DNAReplication: a database of information and resources for the eukaryotic DNA replication community

DNAReplication (at http://www.dnareplication.net) has been set up as a freely available single resource to facilitate access to information on eukaryotic DNA replication. This database summarizes organism-sorted data on replication proteins in the categories of nomenclature, biochemical properties, motifs, interactions, modifications, structure, cell localization and expression, and general comments. Replication concepts are defined and a general model of the steps in DNA replication is presented. Links to relevant websites and homepages of replication labs are provided. The site also has an interactive section where links to recent replication papers are posted and readers are provided with the facility to post comments about each paper. The interactive and links pages are modified weekly and the whole site is updated annually

Sedimentary record of coseismic subsidence in Hersek coastal lagoon (Izmit Bay, Turkey) and the late Holocene activity of the North Anatolian Fault

This research was funded by the European Union in the framework of the REL.I.E.F. (Reliable Information on Earthquake Faulting) project (EVG1‐CT‐2002‐00069). Copyright @ 2011 American Geophysical Union.The late Holocene activity of a restraining bend of the northern strand of the North Anatolian Fault in Izmit Bay was investigated by a sedimentological, geochemical, and paleoecological analysis of sediment cores from Hersek coastal lagoon, NW Turkey. The sediment cores show a succession of sedimentary sequences composed of three units separated by gradual transitions. The first unit is composed of a thin layer of shell debris-rich sediment in abrupt contact with the underlying organic-rich deposits. This unit is over-lain by a thick foraminifera-rich mud deposit, and the sequences are capped by an organic-rich mud unit. These sequences are interpreted as silting up, shallowing upward deposits, typical of a lagoon becoming isolated from the sea. We suggest that they represent the sedimentary signature of coseismic subsidence, which was caused by reverse slip at the Hersek bend, and tsunamis in Izmit Bay. Our radiocarbon-dated paleoseismological record indicates (1) the atypical collapse of the hanging wall during the 740 earthquake and (2) subsidence of the footwall during the 987, 1509, and 1719 earthquakes. This study contributes to the understanding of the dynamics of restraining bends, and it highlights the potential of coastal sediments for reconstructing past earthquakes and tsunamis in regions dominated by strike-slip deformations.This article is available through the Brunel Open Access Publishing Fun

Feasibility of repair of distal penile hypospadias as a day-case surgery

Objective The aim of this study was to present the outcomes of children with distal hypospadias who were operated on outpatient basis.Methods Atotal of 47 consecutive children underwent surgical repair of distal hypospadias in our department. Urethroplasties were performed by the following techniques: stentless meatal advancement-glanuloplasty (MAGPI) or glans approximation procedure (GAP) for glanular hypospadias (14) and tubularized incised plate (TIP) urethroplasty for coronal, subcoronal and midpenil hypospadias with an indwelling urethral catheter or short stent (33). The indwelling urinary catheters were managed by the double diaper technique. Patients were discharged within 6 h after operation. Dressings and catheters were removed on the postoperative day 2 and 6, respectively.Results Voiding difficulty and urinary retention on early postoperative period were observed in 8 patients. Except meatal stenosis in 4 cases and meatal retractions in 2 cases, there were no major complications in any of our patients during the follow-up period, no postoperative fistula or urethral stricture.Conclusion In children, repair of distal penile hypospadias on outpatient basis is feasible. Catheters, urethral stents, drug therapy and dressing are not justifications for hospitalization in such cases.Keywords: hospital stay, hypospadias, outpatient, urethroplasty, wounddressin

The value of laparoscopic classifications in decision on definitive surgery in patients with nonpalpable testes: our experience and review of the literature

Background/purpose The aim of the study was to present our clinical experience with the laparoscopic approach in patients with nonpalpable testes (NPTs) and review the literature on laparoscopic classifications.Materials and methods Between May 2010 and August 2012, 30 boys with NPT (mean age 3.9 years) underwent laparoscopy as a part of diagnosis and treatment in our clinic. The laparoscopic findings were classified into four types according to Castilho. The patients were managed according to the presence or position of the testes and testicular vessels.Results Six patients were excluded from the study. Twenty-six testicular units (19 left, three right, and four bilateral units) in 24 patients were managed laparoscopically. Laparoscopy was terminated in eight patients in whom blind-ending cord structures were detected intra-abdominally. An inguinal canal exploration was performed in 10 cases in whom cord structures were seen entering the internal inguinal ring. No viable testis was found, and testicular remnants were excised for histopathologic examination. Four canalicular testes (peeping) were treated with open orchiopexy. Laparoscopy-assisted orchiopexy without vascular ligation was performed in two testes. Fowler-Stephens orchiopexy in single stage was performed in one testicular unit and in two stages in another unit. All patients were discharged on the same day. The testes were normal in size and found in the scrotum after a mean follow-up period of 14 months.Conclusion The laparoscopic findings in NPT had an important influence on treatment decisions. To be able to interpret the definitive surgery relative to the laparoscopic classification, collaborative studies are required. Keywords: laparoscopy, nonpalpable testis, nubbin, orchiopexy, vas deferen

Reaction Mechanism of Human DNA Repair Excision Nuclease

Nucleotide excision repair consists of removal of the damaged nucleotide(s) from DNA by dual incision of the damaged strand on both sides of the lesion, followed by filling of the resulting gap and ligation. In humans, 14-16 polypeptides are required for the dual incision step. We have purified the required proteins to homogeneity and reconstituted the dual incision activity (excision nuclease) in a defined enzyme/substrate system. The system was highly efficient, removing >30% of the thymine dimers under optimal conditions. All of the six fractions that constitute the excision nuclease were required for dual incision of the thymine dimer substrate. However, when a cholesterol-substituted oligonucleotide was used as substrate, excision occurred in the absence of the XPC-HHR23B complex, reminiscent of transcription-coupled repair in the XP-C mutant cell line. Replication protein A is absolutely required for both incisions. The XPG subunit is essential to the formation of the preincision complex, but the repair complex can assemble and produce normal levels of 3'-incision in the absence of XPF-ERCC1. Kinetic experiments revealed that the 3'-incision precedes the 5'-incision. Consistent with the kinetic data, uncoupled 5'-incision was never observed in the reconstituted system. Two forms of TFIIH were used in the reconstitution reaction, one containing the CDK7-cyclin H pair and one lacking it. Both forms were equally active in excision. The excised oligomer dissociated from the gapped DNA in a nucleoprotein complex. In total, these results provide a detailed account of the reactions occurring during damage removal by human excision nuclease

Role of enzyme-bound 5, 10-methenyltetrahydropteroylpolyglutamate in catalysis by Escherichia coli DNA photolyase.

DNA photolyase catalyzes the photoreversal of pyrimidine dimers. The enzymes from Escherichia coli and yeast contain a flavin chromophore and a folate cofactor, 5,10-methenyltetrahydropteroylpolyglutamate. E. coli DNA photolyase contains about 0.3 mol of folate/mol flavin, whereas the yeast photolyase contains the full complement of folate. E. coli DNA photolyase is reconstituted to a full complement of the folate by addition of 5,10-methenyltetrahydrofolate to cell lysates or purified enzyme samples. The reconstituted enzyme displays a higher photolytic cross section under limiting light. Treatment of photolyase with sodium borohydride or repeated camera flashing results in the disappearance of the absorption band at 384 nm and is correlated with the formation of modified products from the enzyme-bound 5,10-methenyltetrahydrofolate. Photolyase modified in this manner has a decreased photolytic cross section under limiting light. Borohydride reduction results in the formation of 5,10-methylenetetrahydrofolate and 5-methyltetrahydrofolate, both of which are released from the enzyme. Repeated camera flashing results in photodecomposition of the enzyme-bound 5,10-methenyltetrahydrofolate and release of the decomposition products. Finally, it is observed that photolyase binds 10-formyltetrahydrofolate and appears to cyclize it to form the 5,10-methenyltetrahydrofolate chromophore

Blue-light-receptive cryptochrome is expressed in a sponge eye lacking neurons and opsin

Many larval sponges possess pigment ring eyes that apparently mediate phototactic swimming. Yet sponges are not known to possess nervous systems or opsin genes, so the unknown molecular components of sponge phototaxis must differ fundamentally from those in other animals, inspiring questions about how this sensory system functions. Here we present molecular and biochemical data on cryptochrome, a candidate gene for functional involvement in sponge pigment ring eyes. We report that Amphimedon queenslandica, a demosponge, possesses two cryptochrome/photolyase genes, Aq-Cry1 and Aq-Cry2. The mRNA of one gene (Aq-Cry2) is expressed in situ at the pigment ring eye. Additionally, we report that Aq-Cry2 lacks photolyase activity and contains a flavin-based co-factor that is responsive to wavelengths of light that also mediate larval photic behavior. These results suggest that Aq-Cry2 may act in the aneural, opsin-less phototaxic behavior of a sponge

Structure and Function of the UvrB Protein

UvrB plays a central role in (A)BC excinuclease. To identify the regions of UvrB which are involved in interacting with UvrA, UvrC, and DNA, deletion mutants, point mutants, and various fusion forms of UvrB were constructed and characterized. We found that the region encompassing amino acid residues 115-250 of UvrB binds to UvrA, while the region encompassing amino acid residues 547-673 binds to both UvrA and UvrC. In addition, the region between these two domains, which contains the helicase motifs II-VI, was found to be involved in binding to DNA. Within this DNA-binding region, two point mutants, E265A and E338A, were found to be unable to bind DNA while two residues, Phe-365 and Phe-496, were identified to interact with DNA. Furthermore, fluorescence quenching studies with mutants F365W and F496W and repair of thymine cyclobutane dimers by photoinduced electron transfer by these mutants suggest that residues Phe-365 and Phe-496 interact with DNA most likely through stacking interactions