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Timothy Doran's 11-year-old daughter is allergic to eggs. And like about 2% of children worldwide who share the condition, she is unable to receive many routine vaccinations because they are [...]

The splice mutation in the iron-sulfur cluster scaffold protein ISCU is found to cause myopathy with exercise intolerance in patients. The other human diseases that are caused by the defects in iron-sulfur cluster biogenesis are also investigated.

The functional orthology, as well as patholegic significance of the RFT1 protein present in yeast and human bodies are studied. The RFT1 deficiency is found to lead to profound glycosylation disorder in humans.

The possible mechanisms through which Cdk5 regulates differentiation, exocytosis, gene expression and transcription, cell-cell and cell-matrix adhesion, cell migration, tissue regeneration, senescence, apoptosis and hormone regulation in non-neuronal cells are discussed. A summary of the various non-neuronal cell types, cellular activities and genes or proteins affected by Cdk5 activity and a discussion of comparable events in neuronal cells are presented.

An updated view of member of Hu family of Au rich elements-binding proteins known as HuD and its role in multiple aspects of a neurons life including the initial phenotypic commitment and differentiation, as well as synaptic remodeling during learning paradigms and in response to injury and regeneration are presented. The current state of knowledge concerning the molecular and cellular events regulating the expression, activity and function of HuD in neurons is discussed.

As for other mRNA measurement methods, quantitative RT-PCR results need to be normalized relative to stably expressed genes. Widely used normalizing genes include [beta]-actin and glyceraldehyde-3-phosphate dehydrogenase. It has, however, become clear that these and other normalizing genes can display modulated patterns of expression across tissue types and during complex cellular processes such as cell differentiation and cancer progression. Our objective was to set the basis for identifying normalizing genes that displayed stable expression during enterocytic differentiation and between healthy tissue and adenocarcinomas of the human colon. We thus identified novel potential normalizing genes using previously generated cDNA microarray data and examined the alterations of expression of two of these genes as well as seven commonly used normalizing genes during the enterocytic differentiation process and between matched pairs of resection margins and primary carcinomas of the human colon using real-time RT-PCR. We found that ribosomal phosphoprotein P0 was particularly stable in all intestinal epithelial cell extracts, thereby representing a particularly robust housekeeping reference gene for the assessment of gene expression during the human enterocytic differentiation process. On the other hand, [beta]-2-microglobulin generated the best score as a normalizing gene for comparing human colon primary carcinomas with their corresponding normal mucosa of the resection margin, although others were found to represent acceptable alternatives. In conclusion, we identified and characterized specific normalizing genes that should significantly improve quantitative mRNA studies related to both the differentiation process of the human intestinal epithelium and adenocarcinomas of the human colon. This approach should also be useful to validate normalizing genes in other intestinal contexts. mRNA analysis; intestinal cell differentiation; colon cancer cells

Epstein--Barr virus (EBV) nuclear antigen 2 (EBNA2) association with RBP-J[kappa] is essential for regulation of virus and cell gene transcription and B lymphocyte transformation into infinitely proliferating lymphoblastoid cells (LCLs). To identify EBNA2-regulated cell genes in LCLs, an EBV recombinant that expresses EBNA2 with its C terminus fused in frame to a 4-hydroxytamoxifen (4HT)-dependent mutant estrogen receptor (E2HTF) was used to transform primary B lymphocytes to LCLs. In the presence of 4HT, E2HTF expression level and effects on the LMP1 promoter in transfected B JAB lymphoblasts were similar to EBNA2. In 4HT-supplemented medium, E2HTF EBV recombinant infected LCLs were also similar to EBNA2 LCLs in outgrowth but required higher serum and a restricted range of cell concentrations for consistent growth. In medium without 4HT, E2HTF localized to the cytoplasm, c-myc levels substantially decreased within 6 h, cells stopped growing, and levels of other EBNAs and LMP1 remained stable for 24 h. Over this 24-h period, 30 cell RNAs decreased 2-fold, and 51 other RNAs decreased 1.5-fold. These RNAs encode proteins important in cell adhesion or signaling, transcription, RNA processing, cell-cycle regulation, and survival. Real-time RT-PCR confirmed EBNA2-dependent expression of eight RNAs. RBP-J[kappa]/CBF1 | c-myc

The telencephalon shows the greatest degree of size variation in the vertebrate brain. Understanding the genetic cascade that regulates telencephalon growth is crucial to our understanding of how evolution of the normal human brain has supported such a variation in size. Here, we present a simple and quick approach to analyze this cascade that combines caged-mRNA technology and the use of antisense morpholino oligonucleotides in zebrafish embryos. Lhx2, a LIM-homeodomain protein, and Six3s (Six3b and Six3a), another homeodomain proteins, show very similar expression patterns early in forebrain development, and these are known to be involved in the growth of this part of the brain. The telencephalon of six3b and six3a double morphant (six3 morphant) embryos is markedly reduced in size due to impaired cellular proliferation. Head-specific overexpression of Lhx2 by photoactivation of a caged-lhx2 mRNA completely rescued this size reduction, whereas similar head-specific activation of Six3b could not rescue the knockdown effect of lhx2. In the forebrain of medaka embryos, Six3 facilitates cellular proliferation by sequestration of Geminin from Cdtl, a key component in the assembly of the prereplication complex. Our results suggest that Lhx2 may mediate an alternative or parallel pathway for control of cellular proliferation in the developing forebrain via Six3. Keywords: mRNA caging; lhx2; six3; Antisense morpholinos; Forebrain; Cell proliferation; Zebrafish

RNA editing adds and deletes uridine nucleotides in many pre-edited mRNAs to create translatable mRNAs in the mitochondria of the parasite Trypanosoma brucei. Kinetoplastid RNA editing protein B3 (KREPB3, formerly TbMP61) is part of the multiprotein complex that catalyzes editing in T. brucei and contains an RNase III motif that suggests nuclease function. Repression of KREPB3 expression, either by RNA interference in procyclic forms (PFs) or by conditional inactivation of an ectopic KREPB3 allele in bloodstream forms (BFs) that lack both endogenous alleles, strongly inhibited growth and in vivo editing in PFs and completely blocked them in BFs. KREPB3 repression inhibited cleavage of insertion editing substrates but not deletion editing substrates in vitro, whereas the terminal uridylyl transferase, U-specific exoribonuclease, and ligase activities of editing were unaffected, and [approximately equal to] 20S editosomes were retained. Expression of KREPB3 alleles with single amino acid mutations in the RNase III motif had similar consequences. These data indicate that KREPB3 is an RNA editing endonuclease that is specific for insertion sites and is accordingly renamed KREN2 (kinetoplastid RNA editing endonudease 2). KREN2 | trypanosome | editosome | kinetoplastid

Uridine insertion/deletion RNA editing in trypanosomatid mitochondria is a posttranscriptional RNA modification phenomenon required for translation of mitochondrial mRNAs. This process involves guide RNA-mediated cleavage at a specific site, insertion or deletion of Us from the 3' end of the 5' mRNA fragment, and ligation of the two mRNA fragments. The Leishmania major RNA ligase-containing complex protein 2 expressed in insect cells has a 3'-5' exoribonuclease activity and was therefore renamed RNA editing exonuclease 1 (REX1). Recombinant REX1 specifically trims 3' overhanging Us and stops at a duplex region. Evidence is presented that REX1 is responsible for deletion of the 3' overhanging Us from the bridged mRNA 5' cleavage fragment and that RNA editing ligase 1 is responsible for the ligation of the two mRNA cleavage fragments in U-deletion editing. The evidence involves both in vivo down-regulation of REX1 expression in Trypanosoma brucei by RNA interference and the reconstitution of precleaved U-deletion in vitro editing with only two recombinant enzymes: recombinant REX1 and recombinant RNA editing ligase 1. ligase | trypanosomes | REX1 | editing

mRNAs and major spliceosomal U snRNAs have many structural similarities to the different RNAs, yet they are exported by distinct factors. It is shown that the export switch depends on the length of the insertion but not on the position, indicating unequivocally that the switch is the result of the RNA length.

The hypochromicity data shows that DNA hairpin exhibits the best stacking interactions followed by all-RNA hairpin and last by all -2',5'-RNA hairpin. The regio isomeric 2',5'-linked RNA tetra loop can form super stable hairpin structures of comparable thermodynamic stabilities.

Cajal bodies are nuclear sites of small ribonucleoprotein (RNP) remodeling and maturation. A recent study describes the discovery of the Drosophila Cajal body, revealing some interesting insights into the subnuclear organization of RNA processing machineries among different species.

Several studies are conducted to explain the structure, as well as the activity relationships present in the RNA-editing adenosine deaminases (ADARs) reactions. The significance of the active site and the substrate structures in these RNA editing reactions is also determined.

Completion of the initial Monodelphis domestica genome assembly presents an opportunity to examine genome-wide phenomena in a marsupial. 105 MicroRNA loci containing 137 MicroRNAs were identified and annotated and 98 of the loci were mapped to the M. domestica genome,

Seven well-known genetic processes are discussed to detect parallels between molecules and organismal genetic phenomena. This knowledge will help in looking for patterns in nature leading to the discovery of shared evolutionary provenances.

Several genome-wide studies are conducted to explain the cell identity functions of the ladybird genes. The diversification of muscle and heart precursors is found to be a multistep process in ladybirds.

The C-terminal domain of the archaeal leucyl-tRNA synthetase (LeuRS_[DELTA](811-967)) has displayed a robust deacylation activity against Ile-t[RNA.sup.Ile], correctly formed by isoleucyl-tRNA synthetase. The analysis has shown that the requirement of the C-terminal domain for misediting prevention is unique to LeuRS, which has not recognized the anticodon of the cognate tRNA.

The region of DEAD-box protein CYT-19 responsible for binding nonspecifically to the adjacent RNA structure is examined by constructing a C-terminal truncation variant that lacks 49 amino acids and terminates at a domain boundary. The DExD/H-box proteins have contained arginine-rich ancillary domains, which function similarly as nonspecific RNA-binding elements that enhance general RNA chaperone activity.

The functions of microribonucleic acids (miRNAs) during early mammalian development are discussed. The impact of the loss of maternal inheritance of the miRNAs following specific deletions from growing oocytes is investigated, and it is concluded that maternal genes are largely controlled by miRNAs and are essential for the earliest stages of mouse embryonic development.

A study describes the importance of cytoplasmic processing bodies (PBs) in regulating the decay of mRNA (micro-ribonucleic acid) which consists of an adenine/uridine-rich element (ARE). It was found that ARE promotes the translational silencing and polysome disassembly of the mRNAs.

A protein (CsrD) that controls the degradation of CsrB/C RNAs is described. Analysis of the decay of CsrB RNA, both in vitro and in viro, suggested that CsrD is not a ribonuclease.

Advances of the structure, mechanism, regulation and biological functions of the adenosine deaminases that act on RNA enzymes are highlighted. A brief overview is presented on RNA editing by adenosine deamination, which refers to a variety of modification reactions that change the coding properties of RNA molecules from that encoded in their corresponding gene sequences.

The modifications of earlier published chromatin immunoprecipitation assay, is used to show that cotranscriptional splicing occurs approximately 1 kb after transcription of 3' splice site. This protects intron-containing nascent transcripts from effects of cleavage by intronic hammerhead ribozyme and suggests that high percentage of introns are recognized cotranscriptionally.

Study is conducted to show that depletion of GW182 leads to changes in mRNA expression profiles indicating that GW182 is a genuine component of miRNA pathway and that GW182 triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via a deadenylation and decapping mechanism. Evidence is also provided to show that mRNA degradation by miRNAs requires GW182, the CCR4:NOT dedenylase, and the DCP1:DCP2 decapping complexes.

An overview of earlier studies as well as recent findings that support the existence of an evolutionarily conserved role for cotranscriptional processes in the maintenance of genome stability is presented. The way by which different species protect the integrity of their genomes from potentially disastrous effects of nascent transcripts by diverse mechanisms and the possible mechanisms by which if unchecked, nascent transcripts can lead to genome instability is discussed.

RNA fluorescence in situ hybridization (RNA-FISH) together with protein immunolocalization is used to present evidence for the Arabidopsis chromatin-modifying small interfering RNS (siRNA) processing centers associated with nucleolus. The results have shown that maintenance of the heterochromatic state involves locus-specific nuclear RNA polymerase IV (Pol IVa) transcription followed by siRNA production and assembly of ARGONAUTE4 (AGO-4) and the largest-subunit genes (NRPD1b)-containing silencing complexes within nucleolar processing centers.

Five different amide-linked dimers including structures with homochiral linkers of the type X3'-C*H(CH3)-CO-NH-CH2 (X=O, CH2) as well as the corresponding analogues carrying methoxy groups at the 2'-position of the 3'-nucleoside were synthesized to analyze the influence of various chemistries of such five-atom linkers on the RNA-binding affinity. It was found that some of the five-atom-linked dimers lead to significantly higher RNA-binding affinities compared with that of native DNA.

The beta-glucuronidase (GUS) gene was introduced into acdS so that GUS was expressed under control of the acdS promoter and the disruption mutants were generated with mutations in a nitrogen fixation regulator gene, nifA. The main aim behind the effort was to examine the regulation of the acdS gene encoding 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase in Mesorhizobium loti MAFF303099 during symbiosis with the host legume Lotus japonicus.

A development and evaluation of a DNA microarray platform for the characterization of bacterial communities is presented in freshwater sediments based on a heterogeneous set of 70 16S rRNA-targeted oligonucleotide probes and directly labeled environmental RNA. Hybridization from environmental samples were validated by parallel fluorescence in situ hybridization combined with catalyzed reported deposition for maximizing sensitivity of the analysis.

The first study of RNA refolding in an unperturbed dynamic equilibrium was carried out by developing a new [1.sup.H]/[15.sup.N]-heteronuclear exchange-sensitive NMR method. It was found that the refolding rates are strongly affected by an entropically favorable preorientation of the replacing strand.

A study developing a strategy to encapsidate gold nanoparticles within a Red Clover necrotic mosaic virus (RCNMV) coat protein (CP) shell was conducted. The binding of the CP to the origin of assembly (OAS) initiates the assembly process that results in the encapsidation of the viral genome and insertion or attachment of the RCNMV RNA-2 stem loop to a foreign RNA into virions possessing a wild-type morphology.

A quantitative real-time PCR (qPCR) approach targeting 16S rRNA genes and three Dehalococcoides reductive dehalogenase (RDase) genes with assigned function is designed and evaluated. A large number of Dehalococcoides spp. contains as-yet-unidentified RDase genes, indicating that the current understanding of the dechlorinating Dehalococcoides community is incomplete.

By activating a suite of genes using the gene-targeting tool CRISPR-Cas9, researchers have turned connective-tissue cells called fibroblasts directly into neurons. Directly reprogramming cells from one identity to another could [...]