The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes

In Arabidopsis thaliana (Arabidopsis), DICER-LIKE1 (DCL1) functions together with the double-stranded RNA binding protein (dsRBP), DRB1, to process microRNAs (miRNAs) from their precursor transcripts prior to their transfer to the RNA-induced silencing complex (RISC). miRNA-loaded RISC directs RNA silencing of cognate mRNAs via ARGONAUTE1 (AGO1)-catalyzed cleavage. Short interefering RNAs (siRNAs) are processed from viral-derived or transgene-encoded molecules of double-stranded RNA (dsRNA) by the DCL/dsRBP partnership, DCL4/DRB4, and are also loaded to AGO1-catalyzed RISC for cleavage of complementary mRNAs. Here, we use an artificial miRNA (amiRNA) technology, transiently expressed in Nicotiana benthamiana, to produce a series of amiRNA duplexes with differing intermolecular thermostabilities at the 5' end of duplex strands. Analyses of amiRNA duplex strand accumulation and target transcript expression revealed that strand selection (amiRNA and amiRNA*) is directed by asymmetric thermostability of the duplex termini. The duplex strand possessing a lower 5' thermostability was preferentially retained by RISC to guide mRNA cleavage of the corresponding target transgene. In addition, analysis of endogenous miRNA duplex strand accumulation in Arabidopsis drb1 and drb2345 mutant plants revealed that DRB1 dictates strand selection, presumably by directional loading of the miRNA duplex onto RISC for passenger strand degradation. Bioinformatic and Northern blot analyses of DCL4/DRB4-dependent small RNAs (miRNAs and siRNAs) revealed that small RNAs produced by this DCL/dsRBP combination do not conform to the same terminal thermostability rules as those governing DCL1/DRB1-processed miRNAs. This suggests that small RNA processing in the DCL1/DRB1-directed miRNA and DCL4/DRB4-directed sRNA biogenesis pathways operates via different mechanisms.

Transient high glycaemic intake in the last trimester of pregnancy increases offspring birthweight and postnatal growth rate in sheep: a randomised control trial

OBJECTIVE

Investigate the effect of transient hyperglycemic intake (analogous to snacking on high glycaemic foods) in the third trimester of pregnancy on offspring birthweight and subsequent growth in sheep.

DESIGN

Randomised trial.

SETTING

University research farm.

SAMPLE

Third trimester pregnant ewes.

METHODS

Ewes were blocked on weight, age and litter size and were randomly assigned to receive oral administration of 100 ml of propylene glycol (PG; n = 51) or 100 ml of water (control, C; n = 53) twice/day. Twice during treatment, 12 ewes from each group were selected and blood samples collected to determine the glucose and insulin response to treatment.

MAIN OUTCOME MEASURES

At birth, blood was collected from the lambs, their body dimensions measured and body weights recorded at 0, 6 and 12 weeks of age after which lambs were slaughtered when they reached 40 kg live weight.

RESULTS

Administration of PG elevated (P < 0.05) plasma glucose and insulin concentrations for 2 hours post administration compared with control ewes. Lambs (C: n = 80; PG: n = 70) born to ewes fed high glycaemic meals had higher birthweights (C: 5.01 +/- 0.18 kg; PG: 5.27 +/- 0.22 kg, P = 0.032), plasma glucose concentrations (P = 0.001) and ponderal index (weight/height(3), P = 0.043) and reached a similar (P > 0.05) slaughter carcass weight (C: 20.0 +/- 0.51 kg; PG: 20.6 +/- 0.55 kg) at an earlier age (PG: 166.0 +/- 13.2; C: 183.4 +/- 13.8 days, P = 0.039) compared with control lambs.

CONCLUSIONS

Transient high glycaemic intakes in the third trimester of pregnancy resulted in heavier offspring at birth that had faster growth rates in early postnatal life. This animal model is relevant for studying the relationship between maternal diet, fetal size and the risk of childhood obesity.

The effect of breast support on kinetics during overground running performance

Changes in ground reaction forces that result from different breast support conditions may have implications for sports performance and transmission of forces through the skeleton. The aim of this investigation was to compare kinetic variables and breast motion in a no-bra, everyday-bra and two sports-bra conditions. Following ethical approval, eight female participants with D-cup breasts had retro-reflective markers placed on the left and right nipples, anterior superior iliac spines and clavicles. Five calibrated ProReflex infra-red cameras (100 Hz; Qualisys) measured 3-D displacement of markers and synchronised kinetic data were collected using a force platform (500 Hz, Kistler 9281CA). A repeated measures one-way ANOVA revealed a significantly higher medial impact force in the no-bra condition (0.15 times body weight) compared with the compression sports-bra condition (0.12 times body weight) (F = 3.64 (3,21), p = 0.03). Findings suggest that inadequate breast support affects a female's running kinetics, which may have negative physiological consequences on sports performance.

Necrotizing fasciitis: a case of hip disarticulation in a postnatal intravenous drug abuser

An interesting case of necrotizing fasciitis of the leg following emergency caesarian section in a known intravenous drug user. Postnatal day two she developed pain and swelling in the left leg. In view of her previous history, deep vein thrombosis (DVT) was the initial diagnosis. But, due to clinically worsening symptoms and no response to anticoagulation, further investigations were done which showed necrotizing fasciitis. Due to disease progression, a hip disarticulation was performed and the patient went on to full recovery.

Synthesis of complementary RNA by RNA-dependent RNA polymerases in plant extracts is independent of an RNA primer

RNA-dependent RNA polymerase (RDR) activities were readily detected in extracts from cauliflower and broccoli florets, Arabidopsis thaliana (L.) Heynh callus tissue and broccoli nuclei. The synthesis of complementary RNA (cRNA) was independent of a RNA primer, whether or not the primer contained a 3' terminal 2'-O-methyl group or was phosphorylated at the 5' terminus. cRNA synthesis in plant extracts was not affected by loss-of-function mutations in the DICER-LIKE (DCL) proteins DCL2, DCL3, and DCL4, indicating that RDRs function independently of these DCL proteins. A loss-of-function mutation in RDR1, RDR2 or RDR6 did not significantly reduce the amount of cRNA synthesis. This indicates that these RDRs did not account for the bulk RDR activities in plant extracts, and suggest that either the individual RDRs each contribute a fraction of polymerase activity or another RDR(s) is predominant in the plant extract.

Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis

In plants, silencing of mRNA can be transmitted from cell to cell and also over longer distances from roots to shoots. To investigate the long-distance mechanism, WT and mutant shoots were grafted onto roots silenced for an mRNA. We show that three genes involved in a chromatin silencing pathway, NRPD1a encoding RNA polymerase IVa, RNA-dependent RNA polymerase 2 (RDR2), and DICER-like 3 (DCL3), are required for reception of long-distance mRNA silencing in the shoot. A mutant representing a fourth gene in the pathway, argonaute4 (ago4), was also partially compromised in the reception of silencing. This pathway produces 24-nt siRNAs and resulted in decapped RNA, a known substrate for amplification of dsRNA by RDR6. Activation of silencing in grafted shoots depended on RDR6, but no 24-nt siRNAs were detected in mutant rdr6 shoots, indicating that RDR6 also plays a role in initial signal perception. After amplification of decapped transcripts, DCL4 and DCL2 act hierarchically as they do in antiviral resistance to produce 21- and 22-nt siRNAs, respectively, and these guide mRNA degradation. Several dcl genotypes were also tested for their capacity to transmit the mobile silencing signal from the rootstock. dcl1-8 and a dcl2 dcl3 dcl4 triple mutant are compromised in micro-RNA and siRNA biogenesis, respectively, but were unaffected in signal transmission.

RNA interference-inducing hairpin RNAs in plants act through the viral defence pathway

RNA interference (RNAi) is widely used to silence genes in plants and animals. It operates through the degradation of target mRNA by endonuclease complexes guided by approximately 21 nucleotide (nt) short interfering RNAs (siRNAs). A similar process regulates the expression of some developmental genes through approximately 21 nt microRNAs. Plants have four types of Dicer-like (DCL) enzyme, each producing small RNAs with different functions. Here, we show that DCL2, DCL3 and DCL4 in Arabidopsis process both replicating viral RNAs and RNAi-inducing hairpin RNAs (hpRNAs) into 22-, 24- and 21 nt siRNAs, respectively, and that loss of both DCL2 and DCL4 activities is required to negate RNAi and to release the plant's repression of viral replication. We also show that hpRNAs, similar to viral infection, can engender long-distance silencing signals and that hpRNA-induced silencing is suppressed by the expression of a virus-derived suppressor protein. These findings indicate that hpRNA-mediated RNAi in plants operates through the viral defence pathway.

The evolution and diversification of Dicers in plants

Most multicellular organisms regulate developmental transitions by microRNAs, which are generated by an enzyme, Dicer. Insects and fungi have two Dicer-like genes, and many animals have only one, yet the plant, Arabidopsis, has four. Examining the poplar and rice genomes revealed that they contain five and six Dicer-like genes, respectively. Analysis of these genes suggests that plants require a basic set of four Dicer types which were present before the divergence of mono- and dicotyledonous plants ( approximately 200 million years ago), but after the divergence of plants from green algae. A fifth type of Dicer seems to have evolved in monocots.

On the role of RNA silencing in the pathogenicity and evolution of viroids and viral satellites

Viroids and most viral satellites have small, noncoding, and highly structured RNA genomes. How they cause disease symptoms without encoding proteins and why they have characteristic secondary structures are two longstanding questions. Recent studies have shown that both viroids and satellites are capable of inducing RNA silencing, suggesting a possible role of this mechanism in the pathology and evolution of these subviral RNAs. Here we show that preventing RNA silencing in tobacco, using a silencing suppressor, greatly reduces the symptoms caused by the Y satellite of cucumber mosaic virus. Furthermore, tomato plants expressing hairpin RNA, derived from potato spindle tuber viroid, developed symptoms similar to those of potato spindle tuber viroid infection. These results provide evidence suggesting that viroids and satellites cause disease symptoms by directing RNA silencing against physiologically important host genes. We also show that viroid and satellite RNAs are significantly resistant to RNA silencing-mediated degradation, suggesting that RNA silencing is an important selection pressure shaping the evolution of the secondary structures of these pathogens.

Used leucodepletion filters as a source of large quantities of DNA suitable for the study of genetic variations in human populations

A simple technique for developing large control panels with large quantities of DNA suitable for studies in population genetics was established.

BACKGROUND AND OBJECTIVES

Both a lack of suitable controls and insufficient quantities of DNA for repeated analysis of the same control group often hamper the investigation of genetic markers for disease.

MATERIALS AND METHODS

Using a waste product from routine blood donation, we describe a simple method that allows the investigator to extract large amounts of DNA.

RESULTS

A mean of 1520 microg of DNA per sample was obtained. The DNA obtained remains suitable for polymerase chain reaction and sequencing techniques after 2 years of storage at both 4 degrees C and -40 degrees C.

CONCLUSION

This technique allows the development of a large panel of controls with sufficient quantities of genomic DNA for thousands of tests.

Chlamydial co-infection among patients with gonorrhoea

The objective was to determine how often gonococcal (GC) infection is accompanied by chlamydial co-infection and to determine risk factors for dual infection. All GC-positive cultures were identified between 24 April and 9 September 1998, among patients seen at the three genitourinary medicine (GUM) clinics across the Chelsea and Westminster Directorate. Chlamydia trachomatis was diagnosed using an enzyme-linked immunosorbent assay (ELISA) (Dade-Behring). One hundred and fifty-three episodes of gonorrhoea were identified. Information on chlamydial infection was available for 149 cases of GC of whom 16 (10.7%) were found to be co-infected with C. trachomatis. In univariate analysis, chlamydial co-infection was exclusively diagnosed in heterosexuals, and was more likely to be diagnosed among females, in younger individuals and in individuals of black Caribbean ethnic group. In multivariable analyses, however, only the sex and age of the individual were independently associated with chlamydial co-infection. The rate of co-infection was 10.7%. Independent risk factors were being less than 20 years old and being female.

Lateral epicondylitis in a hospital phlebotomist--an ergonomic solution

This report outlines a case of lateral epicondylitis in a hospital phlebotomist thought to be due to the forceful gripping, and repetitive twisting, involved in breaking the seals on green vacutainer needles. An ergonomic solution in the form of a device to aid breaking of the vacutainer seals is presented. The importance of seeking ergonomic solutions with manufacturers is highlighted.

Construct design for efficient, effective and high-throughput gene silencing in plants

Post-transcriptional silencing of plant genes using anti-sense or co-suppression constructs usually results in only a modest proportion of silenced individuals. Recent work has demonstrated the potential for constructs encoding self-complementary 'hairpin' RNA (hpRNA) to efficiently silence genes. In this study we examine design rules for efficient gene silencing, in terms of both the proportion of independent transgenic plants showing silencing, and the degree of silencing. Using hpRNA constructs containing sense/anti-sense arms ranging from 98 to 853 nt gave efficient silencing in a wide range of plant species, and inclusion of an intron in these constructs had a consistently enhancing effect. Intron-containing constructs (ihpRNA) generally gave 90-100% of independent transgenic plants showing silencing. The degree of silencing with these constructs was much greater than that obtained using either co-suppression or anti-sense constructs. We have made a generic vector, pHANNIBAL, that allows a simple, single PCR product from a gene of interest to be easily converted into a highly effective ihpRNA silencing construct. We have also created a high-throughput vector, pHELLSGATE, that should facilitate the cloning of gene libraries or large numbers of defined genes, such as those in EST collections, using an in vitro recombinase system. This system may facilitate the large-scale determination and discovery of plant gene functions in the same way as RNAi is being used to examine gene function in Caenorhabditis elegans.

Antiretroviral therapy for HIV-2 infected patients

OBJECTIVES

To evaluate clinical and RNA load response to antiretroviral therapy amongst patients infected with HIV-2 and to study the development of drug resistance.

METHODS

Seven HIV-2 seropositive patients were monitored with clinical examination, CD4 cell count and HIV-2 viral RNA load. Viruses from four subjects were genotyped and in vitro recovery of virus by co-cultivation with PBMCs and HVS T-cells was attempted. Viruses isolated from two subjects were assayed for phenotypic antiviral resistance. The main outcome measures were the relationship between disease stage, viral load, CD4 cell count, viral subtype and the clinical course of HIV-2 infection and the effect of combination antiretroviral therapy on disease progression, CD4 cell count, HIV-2 RNA viral load and drug resistance.

RESULTS

The median time of follow-up was 3 years (range 0-8 years). Three patients had AIDS, and one had symptomatic disease. Of the four patients genotyped, three were infected with HIV-2 subtype B and one with subtype A. Viraemia was detectable only at CD4 counts of less than 300 x 10(6)/ml. Two patients with high viral loads failed to respond to antiretroviral therapy although their treatment may not have been optimal. One developed in vitro phenotypic antiviral resistance. The genotype of this patient's viral reverse transcriptase is being analysed.

CONCLUSIONS

In contrast to HIV-1, HIV-2 RNA levels were often undetectable despite advanced disease and low CD4 cell counts. However, HIV-2 was clearly capable of causing CD4 cell depletion resulting in symptomatic disease. The principles of highly active antiretroviral therapy seem to apply to HIV-2 and suboptimal therapy may lead to drug resistance. The timing of therapy initiation, monitoring of response and the measurement of resistance remain unresolved issues and conclusions cannot be extrapolated from HIV-1.

Replicating satellite RNA induces sequence-specific DNA methylation and truncated transcripts in plants

Tobacco plants were transformed with a chimeric transgene comprising sequences encoding beta-glucuronidase (GUS) and the satellite RNA (satRNA) of cereal yellow dwarf luteovirus. When transgenic plants were infected with potato leafroll luteovirus (PLRV), which replicated the transgene-derived satRNA to a high level, the satellite sequence of the GUS:Sat transgene became densely methylated. Within the satellite region, all 86 cytosines in the upper strand and 73 of the 75 cytosines in the lower strand were either partially or fully methylated. In contrast, very low levels of DNA methylation were detected in the satellite sequence of the transgene in uninfected plants and in the flanking nonsatellite sequences in both infected and uninfected plants. Substantial amounts of truncated GUS:Sat RNA accumulated in the satRNA-replicating plants, and most of the molecules terminated at nucleotides within the first 60 bp of the satellite sequence. Whereas this RNA truncation was associated with high levels of satRNA replication, it appeared to be independent of the levels of DNA methylation in the satellite sequence, suggesting that it is not caused by methylation. All the sequenced GUS:Sat DNA molecules were hypermethylated in plants with replicating satRNA despite the phloem restriction of the helper PLRV. Also, small, sense and antisense approximately 22 nt RNAs, derived from the satRNA, were associated with the replicating satellite. These results suggest that the sequence-specific DNA methylation spread into cells in which no satRNA replication occurred and that this was mediated by the spread of unamplified satRNA and/or its associated 22 nt RNA molecules.

Anticoagulant-induced pseudothrombocytopenia in a patient presenting for coronary artery bypass grafting

A 73-yr-old man with severe ischaemic heart disease presented for coronary artery bypass grafting. His preoperative platelet count, obtained from an ethylene diamine tetraacetic acid (EDTA) sampling bottle, was 61 x 10(9) litre-1, but he had no history of bleeding problems. Previous platelet counts demonstrated results ranging from 16 x 10(9) litre-1 to 254 x 10(9) litre-1 with variable degrees of in vitro platelet clumping. Preoperative thrombelastography reflected a normal coagulation profile. The laboratory findings and the absence of a history of haemorrhagic complications suggested a diagnosis of EDTA-dependent pseudothrombocytopenia. We present the perioperative implications of this in vitro phenomenon and methods of detecting the functional and numerical integrity of circulating platelets.