Localization and processing from a polycistronic precursor of novel snoRNAs in maize

We have shown previously that groups of U14 snoRNA genes are clustered with other, novel snoRNAs in maize. These genes are transcribed polycistronically from an upstream promoter to give a precursor snoRNA, which is processed by a splicing-independent mechanism. The clusters contain both box C/D snoRNAs, thought to guide rRNA O-ribose methylations, and the first plant box H/ACA snoRNA so far identified, thought to guide an rRNA pseudo-uridylation. Here we show that four novel snoRNAs identified as members of U14-containing gene clusters each show distinct sub-nucleolar localizations. Two of the snoRNAs (snoR2, a box H/ACA snoRNA, and snoR3, a box C/D snoRNA) colocalise closely with nucleolar rDNA transcription sites. A third box C/D snoRNA, U49, is localised to a more extended region which includes the transcription sites. On the other hand snoR1, another box C/D snoRNA, is located in a quite different region of the nucleolus, and shows a similar distribution to that of 7–2/MRP, a snoRNA involved in the later pre-rRNA cleavage reactions. This may indicate that this snoRNA is involved at later stages of processing, whereas the other snoRNAs are involved early or cotranscriptionally. Probes to intergenic spacer regions of the precursor snoRNA have been used to determine the location of the precursor. This shows a clear labelling of both the dense fibrillar component of the nucleolus, and of coiled bodies. This distribution implies that the polycistronic precursor is imported into the nucleolus for processing to the mature snoRNAs, and that the import or processing pathway involves coiled bodies.

Characterization of exon skipping mutants of the COP1 gene from Arabidopsis

The removal of introns from pre-mRNA requires accurate recognition and selection of the intron splice sites. Mutations which alter splice site selection and which lead to skipping of specific exons are indicative of intron/exon recognition mechanisms involving an exon definition process. In this paper, three independent mutants to the COP1 gene in Arabidopsis which show exon skipping were identified and the mutations which alter the normal splicing pattern were characterized. The mutation in cop1-1 was a G-->A change 4 nt upstream from the 3' splice site of intron 5, while the mutation in cop1-2 was a G-->A at the first nucleotide of intron 6, abolishing the conserved G within the 5' splice site consensus. The effect of these mutations was skipping of exon 6. The mutation in cop1-8 was G-->A in the final nucleotide of intron 10 abolishing the conserved G within the 3' splice site consensus and leading to skipping of exon 11. The splicing patterns surrounding exons 6 and 11 of COP1 in these three mutant lines of Arabidopsis provide evidence for exon definition mechanisms operating in plant splicing.

U14snoRNAs of the fern, Asplenium nidus, contain large sequence insertions compared with those of higher plants

Northern analyses of U14snoRNAs in different plant species showed the expected hybridising band of approximately 120 nt in monocotyledonous and dicotyledonous angiosperms. In the lower plant, Bird's nest fern (Asplenium nidus), U14s were larger and three hybridising RNAs of approximately 190, 210 and 250 nt were observed. RT-PCR cloning of all three size variants using primers to the conserved 5' and 3' ends of higher plant U14snoRNAs showed large insertions in one of the plant-specific regions corresponding in position to the yeast U14-specific Y-domain. The insertions are pyrimidine-rich in their 5' halves and purine-rich in their 3' halves and are likely to be sequestered in stem structures consistent with the proposed model of U14snoRNA secondary structure. The 5' flanking regions of one of the fern U14 variants was generated by PCR and lacked classical plant snRNA promoter elements.

Processing of vertebrate box C/D small nucleolar RNAs in plant cells

The recent isolation of a number of plant box C/D small nucleolar (sno)RNAs demonstrates the conservation in plants of sequence and structural elements of processed box C/D snoRNAs. Boxes C and D, and terminal inverted repeats are known to be essential for accumulation and processing in vertebrates and yeast. Processing of vertebrate box C/D snoRNAs was examined by expression of various mouse hsc70 intron 5-U14 constructs in tobacco protoplasts. Full-length U14 and internally deleted U14 accumulated in the plant cells. Human U3 and U8 fragments, consistent with processing to internal box C/C' sequences, also accumulated in the plant cells. The similarity of processing behaviour of the vertebrate box C/D constructs in tobacco protoplasts and Xenopus oocytes suggests the mechanism of processing, involving recognition and association of proteins, is conserved in plants.

Dilutional and modified ultrafiltration reduces pulmonary hypertension after operations for congenital heart disease: a prospective randomized study

OBJECTIVE

A prospective randomized study was performed to test whether removal of endothelin-1, by ultrafiltration techniques, will reduce pulmonary hypertension after operations for congenital heart disease.

METHODS

Twenty-four patients with pulmonary hypertension (systolic pulmonary/systemic arterial pressure ratio > 60%) undergoing cardiac operations were randomized into a control group (n = 12) having conventional ultrafiltration and an experimental group (n = 12) undergoing dilutional ultrafiltration during and modified ultrafiltration after cardiopulmonary bypass. Plasma endothelin-1, nitric oxide metabolites, and cyclic guanosine monophosphate were assayed before bypass, 10 minutes into bypass, after bypass, and 0, 3, 6, and 12 hours after the operation in both groups, as well as in the ultrafiltrates and after modified ultrafiltration in the experimental group. Both groups received alpha-blockers (chlorpromazine and/or prazosin) postoperatively using the same guidelines.

RESULTS

The ultrafiltrates contained significant amounts of endothelin-1 (1.81 +/- 0.86 pg/ml, dilutional, and 6.44 +/- 1.82 pg/ml, modified ultrafiltrate). Endothelin-1 and the pulmonary/systemic pressure ratio were significantly lower in experimental compared with control patients. Nitric oxide metabolites and cyclic guanosine monophosphate increased similarly in both groups for 12 hours after the operation (p = not significant). Three of 12 control patients (25%) but no experimental patients had pulmonary hypertensive crises (p = 0.07). The experimental patients required significantly less ventilatory support (67 +/- 47 hours vs 178 +/- 139 hours for control patients, p = 0.048).

CONCLUSIONS

Dilutional and modified ultrafiltration reduce endothelin-1 and the pulmonary/systemic pressure ratio postoperatively and may become an important adjunct for preventing pulmonary hypertension after operations for congenital heart disease in high-risk patients.

Metabolic and membrane-altering toxins, molecular differentiation factors, and pheromones in the evolution and operation of endocrine-signalling systems

The endocrine systems of vertebrates and higher invertebrates may have evolved functionally from as far back on the evolutionary scale as bacteria and early multicellular organisms and their biological communities, which have been shown to produce a variety of cyclic nucleotides, peptides, fatty acids, prostaglandins and sterols with endocrine-altering effects in primative as well as more highly evolved species.

An emerging superbug. Staphylococcus aureus becomes less susceptible to vancomycin

The name staphylococcus aureus comes from the Greek, staphyle (a bunch of grapes), kokkos (berry shaped), and aureus (golden). Morphologically, the pathogen resembles grapelike clusters of gram-positive cocci. The illustration here shows the bacteria infecting nasal epithelial tissue, and causing cell damage and inflammation. S. aureus has been knocking down our antibiotic defenses one by one, with some strains becoming dangerously less susceptible to vancomycin. Epidemiologists warn that these strains are coming soon to a hospital near you; be prepared by knowing how to identify the bug, notify infection control authorities, and use basic infection control procedures.

The ribonuclease P database

Ribonuclease P is responsible for the 5'-maturation of tRNA precursors. Ribonuclease P is a ribonucleoprotein, and in bacteria the RNA subunit alone is catalytically active in vitro , i.e., it is a ribozyme. The Ribonuclease P Database is a compilation of ribonuclease P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information, available via the World Wide Web (http: //www.mbio.ncsu.edu/RNaseP/home.html ).

Dynamic changes of endothelin-1, nitric oxide, and cyclic GMP in patients with congenital heart disease

BACKGROUND

Pulmonary hypertension causes major morbidity and mortality after congenital heart surgery, but its mechanism remains unclear.

METHODS AND RESULTS

Plasma endothelin-1 (ET-1), nitric oxide (NO), and cyclic GMP (cGMP) were assayed at 6 intervals in 50 children undergoing cardiopulmonary bypass (CPB): before CPB, 10 minutes into CPB, and 0, 3, 6, and 12 hours after CPB. Three groups based on pulmonary flow and pressure were analyzed: low flow (LF, n=21), high flow/low pressure (systolic pulmonary pressure/systemic pressure ratio, Pp/Ps<50%, HF-LP, n=11), and high flow/high pressure (Pp/Ps> or =50%, HF-HP, n=19). HF-HP and HF-LP received alpha-blockers (chlorpromazine and/or prazosin). HF-HP patients received nitric oxide donors (nitroglycerin/sodium nitroprusside). ET-1 peaked at 6 hours, with its highest level in the HF-HP group (P<.01, by ANOVA). ET-1 correlated significantly with Pp/Ps at 6 hours (r2=.43, P<.005). In the HF-HP group, ET-1 remained above the other groups at 12 hours (12.7+/-2.5 pg/mL versus 6.4+/-1.1 pg/mL versus 6.5+/-3.8 pg/mL P<.05 by ANOVA). NO metabolites were elevated equivalently for the HF-HP and HF-LP groups (5.7+/-2.6 micromol/L versus 0.3.5+/-2.5 micromol/L at 12 hours, P=NS) despite nitric oxide donors and the excess ET-1 in HF-HP patients. Levels of cGMP were similarly elevated in HF-HP and HF-LP patients during this study.

CONCLUSIONS

Endogenous NO may decrease vascular tone and maintain low pulmonary pressure in HF-LP patients. High levels of ET-1, inadequate NO production, and/or impaired responses to NO may increase pulmonary pressure in HF-HP patients.

Role of passenger leukocytes in allograft rejection: effect of depletion of donor alveolar macrophages on the local production of TNF-alpha, T helper 1/T helper 2 cytokines, IgG subclasses, and pathology in a rat model of lung transplantation

Acute lung allograft rejection is believed to be initiated by passenger leukocytes, such as alveolar macrophages (AM), in the donor organ, which release TNF-alpha, and present alloantigens to host lymphocytes, to up-regulated Th1 cellular and humoral immunity. However, the role of donor AM in local TNF-alpha synthesis, and their ability to induce local Th1 cellular and humoral immunity have not been evaluated. By depleting Brown Norway (BN, RT1n) rat lung allografts of AM before transplantation into Lewis rat (LEW, RT1(1)) recipients, the current study determined the role of donor AM in including the production of TNF-alpha, IFN-gamma (Th1 cytokine), IL-4 (Th2 cytokine), IgG subtypes, and rejection pathology in the allograft. The data show that compared with untreated BN allografts, pretransplant depletion of donor lung AM resulted in significantly less TNF-alpha, and IFN-gamma production in allograft bronchoalveolar lavage fluid with variable effects on local IL-4 production. Depletion of AM in the donor lung before transplantation affected the local production of several IgG subclasses. However, pretransplant depletion of donor AM had no effect on the development of the pathology of severe acute rejection. These data show that donor AM have a central role in the local synthesis of TNF-alpha and induce the production of IFN-gamma and IgG subtypes, locally, during acute lung allograft rejection. However, depletion of AM before transplantation does not prevent the development of severe acute rejection in BN rat lungs, transplanted into LEW recipients.

Role of passenger leukocytes in allograft rejection: effect of depletion of donor alveolar macrophages on the local production of TNF-alpha, T helper 1/T helper 2 cytokines, IgG subclasses, and pathology in a rat model of lung transplantation

Acute lung allograft rejection is believed to be initiated by passenger leukocytes, such as alveolar macrophages (AM), in the donor organ, which release TNF-alpha, and present alloantigens to host lymphocytes, to up-regulated Th1 cellular and humoral immunity. However, the role of donor AM in local TNF-alpha synthesis, and their ability to induce local Th1 cellular and humoral immunity have not been evaluated. By depleting Brown Norway (BN, RT1n) rat lung allografts of AM before transplantation into Lewis rat (LEW, RT1(1)) recipients, the current study determined the role of donor AM in including the production of TNF-alpha, IFN-gamma (Th1 cytokine), IL-4 (Th2 cytokine), IgG subtypes, and rejection pathology in the allograft. The data show that compared with untreated BN allografts, pretransplant depletion of donor lung AM resulted in significantly less TNF-alpha, and IFN-gamma production in allograft bronchoalveolar lavage fluid with variable effects on local IL-4 production. Depletion of AM in the donor lung before transplantation affected the local production of several IgG subclasses. However, pretransplant depletion of donor AM had no effect on the development of the pathology of severe acute rejection. These data show that donor AM have a central role in the local synthesis of TNF-alpha and induce the production of IFN-gamma and IgG subtypes, locally, during acute lung allograft rejection. However, depletion of AM before transplantation does not prevent the development of severe acute rejection in BN rat lungs, transplanted into LEW recipients.

Clusters of multiple different small nucleolar RNA genes in plants are expressed as and processed from polycistronic pre-snoRNAs

Small nucleolar RNAs (snoRNAs) are involved in many aspects of rRNA processing and maturation. In animals and yeast, a large number of snoRNAs are encoded within introns of protein-coding genes. These introns contain only single snoRNA genes and their processing involves exonucleolytic release of the snoRNA from debranched intron lariats. In contrast, some U14 genes in plants are found in small clusters and are expressed polycistronically. An examination of U14 flanking sequences in maize has identified four additional snoRNA genes which are closely linked to the U14 genes. The presence of seven and five snoRNA genes respectively on 2.05 and 0.97 kb maize genomic fragments further emphasizes the novel organization of plant snoRNA genes as clusters of multiple different genes encoding both box C/D and box H/ACA snoRNAs. The plant snoRNA gene clusters are transcribed as a polycistronic pre-snoRNA transcript from an upstream promoter. The lack of exon sequences between the genes suggests that processing of polycistronic pre-snoRNAs involves endonucleolytic activity. Consistent with this, U14 snoRNAs can be processed from both non-intronic and intronic transcripts in tobacco protoplasts such that processing is splicing independent.

Intracellular localization and unique conserved sequences of three small nucleolar RNAs

Three human small nucleolar RNAs (snoRNAs), E1, E2 and E3, were reported earlier that have unique sequences, interact directly with unique segments of pre-rRNA in vivo and are encoded in introns of protein genes. In the present report, human and frog E1, E2 and E3 RNAs injected into the cytoplasm of frog oocytes migrated to the nucleus and specifically to the nucleolus. This indicates that the nucleolar and nuclear localization signals of these snoRNAs reside within their evolutionarily conserved segments. Homologs of these snoRNAs from several vertebrates were sequenced and this information was used to develop RNA secondary structure models. These snoRNAs have unique phylogenetically conserved sequences.

Aggressive surgical management of sternoclavicular joint infections

BACKGROUND

Although the sternoclavicular joint is an unusual site for infection, thoracic surgeons may preferentially be called on to coordinate management of cases refractory to antibiotic therapy because of the anatomic relationship of this joint to major vascular structures.

METHODS

Since 1994 we have surgically managed nine sternoclavicular joint infections in eight patients. Associated medical problems were frequent and included diabetes mellitus (n = 2), end-stage renal disease (n = 2), hematologic disorders (n = 2), and multiple joints affected by sepsis (n = 4). Open joint exploration with drainage and débridement with the use of general anesthesia was performed in four patients. The remaining four patients (one with bilateral sternoclavicular joint infections) had computed tomographic evidence of diffuse joint and surrounding bone destruction with infection extending into mediastinal soft tissues. Surgical therapy for these five joint infections involved en bloc resection of the sternoclavicular joint with an ipsilateral pectoralis major muscle covering the bony defect.

RESULTS

There were two deaths unrelated to the surgical procedure. After a mean follow-up of 20 months, the remaining six survivors (seven joints) have complete healing with no apparent limitation in the range of motion even after en bloc resection.

CONCLUSIONS

Most cases of early sternoclavicular joint infections will respond to conservative measures. However, when radiographic evidence of infection beyond the sternoclavicular joint is present, en bloc resection, although seemingly aggressive, results in immediate eradication of all infection with negligible functional morbidity. Prolonged antibiotic therapy or continued local drainage procedures appear to have little value in these cases, adding only to patient care costs and the potential sequelae of chronic infections.

The ribonuclease P database

Ribonuclease P is responsible for the removal of leader sequences from tRNA precursors. Ribonuclease P is a ribonucleoprotein, and in bacteria the RNA subunit alone is catalytically active in vitro, i.e. it is a ribozyme. The Ribonuclease P Database is a compilation of ribonuclease P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information, available via the World Wide Web.

MHC class II expression--a new tool to assess dignity in adrenocortical tumours

One in seventy randomly selected individuals is supposed to host an adrenal mass. The increasing number of incidentally detected adrenocortical adenomas requires the effective and reliable evaluation of dignity. So far this has been determined through a difficult multi-parametric analysis. Since MHC class II antigens are expressed in the normal adrenal cortex with a restriction to the zona reticularis, we examined 28 adrenocortical incidentalomas, 10 adenomas, 13 cortical carcinomas, 2 metastases, 10 controls as well as the adrenocortical carcinoma cell line NCI-H295 immunohistochemically for the expression of HLA class II antigens. We showed, that the majority of the adenomas still express class II antigens, whereas the expression is abrogated in all carcinomas examined. Our results indicate, that the detection of HLA class II positive tumour cells excludes malignancy. Therefore, MHC class II antigens may serve as a novel tumour marker in the evaluation of dignity in adrenocortical tumours. These findings could change the strategy for the assessment of adrenal masses.

Structure and evolution of ribonuclease P RNA in Gram-positive bacteria

The sequences and structures of RNase P RNAs of some Gram-positive bacteria, e.g. Bacillus subtilis, are very different than those of other bacteria. In order to expand our understanding of the structure and evolution of RNase P RNA in Gram-positive bacteria, gene sequences encoding RNase P RNAs from 10 additional species from this evolutionary group have been determined, doubling the number of sequences available for comparative analysis. The enlarged data set allows refinement of the secondary structure model of these unusual RNase P RNAs and the identification of potential tertiary interactions between P10.1 and L12, and between L5.1 and L15.1. The newly-obtained sequences suggest that RNase P RNA underwent an abrupt, dramatic restructuring in the ancestry of the low-G+C Gram-positive bacteria after the divergence of the branches leading to the 'Clostridia and relatives' and the remaining low-G+C Gram-positive species. The unusual structures of the RNase P RNAs of Mycoplasma hyopneumoniae and M.floccularre are apparently derived from RNAs with Bacillus-like structure rather than from intermediate, partially restructured ancestral RNAs. The structure of the RNase P RNA from the photosynthetic Heliobacillus mobilis supports the relationship of this specie with Bacillus and Staphylococcus rather than the 'Clostridia and relatives' as suggested by the sequences of their small-subunit ribosomal RNAs.

Pulmonary hypertension after operations for congenital heart disease: analysis of risk factors and management

BACKGROUND

Management of pulmonary hypertension, a potentially fatal complication of operations to correct congenital heart disease, has evolved through the last 15 years. Monitoring of pulmonary arterial pressure and mixed venous saturation became available, and prophylactic use of alpha-blockers and other vasodilators increased. This study examines risk factors for morbidity and mortality from pulmonary hypertension after operations to correct congenital heart disease and evaluates the impact of management changes on outcomes.

METHODS

By means of multivariable logistic regression analysis, 880 high-risk patients with congenital heart disease (of 2484 patients undergoing cardiopulmonary bypass between January 1980 and December 1994) were analyzed to determine which were at risk for postoperative pulmonary hypertension and its associated morbidity and mortality.

RESULTS

Patients with atrioventricular canal (n = 182), truncus arteriosus (n = 47), total anomalous pulmonary venous connection (n = 90), transposition of great arteries (n = 97), hypoplastic left heart syndrome (n = 50), and ventricular septal defect (n = 414) demonstrated a higher risk of postoperative pulmonary hypertension. By multivariable logistic regression, preoperative pulmonary hypertension (p < 0.0001), absence of mixed venous saturation monitoring (p < 0.0001), and absence of prophylactic alpha-blockade (p = 0.0004) significantly increased postoperative pulmonary hypertension. Preoperative pulmonary hypertension (p < 0.001) and absence of prophylactic alpha-blockers (p = 0.0004) were significant risk factors for in-hospital death related to pulmonary hypertension. Repair at older age (except in the case of total anomalous pulmonary venous connection) was a significant risk for postoperative pulmonary hypertension (p = 0.03).

CONCLUSION

Mixed venous saturation monitoring and alpha-receptor blockade reduced the incidence of pulmonary hypertension after operations for congenital heart disease. Early definitive repair reduced morbidity and mortality from postoperative pulmonary hypertension.

Arabidopsis consensus intron sequences

We have analysed 998 Arabidopsis intron sequences in the EMBL database. All Arabidopsis introns to adhere to the :GU ... AG: rule with the exception of 1% of introns with :GC at their 5' ends. Virtually all of the introns contained a putative branchpoint sequence (YUNAN) 18 to 60 nt upstream of the 3' splice site. Although a polypyrimidine tract was much less apparent than in vertebrate introns, the most common nucleotide in the region upstream of the 3' splice site was uridine. Consensus sequences for 5' and 3' splice sites and branchpoint sequences for Arabidopsis introns are presented.

Evaluation of apoptotic parameters in normal and neoplastic human adrenal

The migration and proliferation of adrenocortical cells is accompanied by mechanisms of cellular knock-out. We compared the programmed cell death of normal and malignant adrenocortical tissues on the basis of apoptotic rates by the nonradioactive in situ end-labelling of DNA-fragments, immunohistochemistry against PCNA, CD95 and ultrastructural analysis. The highest labelling index (LI) was detectable in the outermost zones of the adrenal cortex of normal adrenals. Average LI in normal adrenal cortex was 20% whereas only 2% was detectable in adrenocortical neoplasms. MHC class II, which was previously shown to be involved in programmed cell death in lymphocyte populations (1), was detectable in normal and benign but not in malignant adrenocortical neoplastic cells. In conclusion, the analysis of apoptosis provides new aspects of normal adrenal zonation and allows the differentiation between normal and neoplastic adrenal cortex although the differentiation between malignant and benign neoplasms requires further markers.