Three-stranded DNA structure; is this the secret of DNA homologous recognition?

A novel type of triple-stranded DNA structure was proposed by several groups to play a crucial role in homologous recognition between single- and double-stranded DNA molecules. In this still putative structure a duplex DNA was proposed to co-ordinate a homologous single strand in its major groove side. In contrast to the well-characterized pyrimidine-purine-pyrimidine triplexes in which the two like strands are antiparallel and which are restricted to poly-pyrimidine-containing stretches, the homology-specific triplexes would have like strands in parallel orientation and would not be restricted to any particular sequence provided that there is a homology between interacting DNA molecules. For many years the stereo-chemical possibility of forming homology-dependent three- or four-stranded DNA structures during the pairing stage of recombination reactions was seriously considered in published papers. However, only recently has there been a marked increase in the number of papers that have directly tested the formation of triple-stranded DNA structures during the actual pairing stage of the recombination reaction. Unfortunately the results of these tests are not totally clear cut; while some laboratories presented experimental evidence consistent with the formation of triplexes, others studying the same or very similar systems offered alternative explanations. The aim of this review is to present the current state of the central question in the mechanism of homologous recombination, namely, what kind of DNA structure is responsible for DNA homologous recognition. Is it a novel triplex structure or just a classical duplex?

Report on initial experience with local anaesthesia for carotid artery endarterectomy.

PURPOSE OF THE STUDY: This prospective study reports our preliminary results with local anaesthesia (LA) for carotid endarterectomy (CEA). MATERIAL AND METHODS: Twenty CEA in nineteen patients were performed using a three-stage local infiltration technique. CEA were performed through a short Duplex-assisted skin incision (median length: 55 mm) using a retro-jugular approach and polyurethane patch closure (median length: 35 mm). RESULTS: There were 13 men and 6 women with a mean age of 71.2 years. The indications of CEA were asymptomatic lesions in 11 cases, stroke in 7 cases and transient ischaemic attack in 2 cases. The median degree of internal carotid artery stenosis was 90%. One patient (5%) required an intraluminal shunt. There were no peri-operative deaths, stroke or conversion to general anaesthesia (GA). The median length of stay was 3 days. CONCLUSIONS: LA is a good alternative to GA. It can be used after a feasibility study and a short teaching procedure. In our centre, it is a safe and effective procedure associated with low morbidity, high acceptance by patients and a short hospital stay.

Conformational changes modulate the activity of human RAD51 protein.

Homologous recombination provides a major pathway for the repair of DNA double-strand breaks in mammalian cells. Defects in homologous recombination can lead to high levels of chromosomal translocations or deletions, which may promote cell transformation and cancer development. A key component of this process is RAD51. In comparison to RecA, the bacterial homologue, human RAD51 protein exhibits low-level strand-exchange activity in vitro. This activity can, however, be stimulated by the presence of high salt. Here, we have investigated the mechanistic basis for this stimulation. We show that high ionic strength favours the co-aggregation of RAD51-single-stranded DNA (ssDNA) nucleoprotein filaments with naked duplex DNA, to form a complex in which the search for homologous sequences takes place. High ionic strength allows differential binding of RAD51 to ssDNA and double-stranded DNA (dsDNA), such that ssDNA-RAD51 interactions are unaffected, whereas those between RAD51 and dsDNA are destabilized. Most importantly, high salt induces a conformational change in RAD51, leading to the formation of extended nucleoprotein filaments on ssDNA. These extended filaments mimic the active form of the Escherichia coli RecA-ssDNA filament that exhibits efficient strand-exchange activity.

Complex formation by the human RAD51C and XRCC3 recombination repair proteins.

In vertebrates, the RAD51 protein is required for genetic recombination, DNA repair, and cellular proliferation. Five paralogs of RAD51, known as RAD51B, RAD51C, RAD51D, XRCC2, and XRCC3, have been identified and also shown to be required for recombination and genome stability. At the present time, however, very little is known about their biochemical properties or precise biological functions. As a first step toward understanding the roles of the RAD51 paralogs in recombination, the human RAD51C and XRCC3 proteins were overexpressed and purified from baculovirus-infected insect cells. The two proteins copurify as a complex, a property that reflects their endogenous association observed in HeLa cells. Purified RAD51C--XRCC3 complex binds single-stranded, but not duplex DNA, to form protein--DNA networks that have been visualized by electron microscopy.

Salvage treatment for venous aneurysm complicating vascular access arteriovenous fistula: use of an exoprosthesis to reinforce the vein after aneurysmorrhaphy.

OBJECTIVES: We report a new salvage technique for treating venous aneurysms (VAs) complicating vascular access arteriovenous fistula (AVF) using externally reinforced venous aneurysmorrhaphy. DESIGN: A retrospective study over a 20-month period from a single centre. PATIENTS: Patients presenting to the vascular surgery department, Bordeaux University Hospital for revision of a vascular access AVF were included. METHODS: Reinforced venous aneurysmorrhaphy consisted in removal of redundant vessel wall followed by reinforcement using an external prosthetic graft. Patency, diameter and flow were assessed by duplex ultrasound at 1, 6 and 12 months after salvage. RESULTS: Thirty-eight eligible patients were identified. Five were excluded because VA was associated with central vein stenosis; the remaining 33 underwent salvage. Indications were rapidly expanding or painful VA in seven cases; VA with frequent bleeding or damaged overlying skin in eight; VA in close relation to a stenosis in two; and VA associated with high-flow rate in 16. Cannulation was attempted after 30 days. Mean follow-up time was 12 S.D. 5 months (range: 4-22). Two repaired AVFs failed. Primary 1-year patency was 93%. No aneurysm or infection occurred. Reduction of high flow was successful in 12 of 16 patients. The remaining four required re-operation. CONCLUSIONS: Reinforced venous aneurysmorrhaphy is effective in controlling venous dilation and achieving patency. Reduction of high-flow rates was not always achieved. Further study is needed to evaluate long-term efficacy of this treatment.

In situ aortobiiliac reconstruction of infected aneurysm using a single superficial femoral vein.

Objective: To demonstrate successful in situ aortoiliac reconstruction of an infected infrarenal aneurysm using one single superficial femoral vein (SFV). Methods: In situ reconstruction using the right SFV sutured in end-to-end anastomosis with the aorta and distally with the right common iliac artery and in end-to-side anastomosis with the left common iliac artery. Results: The operating time was less than reported for aortic in situ reconstruction with bilateral SFV harvesting. The duplex scan 3 months postoperatively showed permeability of the bypass without any anastomotic stenosis or pseudoaneurysm. The right common femoral, popliteal, and greater saphenous veins were patent without thrombus, and the patient did not complain about peripheral edema. Conclusions: The use of only one instead of both the SFVs for aortobiiliac in situ reconstruction might be a way to reduce operating time and allow autogenous venous reconstruction even in patients with limited availability of venous material.

A topological view of the replicon.

The replication of circular DNA faces topological obstacles that need to be overcome to allow the complete duplication and separation of newly replicated molecules. Small bacterial plasmids provide a perfect model system to study the interplay between DNA helicases, polymerases, topoisomerases and the overall architecture of partially replicated molecules. Recent studies have shown that partially replicated circular molecules have an amazing ability to form various types of structures (supercoils, precatenanes, knots and catenanes) that help to accommodate the dynamic interplay between duplex unwinding at the replication fork and DNA unlinking by topoisomerases.

Infrainguinal bypass for peripheral arterial occlusive disease: when arms save legs.

OBJECTIVES: Determine if arm veins are good conduits for infrainguinal revascularisation and should be used when good quality saphenous vein is not available. DESIGN: Retrospective study. MATERIALS AND METHODS: We evaluated a consecutive series of infrainguinal bypass (IB) using arm vein conduits from March 2001 to December 2006.We selected arm vein by preoperative ultrasound mapping to identify suitable veins. We measured vein diameter and assessed vein wall quality. We followed patients with systematic duplex imaging at 1 week, 1, 3, 6 and 12 months, and annually thereafter. We treated significative stenoses found during the follow-up. RESULTS: We performed 56 infrainguinal revascularisation using arm vein conduits in 56 patients. Primary patency rates at 1, 2 and 3 years were 65%, 51% and 47%. Primary assisted patencies at 1, 2 and 3 years were 96%, 96% and 82%. Secondary patency rates at 1, 2 and 3 years were 92%, 88% and 88%. The three-year limb salvage rate was 88%. CONCLUSIONS: We conclude that infrainguinal bypass using arm vein for conduits gives good patency rates, if selected by a preoperative US mapping to use the best autogenous conduit available.

Intrinsic subspace convergence in TDD MIMO communication

In numerical linear algebra, students encounter earlythe iterative power method, which finds eigenvectors of a matrixfrom an arbitrary starting point through repeated normalizationand multiplications by the matrix itself. In practice, more sophisticatedmethods are used nowadays, threatening to make the powermethod a historical and pedagogic footnote. However, in the contextof communication over a time-division duplex (TDD) multipleinputmultiple-output (MIMO) channel, the power method takes aspecial position. It can be viewed as an intrinsic part of the uplinkand downlink communication switching, enabling estimationof the eigenmodes of the channel without extra overhead. Generalizingthe method to vector subspaces, communication in thesubspaces with the best receive and transmit signal-to-noise ratio(SNR) is made possible. In exploring this intrinsic subspace convergence(ISC), we show that several published and new schemes canbe cast into a common framework where all members benefit fromthe ISC.

Reconstitution of the strand invasion step of double-strand break repair using human Rad51 Rad52 and RPA proteins.

The human Rad51 recombinase is essential for the repair of double-strand breaks in DNA that occur in somatic cells after exposure to ionising irradiation, or in germ line cells undergoing meiotic recombination. The initiation of double-strand break repair is thought to involve resection of the double-strand break to produce 3'-ended single-stranded (ss) tails that invade homologous duplex DNA. Here, we have used purified proteins to set up a defined in vitro system for the initial strand invasion step of double-strand break repair. We show that (i) hRad51 binds to the ssDNA of tailed duplex DNA molecules, and (ii) hRad51 catalyses the invasion of tailed duplex DNA into homologous covalently closed DNA. Invasion is stimulated by the single-strand DNA binding protein RPA, and by the hRad52 protein. Strikingly, hRad51 forms terminal nucleoprotein filaments on either 3' or 5'-ssDNA tails and promotes strand invasion without regard for the polarity of the tail. Taken together, these results show that hRad51 is recruited to regions of ssDNA occurring at resected double-strand breaks, and that hRad51 shows no intrinsic polarity preference at the strand invasion step that initiates double-strand break repair.

Investigations of a thermosensitive gel to temporarily occlude crural arteries in femoro-distal bypass surgery.

OBJECTIVES: Long occlusions in calcified crural arteries are a major cause of endovascular technical failure in patients with critical limb ischaemia. Therefore, distal bypasses are mainly performed in patients with heavily calcified arteries and with consequently delicate clamping. A new reverse thermosensitive polymer (RTP) is an alternative option to occlude target vessels. The aim of the study is to report our technical experience with RTP and to assess its safety and efficiency to temporarily occlude small calcified arteries during anastomosis time. METHODS: Between July 2010 and December 2011, we used RTP to occlude crural arteries in 20 consecutive patients with 20 venous distal bypasses. We recorded several operative parameters, such as volume of injected RTP, duration of occlusion and anastomotic time. Quality of occlusion was subjectively evaluated. Routine on-table angiography was performed to search for plug emboli. Primary patency, limb salvage and survival rates were reported at 6 months. RESULTS: In all patients, crural artery occlusion was achieved with the RTP without the use of an adjunct occlusion device. Mean volume of RTP used was 0.3 ml proximally and 0.25 ml distally. Mean duration of occlusion was 14.4 ± 4.5 min, while completion of the distal anastomosis lasted 13.4 ± 4.3 min. Quality of occlusion was judged as excellent in eight cases and good in 12 cases. Residual plugs were observed in two patients and removed with an embolectomy catheter, before we amended the technique for dissolution of RTP. At 6 months, primary patency rate was 75% but limb salvage rate was 87.5%. The 30-day mortality rate was 10%. CONCLUSIONS: This study shows that RTP is safe when properly dissolved and effective to occlude small calcified arteries for completion of distal anastomosis.

The structure of human tRNALys3 anticodon bound to HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs

Replication of human immunodeficiency virus (HIV) requires base pairing of the reverse transcriptase primer, human tRNA(Lys3), to the viral RNA. Although the major complementary base pairing occurs between the HIV primer binding sequence (PBS) and the tRNA's 3'-terminus, an important discriminatory, secondary contact occurs between the viral A-rich Loop I, 5'-adjacent to the PBS, and the modified, U-rich anticodon domain of tRNA(Lys3). The importance of individual and combined anticodon modifications to the tRNA/HIV-1 Loop I RNA's interaction was determined. The thermal stabilities of variously modified tRNA anticodon region sequences bound to the Loop I of viral sub(sero)types G and B were analyzed and the structure of one duplex containing two modified nucleosides was determined using NMR spectroscopy and restrained molecular dynamics. The modifications 2-thiouridine, s(2)U(34), and pseudouridine, Psi(39), appreciably stabilized the interaction of the anticodon region with the viral subtype G and B RNAs. The structure of the duplex results in two coaxially stacked A-form RNA stems separated by two mismatched base pairs, U(162)*Psi(39) and G(163)*A(38), that maintained a reasonable A-form helix diameter. The tRNA's s(2)U(34) stabilized the interaction between the A-rich HIV Loop I sequence and the U-rich anticodon, whereas the tRNA's Psi(39) stabilized the adjacent mismatched pairs.

Estudo do jato urinário intravesical com Doppler colorido em pacientes com e sem refluxo vesicoureteral

OBJETIVO: O presente estudo teve como objetivo comparar os achados da uretrocistografia miccional com o ultra-som Doppler duplex colorido, em pacientes com suspeita de refluxo vesicoureteral. MATERIAIS E MÉTODOS: A pesquisa foi realizada através do estudo dos ângulos dos jatos urinários intravesicais, nos planos axial e longitudinal. Foi analisada, também, a distância (em centímetros) entre os meatos ureterais. RESULTADOS: Do total de 32 pacientes estudados (com média de idade de 5 anos e 2 meses), 18 pacientes apresentaram refluxo vesicoureteral (10 com refluxo unilateral, sendo 4 no lado direito e 6 no lado esquerdo, e 8 com refluxo bilateral) e 14 pacientes não apresentaram refluxo. Os valores angulares dos jatos urinários intravesicais e as distâncias entre os meatos ureterais foram obtidos para todos os pacientes e foram calculados a média, o desvio-padrão e o coeficiente de variação. CONCLUSÃO: Os dados evidenciaram tendência de que a lateralização do meato ureteral seja sinal de predisposição ao refluxo vesicoureteral. A análise estatística não-paramétrica de Mann-Whitney não evidenciou diferenças significativas (p > 0,05) entre os grupos (ângulos de inclinação dos jatos urinários intravesicais e distância entre os meatos ureterais).

Erwinia amylovora Novel Plasmid pEI70: Complete Sequence, Biogeography, and Role in Aggressiveness in the Fire Blight Phytopathogen

Comparative genomics of several strains of Erwinia amylovora, a plant pathogenic bacterium causal agent of fire blight disease, revealed that its diversity is primarily attributable to the flexible genome comprised of plasmids. We recently identified and sequenced in full a novel 65.8 kb plasmid, called pEI70. Annotation revealed a lack of known virulence-related genes, but found evidence for a unique integrative conjugative element related to that of other plant and human pathogens. Comparative analyses using BLASTN showed that pEI70 is almost entirely included in plasmid pEB102 from E. billingiae, an epiphytic Erwinia of pome fruits, with sequence identities superior to 98%. A duplex PCR assay was developed to survey the prevalence of plasmid pEI70 and also that of pEA29, which had previously been described in several E. amylovora strains. Plasmid pEI70 was found widely dispersed across Europe with frequencies of 5–92%, but it was absent in E. amylovora analyzed populations from outside of Europe. Restriction analysis and hybridization demonstrated that this plasmid was identical in at least 13 strains. Curing E. amylovora strains of pEI70 reduced their aggressiveness on pear, and introducing pEI70 into low-aggressiveness strains lacking this plasmid increased symptoms development in this host. Discovery of this novel plasmid offers new insights into the biogeography, evolution and virulence determinants in E. amylovora

Laserhitsausparametrien vaikutus ruostumattomien terästen hitsin mikrorakenteeseen

Työn teoriaosassa käsitellään ruostumattomia teräksiä ja terästen metallurgiaan vaikuttavia tekijöitä yleisesti, sekä terästen hitsattavuutta. Hitsauksesta teoriassa käydään läpi laser- ja kaasukaarihitsausta ja hitsin metallurgiaan vaikuttavia tekijöitä. Kokeellisessa osassa paneudutaan kahdeksan eri ruostumattoman teräksen hitsien metallurgiaan ja metallurgiassa tapahtuviin muutoksiin hitsausparametrien mukaan. Koemateriaaleina on neljä austeniittista ruostumatonta terästä, 201, 301LN, 316L ja 254 SMO, kaksi austeniittis-ferriittistä ruostumatonta terästä, 2101 LDX ja 2205, sekä kaksi ferriittistä ruostumatonta terästä, 430 ja 1.4003. Hitsien mikrorakenteen tutkimisessa käytettiin sekä valomikroskooppia sekä joissain tapauksissa pyyhkäisyelektronimikroskooppia. Lisäksi työn kokeellisessa osassa paneuduttiin hitsien metallografisiin syövytystekniikoihin. Kokeiden perusteella voidaan sanoa, että hitsin metallurgia riippuu hitsauksen aikaisesta lämpösyklistä ja hitsausparametreilla voidaan vaikuttaa tämän lämpösyklin muotoon. Austeniittis-ferriittisillä teräksillä hitsauksen aikaisesta lämpösyklistä riippuu pitkälti hitsin austeniitti-ferriitti-suhde. Ferriittisillä teräksillä lämpösyklin muoto vaikuttaa hitsiin muodostuvan martensiitin kovuuteen ja määrään sekä rakenteen hienojakoisuuteen. Austeniittisilla teräksillä lämpösyklinmuodon vaikutus riippuu pitkälti teräksen seostusasteesta ja seosaineista. Austeniittisilla teräksillä kokeissa havaittuja muutoksia, parametrien muutosten mukaan oli muun muassa suotautumisen voimakkuuden