HIV-1 RRE RNA acts as an RNA silencing suppressor by competing with TRBP-bound siRNAs

Several proteins and RNAs expressed by mammalian viruses have been reported to interfere with RNA interference (RNAi) activity. We investigated the ability of the HIV-1-encoded RNA elements Trans-Activation Response (TAR) and Rev-Response Element (RRE) to alter RNAi. MicroRNA let7-based assays showed that RRE is a potent suppressor of RNAi activity, while TAR displayed moderate RNAi suppression. We demonstrate that RRE binds to TAR-RNA Binding Protein (TRBP), an essential component of the RNA Induced Silencing Complex (RISC). The binding of TAR and RRE to TRBP displaces small interfering (si)RNAs from binding to TRBP. Several stem-deleted RRE mutants lost their ability to suppress RNAi activity, which correlated with a reduced ability to compete with siRNA-TRBP binding. A lentiviral vector expressing TAR and RRE restricted RNAi, but RNAi was restored when Rev or GagPol were coexpressed. Adenoviruses are restricted by RNAi and encode their own suppressors of RNAi, the Virus-Associated (VA) RNA elements. RRE enhanced the replication of wild-type and VA-deficient adenovirus. Our work describes RRE as a novel suppressor of RNAi that acts by competing with siRNAs rather than by disrupting the RISC. This function is masked in lentiviral vectors co-expressed with viral proteins and thus will not affect their use in gene therapy. The potent RNAi suppressive effects of RRE identified in this study could be used to enhance the expression of RNAi restricted viruses used in oncolysis such as adenoviruses.

A Conserved Target Site in HIV-1 Gag RNA is Accessible to Inhibition by Both an HDV Ribozyme and a Short Hairpin RNA

Antisense-based molecules targeting HIV-1 RNA have the potential to be used as part of gene or drug therapy to treat HIV-1 infection. In this study, HIV-1 RNA was screened to identify more conserved and accessible target sites for ribozymes based on the hepatitis delta virus motif. Using a quantitative screen for effects on HIV-1 production, we identified a ribozyme targeting a highly conserved site in the Gag coding sequence with improved inhibitory potential compared to our previously described candidates targeting the overlapping Tat/Rev coding sequence. We also demonstrate that this target site is highly accessible to short hairpin directed RNA interference, suggesting that it may be available for the binding of antisense RNAs with different modes of action. We provide evidence that this target site is structurally conserved in diverse viral strains and that it is sufficiently different from the human transcriptome to limit off-target effects from antisense therapies. We also show that the modified hepatitis delta virus ribozyme is more sensitive to a mismatch in its target site compared to the short hairpin RNA. Overall, our results validate the potential of a new target site in HIV-1 RNA to be used for the development of antisense therapies.

Ammonium release from a blanket peatland into headwater stream systems

Hydrochemical sampling of South Pennine (UK) headwater streams draining eroded upland peatlands demonstrates these systems are nitrogen saturated, with significant leaching of dissolved inorganic nitrogen (DIN), particularly ammonium, during both stormflow and baseflow conditions. DIN leaching at sub-catchment scale is controlled by geomorphological context; in catchments with low gully densities ammonium leaching dominates whereas highly gullied catchments leach ammonium and nitrate since lower water tables and increased aeration encourages nitrification. Stormflow flux calculations indicate that: approximately equivalent amounts of nitrate are deposited and exported; ammonium export significantly exceeds atmospheric inputs. This suggests two ammonium sources: high atmospheric loadings; and mineralisation of organic nitrogen stored in peat. Downstream trends indicate rapid transformation of leached ammonium into nitrate. It is important that low-order headwater streams are adequately considered when assessing impacts of atmospheric loads on the hydrochemistry of stream networks, especially with respect to erosion, climate change and reduced precipitation.

Characterization of the TRBP domain required for dicer interaction and function in RNA interference

BACKGROUND

Dicer, Ago2 and TRBP are the minimum components of the human RNA-induced silencing complex (RISC). While Dicer and Ago2 are RNases, TRBP is the double-stranded RNA binding protein (dsRBP) that loads small interfering RNA into the RISC. TRBP binds directly to Dicer through its C-terminal domain.

RESULTS

We show that the TRBP binding site in Dicer is a 165 amino acid (aa) region located between the ATPase and the helicase domains. The binding site in TRBP is a 69 aa domain, called C4, located at the C-terminal end of TRBP. The TRBP1 and TRBP2 isoforms, but not TRBPs lacking the C4 site (TRBPsDeltaC4), co-immunoprecipitated with Dicer. The C4 domain is therefore necessary to bind Dicer, irrespective of the presence of RNA. Immunofluorescence shows that while full-length TRBPs colocalize with Dicer, TRBPsDeltaC4 do not. tarbp2-/- cells, which do not express TRBP, do not support RNA interference (RNAi) mediated by short hairpin or micro RNAs against EGFP. Both TRBPs, but not TRBPsDeltaC4, were able to rescue RNAi function. In human cells with low RNAi activity, addition of TRBP1 or 2, but not TRBPsDeltaC4, rescued RNAi function.

CONCLUSION

The mapping of the interaction sites between TRBP and Dicer show unique domains that are required for their binding. Since TRBPsDeltaC4 do not interact or colocalize with Dicer, we suggest that TRBP and Dicer, both dsRBPs, do not interact through bound dsRNA. TRBPs, but not TRBPsDeltaC4, rescue RNAi activity in RNAi-compromised cells, indicating that the binding of Dicer to TRBP is critical for RNAi function.

Arsenic retention and release in ombrotrophic peatlands

Organic matter can play an important role in the mobility and fate of As in the environment, but there is a lack of data on As biogeochemistry in ombrotrophic peatlands. The aim of this study was to investigate As retention and release in atmospherically contaminated ombrotrophic peat soils in the Peak District National Park (UK). Solid phase As concentrations in the peat soils exceed 25 mg kg(-1). Solid phase As and Fe concentrations are closely correlated at sites where the peat is subjected to drying and oxic conditions. In a wetter zone of the bog, solid phase As and Fe distributions are decoupled, suggesting that As retention in these systems is not solely controlled by the presence of Fe oxides. Comparison of solid phase As and Pb distributions reveals that As has been subjected to post-depositional mobility in areas of water table fluctuation. Conversely, at permanently waterlogged locations As is immobile. Detailed stream water sampling reveals that As is released from the organic-rich uplands soils into the fluvial system. Dissolved As concentrations are highly variable, with values ranging from 0.20 to 7.28 microg l(-1). Stream water As concentrations are elevated during late summer stormflow periods when there has been re-wetting of the peat after significant water table draw-down. Dissolved As is strongly correlated to dissolved organic carbon under stormflow and baseflow. The results of this study suggest that organic matter plays an important role in As dynamics in ombrotrophic peatlands, but further work is needed to identify the exact As binding and release mechanisms. Drying and re-wetting of ombrotrophic peat soils and associated changes in redox status has the potential to lead to increased As mobility. Further work is needed to provide information on how predicted climate change will influence As cycling at sites containing a legacy of atmospheric contamination.

Sulphur leaching from headwater catchments in an eroded peatland, South Pennines, U.K

A detailed investigation into sulphur leaching in peatland headwater catchments in the South Pennines, UK shows that, despite significant reductions in sulphur emissions, sulphur remains a key acidifier. This sulphur can be considered as legacy atmospheric pollution, stored within the peat by processes of dissimilatory sulphate reduction and now being leached into the region's surface waters. Persistently lower water tables at gully edge locations define a thick erosional acrotelm that is vulnerable to aeration, oxidation and flushing throughout the year, and not solely confined to periods of drought. Stream discharge behaves as a two-end member system, whereby pre-event water, rich in DOC and sulphate, is diluted by event water as a result of event water flowing through fast flow pathways such as macropores and overland flow. A rapid increase in water table elevation during the storm and a decrease in elevation after the storm indicate that event water has infiltrated the peat and has then been released into the stream. Streamwaters in peat dominated upland catchments with high densities of gullying have high concentrations of sulphate and low concentrations of DOC, whereas the reverse is true for those catchments with low densities of gullying. This is consistent with the concept that high concentrations of sulphate can suppress the solubility of DOC. A significant store of sulphate exists within South Pennine peats, and continued gully erosion will enhance sulphur leaching meaning that the timescale involved for any depletion is uncertain. It is therefore important that models predicting recovery from acidification in these upland systems include an understanding of how this stored sulphur is being leached, especially with respect to gully erosion, climate change and reduced precipitation.

Comparison of psychological symptoms of women requesting removal of breast implants with those of breast cancer patients and healthy controls

Concern about the safety of silicone breast implants has led many women with numerous physical and psychological symptoms to seek breast implant removal. This retrospective group comparison study describes the psychological profile of women requesting breast implant removal compared with two control groups. The Brief Symptom Inventory was used to compare psychological symptoms of three groups of women: a preoperative breast implant group requesting removal of implants (n = 78), a postoperative breast cancer group without breast implants (n = 64), and a control group with no known breast disease and unknown breast implant status (n = 68). Scores were compared on the Global Severity Index of the Brief Symptom Inventory as well as on nine subscales: somatization, obsessive-compulsiveness, interpersonal sensitivity, depression, anxiety, hostility, phobic anxiety, paranoid ideation, and psychoticism. The breast implant group had significantly elevated Global Severity Index scores, as well as somatization, obsessive-compulsiveness, depression, hostility, and anxiety subscale scores, when compared with the other groups. Post hoc data analysis revealed that women who had implants after subcutaneous mastectomy as prophylaxis for breast cancer (n = 18) had a significantly different symptom profile and higher Global Severity Index scores than women who had cosmetic augmentation (n = 53). Additionally, women who had subcutaneous mastectomy and implants had significantly higher subscales of interpersonal sensitivity, phobic anxiety, paranoid ideation, and psychoticism than the cosmetic implant subjects. Women requesting removal of silicone breast implants had greater psychological distress than women who were recently diagnosed with breast cancer or controls with no known breast disease and unknown implant status. Within the implant group, however, women who had subcutaneous mastectomy showed greater psychological disturbance than those who had augmentation mammaplasty.

The relationship of ambulation in labor to operative delivery

An abbreviated version of the Nurse-Midwifery Clinical Data Set was used to gather data on all women (n = 3,049) who began intrapartum care with a nurse-midwife in three sites. Demographic information, intrapartum care, and outcomes were recorded. The association of ambulation in labor with operative delivery was examined in a low-risk sample (n = 1,678) of women who did not receive care measures (epidural anesthesia, oxytocin induction or augmentation) that preclude mobility in labor. Women who ambulated for a significant amount of time during labor (compared with those who did not ambulate) had half the rate of operative delivery (2.7% vs. 5.5%).

Factors related to perineal trauma in childbirth

We conducted an observational cohort study in three nurse-midwifery services to identify patient characteristics and clinical care measures related to perineal trauma at birth. Data were collected on all women who began care with a nurse-midwife in labor, using an adaptation of the Nurse-Midwifery Clinical Data Set (n = 3,049). Study variables included demographics, perineal management techniques and position for birth, and other intrapartum care and events. Univariate and multivariate analyses showed that episiotomy was strongly related to fetal bradycardia, prolonged second stage, ethnic status, and maternal education level. Warm compresses and flexion/counter-pressure to slow delivery were protective. Spontaneous lacerations were influenced by these factors as well. The lateral position for birth was protective, and use of oils or lubricants and the lithotomy position increased lacerations, Multisite studies in nurse-midwifery practices may provide an ideal means of determining effective care measures in healthy populations.

Psychological and rheumatic symptoms of women requesting silicone breast implant removal

In this case series, we describe the psychological and rheumatic symptoms of 52 women requesting breast implant removal. Main outcome measures include psychological evaluation with the Brief Symptom Inventory and the Beck Depression Inventory. Clinical evaluation was performed using a rheumatic symptom survey. Results noted elevation of all Brief Symptom Inventory subscales (highest in Somatization and Obsessive-Compulsive), and the Beck Depression Inventory showed mild depression. Rheumatic survey noted a mean of 12 of 23 symptoms. In conclusion, psychological distress and mild depression are noted in this group, who also may experience rheumatic symptoms of connective tissue disease. There was a moderate positive correlation between rheumatic symptoms and psychological distress.

The health status of women following cosmetic surgery

A retrospective study was performed to determine the frequency of new symptoms and diseases after silicone breast implantation. Questionnaires were mailed to 826 women who made up a breast implant group (n = 516) and a control group who had undergone blepharoplasty (n = 124), liposuction (n = 111), or rhinoplasty (n = 75). Responses were obtained from 370 women (45 percent); however, 68 of these patients (18 percent) were considered ineligible. The overall response rate was 59 percent for the breast implant group and 46 percent for controls. The 302 eligible women included patients with silicone breast implants (n = 222) and controls (n = 80). Women with implants were significantly younger than controls, the median age of women with breast implants being 37 years compared with 46.5 years for controls (p < 0.0001). We compared the incidence of 23 symptoms and 4 connective-tissue diseases after cosmetic surgery in the two groups. The symptoms of swollen glands under arms (p < 0.05) and tender glands under arms (p < 0.01) were statistically more frequent in the breast implant group. The symptom change in skin color was more common in the controls (p < 0.001). The Bonferroni correction for multiple (27) endpoints adjusts the 5 and 1 percent significance cutoff points to 0.00185 and 0.00037, respectively, leaving only change of skin color significant at the 5 percent level on the adjusted data. No cases of scleroderma or lupus were found, and the incidence of arthritis was not significantly different between the implant and control groups.

Self-inflicted burns: a ten-year retrospective study

In this 10-year retrospective survey of 2216 admissions to a regional burn center, 15 patients (0.67%) had self-inflicted burn wounds. The burns were serious, with a mean abbreviated burn severity index of 11.2, and eight patients died of their injuries. Nine patients had a documented history of psychiatric problems, seven of whom had undergone a previous psychiatric hospitalization. A psychiatric assessment was obtained for 12 patients immediately after self-immolation, and all but one had a major psychiatric disorder. Seven patients had major depression and four had chronic paranoid schizophrenia. Motives were assessed, both by chart review and by interview of five available survivors and of relatives of nonsurvivors. Fewer than half actually intended to kill themselves; equally important was the theme of attempting to control internal psychotic states.

Auscultated fetal heart rate accelerations. An alternative to the nonstress test

This nonexperimental, descriptive correlational study was conducted to determine whether a significant difference exists between the results of an electronically monitored nonstress test (NST) and those of auscultation for single fetal heart rate acceleration, the auscultated acceleration test (AAT). Of 130 NSTs, both the NST and the AAT were reactive in 105 cases and both were nonreactive in seven cases. Eighteen nonreactive AATs went on to have reactive NSTs (72.00% false-positive rate). There were no reactive AATs that went on to have nonreactive NSTs (0% false-negative rate). Various recommendations are made for future research in an attempt to decrease the false-positive rate. The McNemar's test for data analysis used in previous research indicated that there was a significant difference between the two tests. However, the sensitivity (100%) and specificity (85.37%) of the AAT indicate that the test is valid in predicting the results of the NST and thus appears to be a valid screening tool for fetal well-being and may be a reliable alternative to the NST.

The role of separate molecular domains in the structure of phytochrome from etiolated Avena sativa L

The spectral properties of peptides generated from etiolated-Avana, 124-kDa (kilodalton) phytochrome by endogenous protease(s) have been studied to assess the role of the amino-terminal and the carboxyl-terminal domains in maintaining the proper interaction between protein and chromophore. The amino-terminal, 74-kDa chromopeptide, a degradation product of the far-red absorbing form of the pigment (Pfr), is shown to be spectrally similar to the 124-kDa, undegraded molecule. The minimum and maximum of the difference spectrum (Pr-Pfr) are 730 and 665 nm, respectively, and the spectral-change ratio is unity. Also, like undegraded, 124-kDa phytochrome, the 74-kDa peptide exhibits minimal dark reversion. These data indicate that the 55-kDa, carboxyl-terminal half of the polypeptide does not interact with the chromophore and may not have a role in the structureal integrity of the amino-terminal domain. The 64-kDa chromopeptide can be generated directly from the 74-kDa species by cleavage of 10 kDa from the amino terminus upon incubation of this species as Pr. Accompanying this conversion are changes in the spectral properties, namely, a shift in the difference spectrum minimum to 722-724 nm and a tenfold increase in the capacity for dark reversion. These data indicate that the 6-10 kDa, amino-terminal segment continues to function in its role of maintaining proper chromophore-protein interactions in the 74-kDa peptide as it does in the undegraded molecule. Conversely, removal of this segment upon proteolysis to the 63-kDa species leads to aberrant spectral properties analogous to those observed when this domain is lost from the full-length, 124-kDa molecule, resulting in the 118/114-kDa degradation products. The data also show that photoconversion of the 74-kDa chromopeptide from Pfr to Pr exposes proteolytically susceptible sites in the same way as in the 124-kDa molecule. Thus, the separated, 74-kDa amino-terminal domain undergoes a photoinducible conformational change comparable to that in the intact molecule.

Phytochrome in green tissue: Spectral and immunochemical evidence for two distinct molecular species of phytochrome in light-grown Avena sativa L

A method is described for the extraction of phytochrome from chlorophyllous shoots of Avena sativa L. Poly(ethyleneimine) and salt fractionation are used to reduce chlorophyll and to increase the phytochrome concentration sufficiently to permit spectral and immunochemical analyses. The phototransformation difference spectrum of this phytochrome is distinct from that of phytochrome from etiolated shoots in that the maximum in the red region of the difference spectrum is shifted about 15 nm to a shorter wavelength. Immunochemical probing of electroblotted proteins (Western blotting), using a method sensitive to 50 pg, demonstrates the presence of two polypeptides in green tissue that bind antiphytochrome antibodies: a predominant species with a relative molecular mass (Mr) of 118000 and a lesser-abundant 124000-Mr polypeptide. Under nondenaturing conditions all of the 124000-Mr species is immunoprecipitable, but the 118000-Mr species remains in the supernatant. Peptide mapping and immunochemical analysis with monoclonal antibodies show that the 118000-Mr species has structural features that differ from etiolated-oat phytochrome. Mixing experiments show that these structural differences are intrinsic to the molecular species from these two tissues rather than being the result of post-homogenization modifications or interfering substances in the green-tissue extracts. Together the data indicate that the phytochrome that predominates in green-tissue has a polypeptide distinct from the well-characterized molecule from etiolated tissue.

Monoclonal antibodies to three separate domains on 124 kilodalton phytochrome from Avena

Forty-six monoclonal antibodies have been prepared against 124 kilodalton phytochrome from Avena sativa cv Garry. Clones grown in mice have yielded ascites fluids with antibodies which bind to three distinct regions of the molecule, as visualized by immunoblot analysis of proteolytically produced peptides of the protein. One antibody group (type 1) recognizes an antigenic domain(s) that lies within 6 kilodaltons of the amino terminus of the molecule, a region critical to correct protein-chromophore interaction. The second group (type 2) binds to an antigenic site(s) present within the chromophore-containing half of the molecule that is adjacent to the domain recognized by the type 1 antibodies. The third group (type 3) recognizes an antigenic site(s) that resides in the nonchromophoric, carboxy terminal end of the molecule between 88 and 97 kilodaltons from the amino terminus. One of the type 1 antibodies cross-reacts with apparently undegraded 120 kilodalton phytochrome from zucchini, and therefore may be useful for identifying conserved domains which are essential to the regulatory role of the photoreceptor.

Purification of Phytochrome by Affinity Chromatography on Agarose-Immobilized Cibacron Blue 3GA

The binding of phytochrome to Cibacron Blue 3GA was utilized to develop a new affinity purification procedure for phytochrome. Brushite-purified phytochrome from rye (Secale cereale c.v. Cougar) was bound to agarose-immobilized blue dye in 0.1 molar potassium phosphate (pH 7.8), contaminating proteins washed out with 0.5 molar KCl, and homogeneous phytochrome eluted with 10 millimolar flavin mononucleate. Ninety-five per cent of the phytochrome applied bound, and 60 to 65% was eluted, giving a 25 to 30% yield for the complete one-day procedure. Affinity-purified rye phytochrome was identical to conventionally purified phytochrome in its behavior on sodium dodecyl sulfate gels, in gel exclusion chromatography, in sedimentation in sucrose density gradients and in its spectral properties.