The yeast 2-micron plasmid Rep2 protein has Rep1-independent partitioning function.

Equal partitioning of the multi-copy 2-micron plasmid of the budding yeast Saccharomyces cerevisiae requires association of the plasmid Rep1 and Rep2 proteins with the plasmid STB partitioning locus. Determining how the Rep proteins contribute has been complicated by interactions between the components. Here, each Rep protein was expressed fused to the DNA-binding domain of the bacterial repressor protein LexA in yeast harboring a replication-competent plasmid that had LexA-binding sites but lacked STB. Plasmid transmission to daughter cells was increased only by Rep2 fusion expression. Neither Rep1 nor a functional RSC2 complex (a chromatin remodeler required for 2-micron plasmid partitioning) were needed for the improvement. Deletion analysis showed the carboxy-terminal 65 residues of Rep2 were required and sufficient for this Rep1-independent inheritance. Mutation of a conserved basic motif in this domain impaired Rep1-independent and Rep protein/STB-dependent plasmid partitioning. Our findings suggest Rep2, which requires Rep1 and the RSC2 complex for functional association with STB, directly participates in 2-micron plasmid partitioning by linking the plasmid to a host component that is efficiently partitioned during cell division. Further investigation is needed to reveal the host factor targeted by Rep2 that contributes to the survival of these plasmids in their budding yeast hosts.

The yeast 2-µm plasmid Raf protein contributes to plasmid inheritance by stabilizing the Rep1 and Rep2 partitioning proteins.

The yeast 2-µm plasmid is a remarkable genetic parasite, managing efficient maintenance at high-copy number with minimal impact on the host. Equal partitioning of the plasmid upon host cell division requires plasmid proteins Rep1 and Rep2 and the plasmid STB locus. The Rep proteins and the plasmid-encoded Raf protein also regulate plasmid gene transcription. In this study, protein interaction assays, sequence analyses and mutational approaches were used to identify domains and residues in Rep2 and Raf required for association with Rep1 and Rep2 and to delineate the Rep2 DNA-binding domain. Rep2 and Raf displayed similarities in interactions with Rep1 and Rep2, in having Rep1 promote their STB association in vivo, and in stabilizing Rep protein levels. Rep2 mutants impaired for self-association were competent for transcriptional repression while those deficient for Rep1 association were not. Surprisingly, Rep2 mutants impaired for either Rep1 interaction or self-association were able to maintain efficient plasmid inheritance provided Raf was present and competent for Rep protein interaction. Our findings provide insight into the Rep protein complexes required for partitioning and transcriptional repression, and suggest that in addition to its transcriptional function, Raf stabilization of Rep partitioning proteins contributes to the remarkable persistence of the 2-µm plasmid.

Bootstrap methods for quantifying the uncertainty of binding constants in the hard modeling of spectrophotometric titration data.

Equilibrium hard modeling of spectrophotometric titration data with binding parameters (ΔG° or logK values) involves nonlinear mathematical relationships and correlated experimental uncertainties. Therefore, uncertainty quantification techniques based on standard error computation substantially underestimate the true error for the calculated binding parameters. We show that the bootstrapping technique can provide accurate uncertainty quantification with no a priori knowledge of experimental error levels. Monte Carlo studies on simulated data show that bootstrapping the chemical solutions, whether on the data or residuals, handles absorbance error, transmittance error, and composition error well, producing asymmetric confidence intervals that correctly assess the true uncertainty. Additionally, stock solution error is handled well if it is present with other forms of error. Confidence interval bands for molar absorptivity curves can likewise be calculated. Analogous bootstrapping studies on real datasets confirm that the 95% confidence intervals match the variance observed from experimental replicates, though bootstrapping on the residuals should be used for smaller datasets. Bootstrapping along the titration axis should be used to estimate uncertainty whenever binding parameters are ascertained from titration datasets.

The Manifold Scattering Transform for High-Dimensional Point Cloud Data.

The manifold scattering transform is a deep feature extractor for data defined on a Riemannian manifold. It is one of the first examples of extending convolutional neural network-like operators to general manifolds. The initial work on this model focused primarily on its theoretical stability and invariance properties but did not provide methods for its numerical implementation except in the case of two-dimensional surfaces with predefined meshes. In this work, we present practical schemes, based on the theory of diffusion maps, for implementing the manifold scattering transform to datasets arising in naturalistic systems, such as single cell genetics, where the data is a high-dimensional point cloud modeled as lying on a low-dimensional manifold. We show that our methods are effective for signal classification and manifold classification tasks.

Use of Yeast Plasmids: Transformation and Inheritance Assays.

The use of the budding yeast Saccharomyces cerevisiae as a model genetic organism has been facilitated by the availability of a wide range of yeast shuttle vectors, plasmids that can be propagated in Escherichia coli and also in yeast, where they are stably maintained at low- or high-copy number, depending on the plasmid system. Here we provide an introduction to the low-copy (ARS/CEN) and multi-copy (2-µm-based) plasmids, the marker genes commonly used for plasmid selection in yeast, methods for transforming yeast and monitoring plasmid inheritance, and tips for working with yeast transformants.

The 2 microm plasmid causes cell death in Saccharomyces cerevisiae with a mutation in Ulp1 protease.

The 2 microm circle plasmid confers no phenotype in wild-type Saccharomyces cerevisiae but in a nib1 mutant, an elevated plasmid copy number is associated with cell death. Complementation was used to identify nib1 as a mutant allele of the ULP1 gene that encodes a protease required for removal of a ubiquitin-like protein, Smt3/SUMO, from protein substrates. The nib1 mutation replaces conserved tryptophan 490 with leucine in the protease domain of Ulp1. Complete deletion of ULP1 is lethal, even in a strain that lacks the 2 microm circle. Partial deletion of ULP1, like the nib1 mutation, results in clonal variations in plasmid copy number. In addition, a subset of these mutant cells produces lineages in which all cells have reduced proliferative capacity, and this phenotype is dependent upon the presence of the 2 microm circle. Segregation of the 2 microm circle requires two plasmid-encoded proteins, Rep1 and Rep2, which were found to colocalize with Ulp1 protein in the nucleus and interact with Smt3 in a two-hybrid assay. These associations and the observation of missegregation of a fluorescently tagged 2 microm circle reporter plasmid in a subset of ulp1 mutant cells suggest that Smt3 modification plays a role in both plasmid copy number control and segregation.

The role of a multidisciplinary severe chronic obstructive pulmonary disease hyperinflation service in patient selection for lung volume reduction.

Chronic obstructive pulmonary disease (COPD) is a complex disease and the management is focused on improving breathlessness, quality of life and healthcare utilisation. Our understanding of COPD phenotypes has improved in recent years and there is an increased drive towards delivering phenotype-based therapies. Lung volume reduction can offer the prospect of life changing benefit in breathlessness and quality of life in a select group of patients with severe emphysema already receiving maximum medical treatment. In spite of the available evidence, very few procedures are being performed relative to the disease burden and prevalence of suitable individuals. Currently the major barriers to patient accessibility are lack in standardised multidisciplinary severe COPD services with easy access to lung volume reduction procedures, as well as poorly informed perceptions of healthcare professionals. There is a recognised need to improve such services in many healthcare systems. We share our experiences with setting up and running a successful regional multidisciplinary severe COPD hyperinflation service.

Delayed onset pulmonary glue emboli in a ventilated patient: a rare complication following endoscopic cyanoacrylate injection for gastric variceal haemorrhage.

Cyanoacrylate injection is a recognised endoscopic treatment option for variceal haemorrhage. We describe a 34-year old man with hepatitis B cirrhosis who presented to the hospital with upper gastrointestinal haemorrhage from gastric and oesophageal varices. Haemostasis was achieved via cyanoacrylate injection sclerotherapy and banding. Ten days later, the patient developed acute hypoxia and fever. His chest radiograph showed wide-spread pulmonary shadowing. A non-contrast CT scan confirmed multiple emboli of injected glue material from the varix with parenchymal changes either suggesting acute lung injury or pulmonary oedema. He gradually recovered with supportive treatment and was discharged home. On follow-up, he remained asymptomatic from a chest perspective. This case report discusses the rare complication of pulmonary embolisation of cyanoacrylate glue from variceal injection sites and the diagnostic dilemmas involved. Emphasis is placed on the importance of maintaining high index of clinical suspicion when assessing patients with possible procedure related complications.

Molecular and cytogenetic analysis of the telomeric (TTAGGG)n repetitive sequences in the Nile tilapia, Oreochromis niloticus (Teleostei: Cichlidae).

The majority of chromosomes in Oreochromis niloticus, as with most fish karyotyped to date, cannot be individually identified owing to their small size. As a first step in establishing a physical map for this important aquaculture species of tilapia we have analyzed the location of the vertebrate telomeric repeat sequence, (TTAGGG)n, in O. niloticus. Southern blot hybridization analysis and a Bal31 sensitivity assay confirm that the vertebrate telomeric repeat is indeed present at O. niloticus chromosomal ends with repeat tracts extending for 4-10 kb on chromosomal ends in erythrocytes. Fluorescent in situ hybridization revealed that (TTAGGG)n is found not only at telomeres, but also at two interstitial loci on chromosome 1. These data support the hypothesis that chromosome 1, which is significantly larger than all the other chromosomes in the karyotype, was produced by the fusion of three chromosomes and explain the overall reduction of chromosomal number from the ancestral teleost karyotype of 2n=48 to 2n=44 observed in tilapia.