Genome-scale patterns in the loss of heterozygosity incidence in Saccharomyces cerevisiae

Former studies have established that loss of heterozygosity can be a key driver of sequence evolution in unicellular eukaryotes and tissues of metazoans. However, little is known about whether the distribution of loss of heterozygosity events is largely random or forms discernible patterns across genomes. To initiate our experiments, we introduced selectable markers to both arms of all chromosomes of the budding yeast. Subsequent extensive assays, repeated over several genetic backgrounds and environments, provided a wealth of information on the genetic and environmental determinants of loss of heterozygosity. Three findings stand out. First, the number of loss of heterozygosity events per unit time was more than 25 times higher for growing than starving cells. Second, loss of heterozygosity was most frequent when regions of homology around a recombination site were identical, about a half-% sequence divergence was sufficient to reduce its incidence. Finally, the density of loss of heterozygosity events was highly dependent on the genome’s physical architecture. It was several-fold higher on short chromosomal arms than on long ones. Comparably large differences were seen within a single arm where regions close to a centromere were visibly less affected than regions close, though usually not strictly adjacent, to a telomere. We suggest that the observed uneven distribution of loss of heterozygosity events could have been caused not only by an uneven density of initial DNA damages. Location-depended differences in the mode of DNA repair, or its effect on fitness, were likely to operate as well.     

Intrathecal Morphine Use in Adolescent Idiopathic Scoliosis Surgery is Associated with Decreased Opioid Use and Decreased Length of Stay

BackgroundLength of stay (LOS) in the hospital following posterior spinal fusion (PSF) for adolescent idiopathic scoliosis (AIS) has decreased over the past decade due to well-defined postoperative clinical pathways, earlier mobilization, and improved pain control methods. Historically, liberal use of parenteral and oral opioids for pain control caused side effects, resulting in delayed discharge. Intraoperative intrathecal morphine (ITM) has been posited to reduce the need for postoperative opioids and to expedite the discharge process. This study examines the relationship between the use of ITM with average required postoperative opioid usage and with average LOS.MethodsThis IRB-approved retrospective cohort study examined 105 patients with AIS who received PSF with instrumentation split into two cohorts. One cohort underwent PSF via standard surgical protocol (n=40) while the other cohort received intraoperative ITM with the standard surgical protocol (n=65). Power analysis demonstrated a study power of 0.8. LOS and total postoperative opioid analgesic medication (morphine milligram equivalent, MME) data were collected. Age at surgery, gender, number of spinal levels fused, estimated intraoperative blood loss (EBL), preoperative Cobb angle, and any complications related to the use of ITM were also recorded. Continuous variables were analyzed with Student’s t-test and categorical variables were analyzed with chi-square independent-sample tests using SAS 9.4 (α = 0.05).ResultsPatients who were treated with ITM displayed shorter LOS (p<0.0001) and reduced postoperative analgesic requirement (p<0.0001). Patients who received ITM spent an average of 1.8 fewer midnights in the hospital and received an average of 221.2 MME less than patients who received standard protocol (57% decrease). There were no significant differences between the two groups for any other variable.ConclusionIntraoperative ITM is a simple and effective treatment for scoliosis surgeons to better control postoperative pain in patients, reduce the risk of dependency, and achieve earlier discharge from the hospital. Shortened LOS reduces the overall cost of care, benefitting patients, hospitals, and insurance companies. Based on the results of this study and several earlier studies, the authors recommended that scoliosis surgeons consider incorporating use of ITM into their standard operative protocols. Level of Evidence: IV     

Diet and dentition in tropical ariid catfishes from Australia

Synopsis The diets of 13 species of ariid catfishes from the tropical waters of the Gulf of Carpentaria are described and compared. Fishes were collected from two estuaries and inshore and offshore marine areas. Up to 10 species have been recorded from a single estuary. Although all are carnivorous and consume a variety of prey, diet analyses and statistical ordination reveal three feeding guilds - piscivores, polychaete-eaters and molluscivores. The diets of most species are similar between sites. There are strong relationships between dietary guild and the size and arrangement of the palatine teeth. The piscivorous group of catfish (guild 1) have large mouths with relatively large multiple palatine tooth plates, either in a band or in a triangular pattern and armed with sharp recurved teeth. The primarily polychaete-feeding group (guild 2) have a variable mouth size but it is usually smaller than that of guild 1 fish; their palatine teeth plates are fewer and smaller, and they have small, sharp recurved teeth. Guild 3 eat mainly molluscs, and have a small mouth and large posteriorly situated palatine plates with globular, truncated teeth. Overlaps in diet between species are probably reduced by differential distribution patterns within estuaries and different habitat preferences. The mouth-width and tooth-plate arrangements of ariids in tropical Australia are suitable for dealing with broad classes of prey rather than specific items, conferring dietary flexibility. This probably optimizes the trade-off for most species between occupation of broad feeding niches and the ability to shift diet easily.     

Rebound effects of price differences

Goal, Scope and Background  Traditionally, comparative life cycle assessments (LCA) have not considered rebound effects, for instance in case of significant price differences among the compared products. No justifications have been made for this delimitation in scope. This article shows that price differences and the consequent effects of marginal consumer expenditure may influence the conclusions of comparative LCA significantly. We also show that considerations about rebound effects of price differences can be included in LCAs. Methods  The direct rebound effect of a price difference is marginal consumption. Based on statistical data on private consumption in different income groups (Statistics Denmark 2005a, 2005b), the present article provides an estimate of how an average Danish household will spend an additional 1 DKK for further consumer goods, when the household has gained money from choosing a cheaper product alternative. The approach is to use marginal income changes and the following changes in consumption patterns as an expression for marginal consumption. Secondly, the environmental impact potentials related to this marginal consumption are estimated by the use of environmental impact intensity data from an IO-LCA database (Weidema et al. 2005). Finally, it is discussed whether, and in which ways the conclusions of comparative LCAs can be affected by including the price difference between product alternatives. This is elucidated in a case study of a comparative LCA screening of two different kinds of Danish cheese products (Fricke et al. 2004). Results  Car purchase and driving, use and maintenance of dwelling, clothing purchase and insurance constitutes the largest percentages of the marginal consumption. In a case study of two cheeses, the including the impact potentials related to the price difference results in significant changes in the total impact potentials. Considering the relatively small price difference of the two products, it is likely also to have a significant influence on the results of comparative LCAs more generally. Discussion  The influence of marginal consumption in comparative LCAs is relevant to consider in situations with large differences in the price of the product alternatives being compared, and in situations with minor differences in the impact potentials related to the alternatives. However, different uncertainties are linked to determining the pattern for marginal consumption and the environmental impact potential related to this. These are first of all related to the method used, but also include inaccurate data of consumption in households, aggregation and weighting of income groups, aggregation of product groups, estimation and size of the price difference, and the general applicability of the results. Conclusion  Incorporating marginal consumption in consequential LCAs is possible in practice. In the case study used, including the rebound effects of the price difference has a significant influence on the result of the comparative LCA, as the result for the impact categories acidification and nutrient enrichment changes in favour of the expensive product. Recommendations and Perspectives  It is recommended that the rebound effects of price differences should be included more frequently in LCAs. In order to ensure this, further research in marginal consumption and investment patterns and IO data for different countries or regions is required. Furthermore, this study does not consider the economic distributional consequences of buying an expensive product instead of a cheaper product (e.g. related to how the profit is spent by those who provided the product). It should also be noted, that more expensive products not necessarily result in less consumption, as those who provided the product also will spend the money they have earned from the sale. Ideally, these consequences should also be further investigated. Likewise, the development of databases to include marginal consumption in PC-tools is needed. In general, considerations of marginal consumption would favour expensive product alternatives, depending, however, on the type of consumer. ESS-Submission Editor: Dr. David Hunkeler (david.hunkeler@aquaplustech.ch)     

High-level expression of murine terminal deoxynucleotidyl transferase inEscherichia coli grown at low temperature and overexpressingargU tRNA

Terminal deoxynucleotidyl transferase (TdT) is a highly conserved vertebrate enzyme that possesses the unique ability to catalyze the random addition of deoxynucleoside 5′-triphosphates onto the 3′-hydroxyl group of a single-stranded DNA. It plays an important role in the generation of immunoglobin and T-cell receptor diversity. TdT is usually obtained from animal thymus gland or produced in a baculovirus system, but both procedures are rather tedious, and proteolysis occurs during purification. Attempts to overexpress TdT in bacteria have been unsuccessful or have yielded an enzyme with a lower specific activity. A dearth of TdT has thus hampered detailed structural and functional studies. In the present study, we report that by lowering growth temperature and overexpressing a rare arginyl tRNA, it is possible to boost the production inEscherichia coli of murine TdT with minimal proteolysis and high specific activity.     

Non-invasive diagnosis of cutaneous leishmaniasis by the direct boil loop-mediated isothermal amplification method and MinION™ nanopore sequencing

Cutaneous leishmaniasis (CL) is gaining attention as a public health problem. We present two cases of CL imported from Syria and Venezuela in Japan. We diagnosed them as CL non-invasively by the direct boil loop-mediated isothermal amplification method and an innovative sequencing method using the MinION? sequencer. This report demonstrates that our procedure could be useful for the diagnosis of CL in both clinical and epidemiological settings.     

MHC Class I Immunopeptidome: Past,Present, and Future

In the 35 years since the revelation that short peptides bound to major histocompatibility complex class I and II molecules are the secret of the major histocompatibility complex–restricted nature of T-cell recognition, there has been enormous progress in characterizing the immunopeptidome, the repertoire of peptide presented for immunosurveillance. Here, the major milestones in the journey are marked, the contribution of proteasome-mediated splicing to the immunopeptidome is discussed, and exciting recent findings relating the immunopeptidome to the translatome revealed by ribosome profiling (RiboSeq) is detailed. Finally, what is needed for continued progress is opined about, which includes the infusion of talented young scientists into the antigen-processing field, currently undergoing a renaissance; thanks in part to the astounding success of T-cell–based cancer immunotherapy.     

Effects of two chitin synthesis inhibitors on Thalassiosira fluviatilis and Cyclotella cryptica

Abstract The effects of two commercial chitin synthesis inhibitors, dimilin and polyoxin D, on chitin fiber formation and cell sedimentation for the diatoms Thalassiosira fluviatilis and Cyclotella cryptica (Bacillariophyceae) were investigated. Dimilin treatments for both diatom species were indistinguishable from controls in terms of chitin fiber productions, cell density and sedimentation. Polyoxin D-treated cells of both diatom species completely lacked the characteristic chitin fibers. Polyoxin D cultures were also characterized by a significant decrease in population density, increased sedimentation rates and a strong tendency to clump in comparison with control and dimilin treatments. It was concluded that (1) dimilin does not directly inhibit chitin synthesis in diatoms; (2) polyoxin-D inhibits β-chitin fibril formation, and (3) chitin fibers play an important role in cell separation and cell buoyancy.     

Repression of porin synthesis by salicylate in Escherichia coli, Klebsiella pneumoniae and Serratia marcescens

The synthesis of the OmpF porin in Escherichia coli K-12 was highly and reversibly inhibited by 5 mM salicylate in the bacterial growth medium, and salicylate also inhibited the OmpC porin synthesis, although only weakly. The full expression of the salicylate effect was presumed to require the ompB gene product on comparison between the wild type and ompB mutant strains. The salicylate effect was also observed for the porin protein synthesis in Klebsiella pneumoniae and Serratia marcescens, although an ompB-like gene remains to be identified in both species.