Schizosaccharomyces pombe Rtf2 is important for replication fork barrier activity of RTS1 via splicing of Rtf1.

Arrested replication forks, when restarted by homologous recombination, result in error-prone DNA syntheses and non-allelic homologous recombination. Fission yeast RTS1 is a model fork barrier used to probe mechanisms of recombination-dependent restart. RTS1 barrier activity is entirely dependent on the DNA binding protein Rtf1 and partially dependent on a second protein, Rtf2. Human RTF2 was recently implicated in fork restart, leading us to examine fission yeast Rtf2's role in more detail. In agreement with previous studies, we observe reduced barrier activity upon rtf2 deletion. However, we identified Rtf2 to be physically associated with mRNA processing and splicing factors and rtf2 deletion to cause increased intron retention. One of the most affected introns resided in the rtf1 transcript. Using an intronless rtf1, we observed no reduction in RFB activity in the absence of Rtf2. Thus, Rtf2 is essential for correct rtf1 splicing to allow optimal RTS1 barrier activity.

Prospective Evaluation of Low-Fat Diet Monotherapy in Dogs with Presumptive Protein-Losing Enteropathy.

For dogs with protein-losing enteropathy (PLE) and evidence of lymphangiectasia, the efficacy of low-fat diet as monotherapy or combined with prednisone remains poorly characterized. In this prospective, observational cohort study of 14 dogs with presumptive PLE and ultrasonographic evidence of lymphangiectasia, subjects were placed on various low-fat diets as monotherapy and prednisone was added if response was deemed inadequate. Dogs were assessed and scored at four recheck examinations across a 6 mo study period, including a final recheck ultrasound. Clinical and clinicopathologic variables were collected and dogs were divided into three outcome groups: clinical remission on dietary monotherapy (LOF); clinical remission on dietary therapy plus immunosuppressive prednisone (LOP); and treatment failure (TXF). Eleven of 14 dogs were in clinical remission at the study end date (6 mo after enrollment): 6 LOF dogs and 5 LOP dogs. LOF dogs achieved a significant reduction in Canine Chronic Enteropathy Clinical Activity Index score and a significant increase in serum albumin within 2 wk of beginning dietary monotherapy. Four of 11 dogs in remission also had ultrasonographic evidence of resolution of linear striations. Low-fat diet appears to be an effective monotherapy in some dogs with presumptive PLE and ultrasonographic evidence of lymphangiectasia.

Rice (Oryza sativa) TIR1 and 5'adamantyl-IAA Significantly Improve the Auxin-Inducible Degron System in Schizosaccharomyces pombe.

The auxin-inducible degron (AID) system is a powerful tool to induce targeted degradation of proteins in eukaryotic model organisms. The efficiency of the existing Schizosaccharomyces pombe AID system is limited due to the fusion of the F-box protein TIR1 protein to the SCF component, Skp1 (Skp1-TIR1). Here, we report an improved AID system for S. pombe that uses the TIR1 from Oryza sativa (OsTIR1) not fused to Skp1. Furthermore, we demonstrate that degradation efficiency can be improved by pairing an OsTIR1 auxin-binding site mutant, OsTIR1F74A, with an auxin analogue, 5'adamantyl-IAA (AID2). We provide evidence for the enhanced functionality of the OsTIR1 AID and AID2 systems by application to the essential DNA replication factor Mcm4 and to a non-essential recombination protein, Rad52. Unlike AID, no detectable auxin-independent depletion of AID-tagged proteins was observed using AID2.

Inhibition of MRN activity by a telomere protein motif.

The MRN complex (MRX in Saccharomyces cerevisiae, made of Mre11, Rad50 and Nbs1/Xrs2) initiates double-stranded DNA break repair and activates the Tel1/ATM kinase in the DNA damage response. Telomeres counter both outcomes at chromosome ends, partly by keeping MRN-ATM in check. We show that MRX is disabled by telomeric protein Rif2 through an N-terminal motif (MIN, MRN/X-inhibitory motif). MIN executes suppression of Tel1, DNA end-resection and non-homologous end joining by binding the Rad50 N-terminal region. Our data suggest that MIN promotes a transition within MRX that is not conductive for endonuclease activity, DNA-end tethering or Tel1 kinase activation, highlighting an Achilles' heel in MRN, which we propose is also exploited by the RIF2 paralog ORC4 (Origin Recognition Complex 4) in Kluyveromyces lactis and the Schizosaccharomyces pombe telomeric factor Taz1, which is evolutionarily unrelated to Orc4/Rif2. This raises the possibility that analogous mechanisms might be deployed in other eukaryotes as well.

Live-cell single-molecule tracking highlights requirements for stable Smc5/6 chromatin association in vivo.

The essential Smc5/6 complex is required in response to replication stress and is best known for ensuring the fidelity of homologous recombination. Using single-molecule tracking in live fission yeast to investigate Smc5/6 chromatin association, we show that Smc5/6 is chromatin associated in unchallenged cells and this depends on the non-SMC protein Nse6. We define a minimum of two Nse6-dependent sub-pathways, one of which requires the BRCT-domain protein Brc1. Using defined mutants in genes encoding the core Smc5/6 complex subunits, we show that the Nse3 double-stranded DNA binding activity and the arginine fingers of the two Smc5/6 ATPase binding sites are critical for chromatin association. Interestingly, disrupting the single-stranded DNA (ssDNA) binding activity at the hinge region does not prevent chromatin association but leads to elevated levels of gross chromosomal rearrangements during replication restart. This is consistent with a downstream function for ssDNA binding in regulating homologous recombination.

Replication dynamics of recombination-dependent replication forks.

Replication forks restarted by homologous recombination are error prone and replicate both strands semi-conservatively using Pol δ. Here, we use polymerase usage sequencing to visualize in vivo replication dynamics of HR-restarted forks at an S. pombe replication barrier, RTS1, and model replication by Monte Carlo simulation. We show that HR-restarted forks synthesise both strands with Pol δ for up to 30 kb without maturing to a δ/ε configuration and that Pol α is not used significantly on either strand, suggesting the lagging strand template remains as a gap that is filled in by Pol δ later. We further demonstrate that HR-restarted forks progress uninterrupted through a fork barrier that arrests canonical forks. Finally, by manipulating lagging strand resection during HR-restart by deleting pku70, we show that the leading strand initiates replication at the same position, signifying the stability of the 3' single strand in the context of increased resection.

Short-Term Prospective Clinical Evaluation of a Polyglycolic Acid Tibial Tuberosity Advancement Cage Implant.

This study investigated the short-term radiographic healing of the osteotomy following tibial tuberosity advancement (TTA), maintenance of patellar tendon angle (PTA), and complications in dogs receiving a polyglycolic acid (PGA) TTA cage. Patients diagnosed with unilateral cranial cruciate ligament disease requiring a 9- or 12-mm TTA cage were included. Twenty-six consecutive client-owned dogs were prospectively selected for this clinical study. Age, weight, sex, breed, cage size, surgery date, and follow-up time were recorded. Radiographs were scored for healing and measured for PTA immediately, at 6 wk, and at 10 wk postoperatively. All stifles were assessed for complications throughout the study period. Stifles with PGA cages had similar overall healing scores compared to previously reported values for metallic cages, and the PTA was well maintained at 6 and 10 wk postoperatively. Polyglycolic acid cages were associated with a higher complication rate (10/26, 38%; 95% confidence interval, 0.19-0.61) compared with previously reported complication rates for metallic cages. Despite favorable healing scores and overall PTA maintenance, PGA cage use resulted in a high complication rate. Proposed advantages offered by this particular implant over currently used metallic cages are offset by this high complication rate. Additional investigation of bioabsorbable materials and implant design should be considered.

Long-term outcome following surgical and radiation treatment of vertebral angiomatosis in a cat.

CASE DESCRIPTION A 2-year-old 5.2-kg (11.4-lb) neutered male domestic shorthair cat was referred because of a 6-week history of progressive paraparesis. CLINICAL FINDINGS Neurologic examination revealed moderate ambulatory paraparesis with marked spinal hyperesthesia at the thoracolumbar junction. The lesion was localized to the T3-L3 spinal cord segment. Clinicopathologic testing, thoracic radiography, and abdominal ultrasonography revealed no abnormalities to explain the observed clinical signs. Advanced spinal imaging with MRI revealed an extradural right-lateralized mass originating from the L2 vertebral pedicle and causing severe spinal cord compression. TREATMENT AND OUTCOME Surgical decompression was achieved by performance of a right-sided hemilaminectomy at L2. Histologic examination of biopsy samples obtained from the mass revealed an ill-defined zone of mature vascular proliferation extending through the preexisting vertebral bone, consistent with vertebral angiomatosis. After surgical recovery, adjuvant radiation therapy was initiated with a total dose of 48 Gy administered in 16 fractions of 3 Gy each over a 3-week period. Neurologic function rapidly improved to full ambulation with only minimal monoparesis of the right pelvic limb. Results of neurologic and MRI examination performed 26 months after surgery indicated no change in neurologic status or evidence of recurrence. CLINICAL RELEVANCE To the authors' knowledge, this report was the first to describe the long-term outcome for vertebral angiomatosis in a cat. Surgical decompression and radiation therapy provided an excellent outcome in this case. Vertebral angiomatosis should be considered as a differential diagnosis for any young cat with thoracolumbar myelopathy secondary to a mass associated with the vertebral pedicle.

PCNA ubiquitylation ensures timely completion of unperturbed DNA replication in fission yeast.

PCNA ubiquitylation on lysine 164 is required for DNA damage tolerance. In many organisms PCNA is also ubiquitylated in unchallenged S phase but the significance of this has not been established. Using Schizosaccharomyces pombe, we demonstrate that lysine 164 ubiquitylation of PCNA contributes to efficient DNA replication in the absence of DNA damage. Loss of PCNA ubiquitylation manifests most strongly at late replicating regions and increases the frequency of replication gaps. We show that PCNA ubiquitylation increases the proportion of chromatin associated PCNA and the co-immunoprecipitation of Polymerase δ with PCNA during unperturbed replication and propose that ubiquitylation acts to prolong the chromatin association of these replication proteins to allow the efficient completion of Okazaki fragment synthesis by mediating gap filling.

Prospective Randomized Clinical and Radiographic Evaluation of a Novel Bioabsorbable Biocomposite Tibial Tuberosity Advancement Cage Implant.

OBJECTIVE: To evaluate the suitability of a novel bioabsorbable biocomposite cage (BC) implant for use in tibial tuberosity advancement (TTA) surgery in dogs with cranial cruciate ligament (CrCL) disease and to compare radiographic osteotomy healing scores and complications between groups that received either a BC or stainless steel cage (SSC). STUDY DESIGN: Prospective randomized clinical study. ANIMALS: Dogs with unilateral CrCL rupture (n=56). METHODS: TTA was performed in 60 consecutive dogs using either a BC (30 dogs) or SSC (30 dogs). Patient parameters, 6 week and 6 month postoperative radiographic osteotomy healing scores, time elapsed to postoperative rechecks, and complications were compared between groups. Osteotomy healing was graded using a 5-point (0-4) scale. Data were analyzed using Wilcoxon Rank Sum tests and χ(2) tests with significance set at P<.05. RESULTS: Fifty-six dogs (30 BC, 26 SSC) had complete medical and radiographic records at 6 months for inclusion in data analysis. Three complications occurred in the BC group (1 major, 2 minor) and 2 occurred in the SSC group (2 minor). There was no statistical difference in patient parameters, 6 week healing scores, or complications between BC and SSC groups. Healing scores at 6 months were significantly higher in the BC group (3.3 ± 0.52) compared to the SSC group (2.9 ± 0.69; P=.04). CONCLUSION: Based on improved BC osteotomy healing scores 6 months after surgery with no significant differences in complications compared to SSC, BC TTA cages are a viable alternative to SSC.

Identifying Products of Recombinase-Mediated Cassette Exchange (RMCE) in Schizosaccharomyces pombe.

Homologous recombination is highly efficient when mediated between two identical target sequences by recombination enzymes such as Cre. Exploiting this, recombinase-mediated cassette exchange (RMCE) was developed for the genetic manipulation of eukaryotic cells, including those of Schizosaccharomyces pombe RMCE can be summarized in three stages: (1) A loxP-ura4(+)-loxM3 cassette is introduced into the genome using standard homologous recombination techniques to create a "base strain." (2) A Cre-expression plasmid carrying a protein tag or replacement gene flanked by loxP and loxM3 is introduced into the cell. (3) Cassette exchange between the chromosomal cassette and the plasmid cassette results in either gene tagging or gene replacement. This is selected for by loss of the marker. This protocol explains how to identify the products of the exchange events in the last stage.

Extraction of Chromosomal DNA from Schizosaccharomyces pombe.

Extraction of DNA from Schizosaccharomyces pombe cells is required for various uses, including templating polymerase chain reactions (PCRs), Southern blotting, library construction, and high-throughput sequencing. To purify high-quality DNA, the cell wall is removed by digestion with Zymolyase or Lyticase and the resulting spheroplasts lysed using sodium dodecyl sulfate (SDS). Cell debris, SDS, and SDS-protein complexes are subsequently precipitated by the addition of potassium acetate and removed by centrifugation. Finally, DNA is precipitated using isopropanol. At this stage, purity is usually sufficient for PCR. However, for more sensitive procedures, such as restriction enzyme digestion, additional purification steps, including proteinase K digestion and phenol-chloroform extraction, are recommended. All of these steps are described in detail here.

Colony Polymerase Chain Reaction with Schizosaccharomyces pombe.

When screening a large number of individual Schizosaccharomyces pombe strains by polymerase chain reaction (PCR), a rapid "colony PCR" approach may be used. Numerous colony PCR protocols are available, and fundamental to them all is that the colony must be fresh (grown overnight) and that as few cells as possible are used. In this protocol, we present three reliable methods for preparing S. pombe cells for colony PCR.

Molecular Genetic Tools and Techniques in Fission Yeast.

The molecular genetic tools used in fission yeast have generally been adapted from methods and approaches developed for use in the budding yeast, Saccharomyces cerevisiae Initially, the molecular genetics of Schizosaccharomyces pombe was developed to aid gene identification, but it is now applied extensively to the analysis of gene function and the manipulation of noncoding sequences that affect chromosome dynamics. Much current research using fission yeast thus relies on the basic processes of introducing DNA into the organism and the extraction of DNA for subsequent analysis. Targeted integration into specific genomic loci is often used to create site-specific mutants or changes to noncoding regulatory elements for subsequent phenotypic analysis. It is also regularly used to introduce additional sequences that generate tagged proteins or to create strains in which the levels of wild-type protein can be manipulated through transcriptional regulation and/or protein degradation. Here, we draw together a collection of core molecular genetic techniques that underpin much of modern research using S. pombe We summarize the most useful methods that are routinely used and provide guidance, learned from experience, for the successful application of these methods.

Transformation of Schizosaccharomyces pombe: Electroporation Procedure.

Transformation ofSchizosaccharomyces pombewith DNA requires the conditioning of cells to promote DNA uptake followed by cell growth under conditions that select and maintain the plasmid or integration event. The three main methodologies are electroporation, treatment with lithium cations, and transformation of protoplasts. This protocol describes transformation by electroporation. It involves pretreatingS. pombecells with dithiothreitol (DTT), which increases the transformation efficiency once the electric pulse is applied.

Transformation of Schizosaccharomyces pombe: Lithium Acetate/ Dimethyl Sulfoxide Procedure.

Transformation ofSchizosaccharomyces pombewith DNA requires the conditioning of cells to promote DNA uptake followed by cell growth under conditions that select and maintain the plasmid or integration event. The three main methodologies are electroporation, treatment with lithium cations, and transformation of protoplasts. The lithium acetate method described here is widely used because it is simple and reliable.

Transformation of Schizosaccharomyces pombe: Protoplast Procedure.

Transformation of Schizosaccharomyces pombe with DNA requires the conditioning of cells to promote DNA uptake followed by cell growth under conditions that select and maintain the plasmid or integration event. The three main methodologies are electroporation, treatment with lithium cations, and transformation of protoplasts. The protocol for protoplast transformation, which is described here, is more complicated than those for electroporation or lithium acetate and thus less often used. However, for some strains, it remains the only reliable protocol.

Virtual-'light-sheet' single-molecule localisation microscopy enables quantitative optical sectioning for super-resolution imaging.

Single-molecule super-resolution microscopy allows imaging of fluorescently-tagged proteins in live cells with a precision well below that of the diffraction limit. Here, we demonstrate 3D sectioning with single-molecule super-resolution microscopy by making use of the fitting information that is usually discarded to reject fluorophores that emit from above or below a virtual-'light-sheet', a thin volume centred on the focal plane of the microscope. We describe an easy-to-use routine (implemented as an open-source ImageJ plug-in) to quickly analyse a calibration sample to define and use such a virtual light-sheet. In addition, the plug-in is easily usable on almost any existing 2D super-resolution instrumentation. This optical sectioning of super-resolution images is achieved by applying well-characterised width and amplitude thresholds to diffraction-limited spots that can be used to tune the thickness of the virtual light-sheet. This allows qualitative and quantitative imaging improvements: by rejecting out-of-focus fluorophores, the super-resolution image gains contrast and local features may be revealed; by retaining only fluorophores close to the focal plane, virtual-'light-sheet' single-molecule localisation microscopy improves the probability that all emitting fluorophores will be detected, fitted and quantitatively evaluated.

Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5' flap DNA: basis of interstrand cross-link repair by FAN1.

Fanconi anemia (FA) is an autosomal recessive genetic disorder caused by defects in any of 15 FA genes responsible for processing DNA interstrand cross-links (ICLs). The ultimate outcome of the FA pathway is resolution of cross-links, which requires structure-selective nucleases. FA-associated nuclease 1 (FAN1) is believed to be recruited to lesions by a monoubiquitinated FANCI-FANCD2 (ID) complex and participates in ICL repair. Here, we determined the crystal structure of Pseudomonas aeruginosa FAN1 (PaFAN1) lacking the UBZ (ubiquitin-binding zinc) domain in complex with 5' flap DNA. All four domains of the right-hand-shaped PaFAN1 are involved in DNA recognition, with each domain playing a specific role in bending DNA at the nick. The six-helix bundle that binds the junction connects to the catalytic viral replication and repair (VRR) nuclease (VRR nuc) domain, enabling FAN1 to incise the scissile phosphate a few bases distant from the junction. The six-helix bundle also inhibits the cleavage of intact Holliday junctions. PaFAN1 shares several conserved features with other flap structure-selective nucleases despite structural differences. A clamping motion of the domains around the wedge helix, which acts as a pivot, facilitates nucleolytic cleavage. The PaFAN1 structure provides insights into how archaeal Holliday junction resolvases evolved to incise 5' flap substrates and how FAN1 integrates with the FA complex to participate in ICL repair.