RNAs involved in metal ion homeostasis, TF signaling deficits, decreases in neurotrophic support and activated apoptotic and neuroinflammatory signaling in moderately affected AD hippocampal CA1.

A human gene encoding a protein homologous to ribosomal protein L39 is normally expressed in the testis and derepressed in multiple cancer cells

We identified and characterized a gene encoding a protein that was 92% identical to human ribosomal protein L39. This gene was located on the long arm of chromosome 3, and was composed of three exons and two long introns. Analysis of mRNA expression in 16 types of normal human tissues showed that this gene was expressed specifically in the testis, in sharp contrast to the ubiquitous expression of the ribosomal protein L39 gene. Surprisingly, the new gene was expressed in 19 out of 24 human cancer samples of various tissue origins. When the new gene was expressed in the cell, a translated product was observed by immunofluorescence microscopy in the nucleus, especially strongly in the nucleolus, and in the cytoplasm. Association of this protein with the large subunit of cytoplasmic ribosomes was detected by polyacrylamide-agarose composite gel electrophoresis followed by immunodetection. These immunochemical data suggest a relationship between the new gene and the ribosome.

Genomic responses of the brain to ischemic stroke, intracerebral haemorrhage, kainate seizures, hypoglycemia, and hypoxia

RNA expression profiles in rat brain were examined 24 h after ischemic stroke, intracerebral haemorrhage, kainate-induced seizures, insulin-induced hypoglycemia, and hypoxia and compared to sham- or untouched controls. Rat oligonucleotide microarrays were used to compare expression of over 8000 transcripts from three subjects in each group (n = 27). Of the somewhat less than 4000 transcripts called 'present' in normal or treated cortex, 5-10% of these were up-regulated 24 h after ischemia (415), haemorrhage (205), kainate (187), and hypoglycemia (302) with relatively few genes induced by 6 h of moderate (8% oxygen) hypoxia (15). Of the genes induced 24 h after ischemia, haemorrhage, and hypoglycemia, approximately half were unique for each condition suggesting unique components of the responses to each of the injuries. A significant component of the responses involved immune-process related genes likely to represent responses to dying neurons, glia and vessels in ischemia; to blood elements in haemorrhage; and to the selectively vulnerable neurons that die after hypoglycemia. All of the genes induced by kainate were also induced either by ischemia, haemorrhage or hypoglycemia. This strongly supports the concept that excitotoxicity not only plays an important role in ischemia, but is an important mechanism of brain injury after intracerebral haemorrhage and hypoglycemia. In contrast, there was only a single gene that was down-regulated by all of the injury conditions suggesting there is not a common gene down-regulation response to injury.

Differential gene expression in Entamoeba histolytica isolated from amoebic liver abscess

The majority of human infections with the intestinal protozoan parasite Entamoeba histolytica remain asymptomatic. In a small proportion of infections, however, E. histolytica trophozoites penetrate the intestinal mucosa and disseminate to other organs, most commonly to the liver, where they induce abscess formation. It is believed that the ability of E. histolytica trophozoites to destroy host tissues and to survive within the liver is accomplished by a strong adaptive response, which requires the specific regulation of a number of amoeba proteins. Using differential display polymerase chain reaction (DD-PCR), we compared RNA expression between E. histolytica trophozoites isolated from liver abscesses of infected gerbils and those grown under normal culture conditions. A total of 3000 cDNA-derived amplicons were compared between the two groups of amoebae, which were calculated to represent about one-third of all E. histolytica mRNA species (transcriptome). Among these, 55 were found to be specifically present or absent in abscess-derived amoebae, of which 42 were successfully cloned and sequenced. Database searches and Northern blot analyses revealed that the 42 amplicons correspond to 29 independent E. histolytica genes, of which at least seven are specifically upregulated and five are downregulated in abscess-derived amoebae. Specific expression of most of these genes was not simply the result of a heat shock response, which might be expected during abscess formation, as only five of the genes revealed an expression profile similar to that found in amoebae cultured under elevated temperatures. The two genes specifically downregulated in abscess-derived amoebae encode members of a family of so far unknown proteins, which contain repetitive stretches of sequences that are rich in lysine and glutamic acid residues. In contrast, a diverse set of genes is specifically upregulated, encoding ribosomal proteins (S30, L37A), cyclophilin, ferredoxin 2 and GTP-binding protein RAB7D, supporting the notion that liver abscess formation requires the regulation and concerted action of a variety of amoeba proteins. These proteins are associated with stress response, signal transduction, regulation of transcription and vesicular trafficking. However, transcriptome analysis will not be sufficient to identify all proteins specifically upregulated during abscess formation, as at least an increase in the expression of actin was found to be regulated at the post-transcriptional level.

Optimisation of methods for selecting candidate genes from cDNA array screens: application to rat brain punches and pineal

DNA arrays are potentially powerful experimental tools within neuroscience but application of this technology to in vivo paradigms may, in practice, be limited by the sensitivity of transcript detection and inter-screen variation. Here we describe the use of brain punch micro-sampling, used in combination with commercially available cDNA arrays, for profiling brain gene expression in a mutant strain of rat (GAERS model of absence epilepsy). Furthermore, we describe a multi-step optimisation of analysis methods which provides for improved sensitivity and absence of bias in the selection of candidate genes which may be differentially expressed in the mutant. Our method has been validated through application to a second paradigm, rhythmic gene expression in the rat pineal gland. Our experimental design, and analysis method should therefore be generally applicable to subtle discriminations of transcript abundance within discrete brain areas.