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PubMed2004

Origin, evolution, and mechanism of 5' tRNA editing in chytridiomycete fungi.

5' tRNA editing has been demonstrated to occur in the mitochondria of the distantly related rhizopod amoeba Acanthamoeba castellanii and the chytridiomycete fungus Spizellomyces punctatus. In these organisms, canonical tRNA structures are restored by removing mismatched nucleotides at the first three 5' positions and replacing them with nucleotides capable of forming Watson-Crick base pairs with their 3' counterparts. This form of editing seems likely to occur in members of Amoebozoa other than A. castellanii, as well as in members of Heterolobosea. Evidence for 5' tRNA editing has not been found to date, however, in any other fungus including the deeply branching chytridiomycete Allomyces macrogynus. We predicted that a similar form of tRNA editing would occur in members of the chytridiomycete order Monoblepharidales based on the analysis of complete mitochondrial tRNA complements. This prediction was confirmed by analysis of tRNA sequences using a tRNA circularization/RT-PCR-based approach. The presence of partially and completely unedited tRNAs in members of the Monoblepharidales suggests the involvement of a 5'-to-3' exonuclease rather than an endonuclease in removing the three 5' nucleotides from a tRNA substrate. Surprisingly, analysis of the mtDNA of the chytridiomycete Rhizophydium brooksianum, which branches as a sister group to S. punctatus in molecular phylogenies, did not suggest the presence of editing. This prediction was also confirmed experimentally. The absence of tRNA editing in R. brooksianum raises the possibility that 5' tRNA editing may have evolved twice independently within Chytridiomycota, once in the lineage leading to S. punctatus and once in the lineage leading to the Monoblepharidales.

Chytridiomycota↗
PubMed1998

The mitochondrial ND8 gene from Crithidia oncopelti is not pan-edited.

RNA editing in trypanosomatid mitochondria is a process involving the insertion and deletion of uridine residues within the coding region of maxicircle messenger RNA transcripts. Twelve of the 17 known genes need editing to produce functional molecules. We have analyzed the predicted editing sites for the Crithidia oncopelti mitochondrial NADH-ubiquinone oxidoreductase subunit 8 (ND8) gene based on known mRNAs from other trypanosomatid species. All studied ND8 mRNAs undergo editing throughout the coding (and 3' noncoding) sequences (pan-editing). The 5' part of the C. oncopelti ND8 gene undergoes editing (like in Leishmania tarentolae and Trypanosoma brucei) while the 3' part of the pre-edited gene corresponds to the 3' part of edited ND8 mRNAs from other organisms. The organization of the ND8 gene in C. oncopelti mitochondrial DNA differs from all organisms investigated so far -- this gene is not pan-edited. We have also localized the guide RNA for cytochrome b between 9S rRNA and the ND8 gene. This RNA shows high homology to the gCYb-II gene of L. tarentolae and the gCyb gene of Crithidia fasciculata. A hypothetical editing pattern for the cytochrome b gene in C. oncopelti maxicircles is proposed.

Amino Acid Sequence↗
PubMed1998

In vivo lactate editing with simultaneous detection of choline, creatine, NAA, and lipid singlets at 1.5 T using PRESS excitation with applications to the study of brain and head and neck tumors.

Two T2-independent J-difference lactate editing schemes for the PRESS magnetic resonance spectroscopy localization sequence are introduced. The techniques, which allow for simultaneous acquisition of the lactate doublet (1.3 ppm) and edited singlets upfield of and including choline (3.2 ppm), exploit the dependence of the in-phase intensity of the methyl doublet upon the time interval separating two inversion (BASING) pulses applied to its coupling partner after initial excitation. Editing method 1, which allows for echo times TE = n/J (n = 1, 2, 3, . . . . ), alters the BASING carrier frequency for each of two cycles so that, for one cycle, the quartet is inverted, whereas, for the other cycle, the quartet is unaffected. Method 2, which also provides water suppression, allows for editing for TE > 1/J by alternating, between cycles, the time interval separating the inversion pulses. Experimental results were obtained at 1.5 T using a Shinnar Le-Roux-designed maximum phase inversion pulse with a filter transition bandwidth of 55 Hz. Spectra were acquired from phantoms and in vivo from the human brain and neck. In a neck muscle study, the lipid suppression factor, achieved partly through the use of a novel phase regularization algorithm, was measured to be over 10(3). Spectra acquired from a primary brain and a metastatic neck tumor demonstrated the presence of lactate and choline signals consistent with abnormal spectral patterns. The advantages and limitations of the methods are analyzed theoretically and experimentally, and significance of the results is discussed.

Aspartic Acid↗
PubMed2000

Uridylate addition and RNA ligation contribute to the specificity of kinetoplastid insertion RNA editing.

RNA editing in Trypanosoma brucei inserts and deletes uridylates (U's) in mitochondrial pre-mRNAs under the direction of guide RNAs (gRNAs). We report here the development of a novel in vitro precleaved editing assay and its use to study the gRNA specificity of the U addition and RNA ligation steps in insertion RNA editing. The 5' fragment of substrate RNA accumulated with the number of added U's specified by gRNA, and U addition products with more than the specified number of U's were rare. U addition up to the number specified occurred in the absence of ligation, but accumulation of U addition products was slowed. The 5' fragments with the correct number of added U's were preferentially ligated, apparently by adenylylated RNA ligase since exogenously added ATP was not required and since ligation was eliminated by treatment with pyrophosphate. gRNA-specified U addition was apparent in the absence of ligation when the pre-mRNA immediately upstream of the editing site was single stranded and more so when it was base paired with gRNA. These results suggest that both the U addition and RNA ligation steps contributed to the precision of RNA editing.

Animals↗
PubMed2002

Role of uridylate-specific exoribonuclease activity in Trypanosoma brucei RNA editing.

Editing of mitochondrial mRNAs in kinetoplastid protozoa occurs by a series of enzymatic steps that insert and delete uridylates (U's) as specified by guide RNAs (gRNAs). The characteristics of the 3' exonuclease activity that removes the U's following cleavage during deletion editing were determined by using an in vitro precleaved deletion assay that is based on ATPase subunit 6 pre-mRNA and gA6[14] gRNA. The exonuclease in partially purified editing complexes is specific for U's. The specificity occurs in the absence of gRNA, but its activity is enhanced by the presence of gRNA. The 3' pre-mRNA fragment enhances the specificity, but not the efficiency, of U removal. The activity is sensitive to the 5' phosphate of the 3' fragment, which is not required for U removal. The ability of the 3' U's to base pair with purines in the gRNA protects them from removal, suggesting that the U-specific 3' exonuclease (exoUase) is specific for U's which are not base paired. ExoUase is stereospecific and cannot remove (Rp)alpha-thio-U. The specificity of the exoUase activity thus contributes to the precision of RNA editing.

Animals↗
PubMed1999

In vivo carbon-edited detection with proton echo-planar spectroscopic imaging (ICED PEPSI): [3,4-(13)CH(2)]glutamate/glutamine tomography in rat brain.

A method for in vivo carbon-edited detection with proton echo-planar spectroscopic imaging (ICED PEPSI) is described. This method is composed of an echo-planar based acquisition implemented with (13)C-(1)H J editing spectroscopy and is intended for high temporal and spatial resolution in vivo spectroscopic imaging of (13)C turnover, from D-[1,6-(13)C]glucose to glutamate and glutamine, in the brain. At a static magnetic field strength of 7 T, both in vitro and in vivo chemical shift imaging data are presented with a spatial resolution of 8 microL (i.e., 1.25 x 1.25 x 5.00 mm(3)) and a maximum spectral bandwidth of 5.2 ppm in (1)H. Chemical shift imaging data acquired every 11 minutes allowed detection of regional [4-(13)CH(2)]glutamate turnover in rat brain. The [4-(13)CH(2)]glutamate turnover curves, which can be converted to tricarboxylic acid cycle fluxes, showed that the tricarboxylic acid cycle flux (V(TCA)) in pure gray and white matter can range from 1.2 +/- 0.2 to 0.5 +/- 0.1 micromol/g/min, respectively, for morphine-anesthetized rats. The mean cortical V(TCA) from 32 voxels of 1.0 +/- 0.3 micromol/g/min (N = 3) is in excellent agreement with previous localized measurements that have demonstrated that V(TCA) can range from 0.9-1.1 micromol/g/min under identical anesthetized conditions. Magn Reson Med 42:997-1003, 1999.

Animals↗
PubMed2006

Testing the Paleolithic-human-warfare hypothesis of blood-injection phobia in the Baltimore ECA Follow-up Study--towards a more etiologically-based conceptualization for DSM-V.

OBJECTIVE: The research agenda for the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-V) has emphasized the need for a more etiologically-based classification system, especially for stress-induced and fear-circuitry disorders. Testable hypotheses based on threats to survival during particular segments of the human era of evolutionary adaptedness (EEA) may be useful in developing a brain-evolution-based classification for the wide spectrum of disorders ranging from disorders which are mostly overconsolidationally such as PTSD, to fear-circuitry disorders which are mostly innate such as specific phobias. The recently presented Paleolithic-human-warfare hypothesis posits that blood-injection phobia can be traced to a "survival (fitness) enhancing" trait, which evolved in some females of reproductive-age during the millennia of intergroup warfare in the Paleolithic EEA. The study presented here tests the key a priori prediction of this hypothesis-that current blood-injection phobia will have higher prevalence in reproductive-age women than in post-menopausal women. METHOD: The Diagnostic Interview Schedule (version III-R), which included a section on blood and injection phobia, was administered to 1920 subjects in the Baltimore ECA Follow-up Study. RESULTS: Data on BII phobia was available on 1724 subjects (1078 women and 646 males). The prevalence of current blood-injection phobia was 3.3% in women aged 27-49 and 1.1% in women over age 50 (OR 3.05, 95% CI 1.20-7.73). [The corresponding figures for males were 0.8% and 0.7% (OR 1.19, 95% CI 0.20-7.14)]. CONCLUSIONS: This epidemiological study provides one source of support for the Paleolithic-human-warfare (Paleolithic-threat) hypothesis regarding the evolutionary (distal) etiology of bloodletting-related phobia, and may contribute to a more brain-evolution-based re-conceptualization and classification of this fear circuitry-related trait for the DSM-V. In addition, the finding reported here may also stimulate new research directions on more proximal mechanisms which can lead to the development of evidence-based psychopharmacological preventive interventions for this common and sometimes disabling fear-circuitry disorder.

Adult↗
PubMed1991

ACE: a single-shot method for water-suppressed localization and editing of spectra, images, and spectroscopic images.

A versatile method for localized (1H) NMR spectroscopy is presented. The method intrinsically combines B0-based spatial localization with the possibility of water suppression and spectral editing. With this sequence it is feasible to localize not only single spectra but also phase-encoded images and spectroscopic images. The technique essentially integrates the "Hahn spin-echo" with the "stimulated echo" sequence and is therefore called ACE (acquiring combined echoes). It realizes water-suppressed three-dimensional localization in a single shot and can be used for localized shimming. Studies in which the new method is applied to phantoms with metabolites diluted at low concentrations are presented. Discrimination between lactate and alanine, employing an adapted spectral editing method with complete inversion, combined with simultaneous water suppression and localization of a 0.06-cc volume is shown. The suppression of signals from outside the selected volume is greater than or equal to 24,000. Also, the method is demonstrated by in vivo experiments at 6.3 T. Localized water-suppressed 1H spectra are obtained completely noninvasively, leaving scalp and fur intact, from well-defined volumes of 0.15 cc in the brain of a living rat. Water-suppressed spectroscopic imaging over a localized volume with "body" coil excitation and noninvasive surface coil detection yielded spectra from voxels as small as 25 microliters in the in vivo rat brain.

Animals↗
PubMed1989

An in vitro system for the editing of apolipoprotein B mRNA.

A novel form of RNA editing generates two forms of apolipoprotein B (apo-B) mRNA by converting C at nucleotide 6666 to U or a U-like base. We have established an in vitro system for the editing of apo-B mRNA using synthetic RNAs and S100 extracts from rat hepatoma cells. Editing was detected by a sensitive primer extension assay and confirmed by DNA sequencing. The in vitro editing activity is specific and sensitive to proteinase K. Apo-B100 RNAs were synthesized in vitro from deletion mutants spanning nucleotide 6666. Synthetic RNAs containing 2383, 483, and 55 nucleotides of apo-B mRNA sequence were edited in vitro with similar efficiency, but an RNA containing 26 nucleotides was not edited.

Animals↗
PubMed1996

RNA editing: a mechanism for gRNA-specified uridylate insertion into precursor mRNA.

In the mitochondria of trypanosomatid protozoa the precursors of messenger RNAs (pre-mRNAs) have their coding information remodeled by the site-specific insertion and deletion of uridylate (U) residues. Small trans-acting guide RNAs (gRNAs) supply the genetic information for this RNA editing. An in vitro system was developed to study the mechanism of U insertion into pre-mRNA. U-insertion editing occurs through a series of enzymatic steps that begin with gRNA-directed pre-mRNA cleavage. Inserted U's are derived from free uridine triphosphate and are added to the 3' terminus of a 5' pre-mRNA cleavage product. gRNA specifies edited RNA sequence at the subsequent ligation step by base pairing-mediated juxtaposition of the 3' cleavage product and the processed 5' cleavage product. gRNA/pre-mRNA chimeras, purported intermediates, seem to be abortive end products of the same reaction.

Animals↗
PubMed2002

Distinct functions of two RNA ligases in active Trypanosoma brucei RNA editing complexes.

Trypanosome RNA editing is a unique U insertion and U deletion process that involves cycles of pre-mRNA cleavage, terminal U addition or U removal, and religation. This editing can occur at massive levels and is directed by base pairing of trans-acting guide RNAs. Both U insertion and U deletion cycles are catalyzed by a single protein complex that contains only seven major proteins, band I through band VII. However, little is known about their catalytic functions, except that band IV and band V are RNA ligases and genetic analysis indicates that the former is important in U deletion. Here we establish biochemical approaches to distinguish the individual roles of these ligases, based on their distinctive ATP and pyrophosphate utilization. These in vitro analyses revealed that both ligases serve in RNA editing. Band V is the RNA editing ligase that functions very selectively to seal in U insertion (IREL), while band IV is the RNA editing ligase needed to seal in U deletion (DREL). In combination with our earlier findings about the cleavage and the U-addition/U-removal steps of U deletion and U insertion, these results show that all three steps of these editing pathways exhibit major differences and suggest that the editing complex could have physically separate regions for U deletion and U insertion.

Adenosine Triphosphate↗
PubMed1995

A histogram-based algorithm for semiautomated three-dimensional craniofacial modeling.

RATIONALE AND OBJECTIVES: I conducted a study designed to facilitate thresholding and reduce volume averaging in three-dimensional (3D) computed tomography (CT) craniofacial modeling. METHODS: Three-dimensional CT reconstructions of orbits from two cadavers and seven clinical cases were generated from paired axial and coronal data. A histogram-based algorithm that was based on preliminary phantom and craniofacial specimen trials was applied to orbital data to identify volume averaged regions of thin bone to be used in conjunction with standard bone thresholds. Region-of-interest measurement of the orbital floors on the original two-dimensional slice data assessed algorithm performance. RESULTS: In five of the nine cases (55%), configuration of the superimposed histograms predicted regions of volume averaging. In only one case did such a region localize to the orbital floor. In the remaining four cases, the air-mucosa interface deep to the orbital floor was identified by the histogram method. CONCLUSION: Operator-dependent editing remains superior to this histogram-based algorithm in reducing volume averaging in 3D craniofacial modeling.

Adult↗
PubMed1994

Requirements for editing in the genomic RNA of hepatitis delta virus.

Hepatitis delta virus is a satellite of the hepatitis B virus which provides the surface antigen for the viral coat. The genome of the hepatitis delta virus consists of a single-stranded, circular RNA of 1679 nucleotides which forms a rod structure due to a high extent of self homology and which replicates via synthesis of an antigenomic RNA in a rolling circle mechanism similar to plant viroids. The antigenomic RNA contains the open reading frame for the delta-antigen which exists in two isoforms, p24 and p27. The formation of these two isoforms is explained by RNA editing at nucleotide 1012 which changes the stop translation codon UAG at amino acid residue 196 into the codon UGG for tryptophan and extends the open reading frame for the synthesis of p27. In order to investigate whether the editing occurs cotranscriptionally during RNA replication or is a posttranscriptional base modification in the genomic or antigenomic RNA, replication defective deletion mutants of the HDV genome were constructed and expressed in COS-7 cells. Editing was demonstrated in non-replicating fragments of genomic HDV RNA but not in antigenomic HDV RNA fragments. The sequences from nucleotide position 337-1200 of the genomic RNA were sufficient to enable low levels of editing. Editing at position 1012 required the opposite strand of the RNA rod from nucleotide position 337-783. Replicating circular HDV RNA was much more efficiently edited than non-replicating full length genomic HDV RNA. Expression of delta-antigen in trans did not complement the low editing efficiency of replication defective genomic HDV RNA. These results demonstrate posttranscriptional U to C editing in the genomic HDV RNA and exclude misincorporation during HDV RNA replication as the editing mechanism. The minimal structural requirements for HDV RNA editing reside between nucleotide position 337-1200.

Animals↗
PubMed1995

Accuracy of automated DNA sequencing: a multi-laboratory comparison of sequencing results.

A double-stranded (ds)DNA template of "unknown" sequence was distributed to approximately 80 core DNA sequencing laboratories by the Association of Biomolecular Resource Facilities (ABRF) for automated DNA sequence analysis. Forty-four different facilities responded with 83 usable sequence submissions. These sequences were grouped by both sequencing protocol (dye-primer or dye-terminator) and whether manually edited or not. The sequences were aligned with the known sequence, and the number of correct base calls, insertions, deletions, no-calls and miscalls were determined for each group. The dye-primer sequencing protocol provided the longest and most accurate sequence. The edited dye-primer data were > 95% accurate out to 400-450 bp, while the edited dye-terminator data could call only 300-350 bases at this accuracy. However, 75% of the laboratories in this sampling preferred the dye-terminator protocol, presumably because of its versatility and convenience. Laboratories that manually edited the automatically called data were able to obtain an additional 100 bases of good sequence when the dye-primer protocol was used. Surprisingly though, editing of dye-terminator results did not increase the amount of good sequence, although the dye-terminator protocol had a superior base-calling ability within the first 100 bases of called sequence.

Autoanalysis↗
PubMed2006

Medicare and Medicaid programs; fire safety requirements for certain health care facilities; amendment. Final rule.

This final rule adopts the substance of the April 15, 2004 tentative interim amendment (TIA) 00-1 (101), Alcohol Based Hand Rub Solutions, an amendment to the 2000 edition of the Life Safety Code, published by the National Fire Protection Association (NFPA). This amendment allows certain health care facilities to place alcohol-based hand rub dispensers in egress corridors under specified conditions. This final rule also requires that nursing facilities at least install battery-operated single station smoke alarms in resident rooms and common areas if they are not fully sprinklered or they do not have system-based smoke detectors in those areas. Finally, this final rule confirms as final the provisions of the March 25, 2005 interim final rule with changes and responds to public comments on that rule.

Alcohols↗
PubMed1999

Clinical evaluation of lymph node metastasis in gastric cancer defined by the fifth edition of the TNM classification in comparison with the Japanese system.

BACKGROUND: This study compared the classification of lymph node metastasis according to the number of involved nodes based on the new tumour node metastasis (TNM) system (fifth edition) with the classification by the Japanese Research Society for Gastric Cancer from an anatomical perspective. METHODS: The two classifications were related to long-term results in 1489 patients with gastric cancer who underwent gastrectomy with systematic extended lymphadenectomy. RESULTS: Both classifications performed well as prognostic indicators (5-year survival rates: pathological (p) N0, 89 per cent; pN1, 66 per cent; pN2, 34 per cent; pN3, nil; and M1, 10 per cent by the TNM classification; n0, 89 per cent; n1, 63 per cent; n2, 46 per cent; n3, 20 per cent; and n4, 8 per cent by the Japanese classification). For regional lymph nodes, the TNM classification was a better index of the prognosis. Significant survival differences were observed among patients with M1 disease according to the number of involved lymph nodes (between one and six nodes, 48 per cent; seven to 15 nodes, 12 per cent; more than 15 nodes, 2 per cent), indicating that patients with distant metastatic lymph nodes (M1) should also be classified by the number of involved nodes. On the other hand, the Japanese classification has the added benefit of being a good indicator of the anatomical extent of lymphadenectomy. CONCLUSION: The new TNM classification provided a better index of the prognosis of patients who underwent systematic lymph node dissection. However, both classifications have specific benefits in the surgical treatment of gastric cancer.

Female↗