Cleavage of stalled forks by fission yeast Mus81/Eme1 in absence of DNA replication checkpoint

During replication arrest, the DNA replication checkpoint plays a crucial role in the stabilization of the replisome at stalled forks, thus preventing the collapse of active forks and the formation of aberrant DNA structures. How this checkpoint acts to preserve the integrity of replication structures at stalled fork is poorly understood. In Schizosaccharomyces pombe, the DNA replication checkpoint kinase Cds1 negatively regulates the structure-specific endonuclease Mus81/Eme1 to preserve genomic integrity when replication is perturbed. Here, we report that, in response to hydroxyurea (HU) treatment, the replication checkpoint prevents S-phase-specific DNA breakage resulting from Mus81 nuclease activity. However, loss of Mus81 regulation by Cds1 is not sufficient to produce HU-induced DNA breaks. Our results suggest that unscheduled cleavage of stalled forks by Mus81 is permitted when the replisome is not stabilized by the replication checkpoint. We also show that HU-induced DNA breaks are partially dependent on the Rqh1 helicase, the fission yeast homologue of BLM, but are independent of its helicase activity. This suggests that efficient cleavage of stalled forks by Mus81 requires Rqh1. Finally, we identified an interplay between Mus81 activity at stalled forks and the Chk1-dependent DNA damage checkpoint during S-phase when replication forks have collapsed.     

dN/dS-based methods detect positive selection linked to trade-offs between different fitness traits in the coat protein of potato virus Y

The dN/dS ratio between nonsynonymous and synonymous substitution rates has been used extensively to identify codon positions involved in adaptive processes. However, the accuracy of this approach has been questioned, and very few studies have attempted to validate experimentally its predictions. Using the coat protein (CP) of Potato virus Y (PVY; genus Potyvirus, family Potyviridae) as a case study, we identified several candidate positively selected codon positions that differed between clades. In the CP of the N clade of PVY, positive selection was detected at codon positions 25 and 68 by both the softwares PAML and HyPhy. We introduced nonsynonymous substitutions at these positions in an infectious cDNA clone of PVY and measured the effect of these mutations on virus accumulation in its two major cultivated hosts, tobacco and potato, and on its efficiency of transmission from plant to plant by aphid vectors. The mutation at codon position 25 significantly modified the virus accumulation in the two hosts, whereas the mutation at codon position 68 significantly modified the virus accumulation in one of its hosts and its transmissibility by aphids. Both mutations were involved in adaptive trade-offs. We suggest that our study was particularly favorable to the detection of adaptive mutations using dN/dS estimates because, as obligate parasites, viruses undergo a continuous and dynamic interaction with their hosts that favors the recurrent selection of adaptive mutations and because trade-offs between different fitness traits impede (or at least slow down) the fixation of these mutations and maintain polymorphism within populations.     

Multiplicative genetic effects in scrapie disease susceptibility

Despite experimental evidence that scrapie is an infectious disease of sheep, variations of the occurrence of the natural disease suggest an influence of host genetic factors. It has been established that the genetic polymorphism of the prion protein (PrP) gene is correlated to the incidence of scrapie and to the survival time: five polymorphisms have been described by variations at amino-acid codons 136, 154 and 171. In this paper we study the effect on scrapie susceptibility of the pairing of the five allelic variants known to exist: we show that scrapie susceptibility is given by the produce of the elementary allelic factors. This first well-documented evidence of a multiplicative property of genetic risk factors could give hints on the underlying mechanisms of prion-induced neurodegenerative diseases.     

Modification of alternan by dextranase

Alternan is a unique glucan with a backbone structure of alternating α-(1 → 6) and α-(1 → 3) linkages. Previously, we isolated strains of Penicillium sp. that modify native, high molecular weight alternan in a novel bioconversion process to a lower molecular weight form with solution viscosity properties similar to those of commercial gum arabic. The mechanism of this modification was unknown. Here, we report that these Penicillium sp. strains secrete dextranase during germination on alternan. Furthermore, alternan is modified in vitro by commercial dextranases, and dextranase-modified alternan appears to be identical to bioconversion-modified alternan. This is surprising, since alternan has long been considered to be resistant to dextranase. Results suggest that native alternan may have localized regions of consecutive α-(1 → 6) linkages that serve as substrates for dextranase. Dextranase treatment of native alternan, particularly with GRAS enzymes, may have practical advantages for the production of modified alternan as a gum arabic substitute. U.S. Department of Agriculture—Names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable.     

A Rescue Strategy for Handling Unevaluable Patients in Simon’s Two Stage Design

For phase II oncology trials, Simon’s two-stage design is the most commonly used strategy. However, when clinically unevaluable patients occur, the total number of patients included at each stage differs from what was initially planned. Such situations raise concerns about the operating characteristics of the trial design. This paper evaluates three classical ad hoc strategies and a novel one proposed in this work for handling unevaluable patients. This latter is called the rescue strategy which adapts the critical stopping rules to the number of unevaluable patients at each stage without modifying the planned sample size. blue Simulations show that none of these strategies perfectly match the original target constraints for type I and II error rates. Our rescue strategy is nevertheless the one which best approaches the target error rates requirement. A re-analysis of one real phase II clinical trials on metastatic cancer illustrates the use of the proposed strategy.     

Gaze in Visual Search Is Guided More Efficiently by Positive Cues than by Negative Cues

Visual search can be accelerated when properties of the target are known. Such knowledge allows the searcher to direct attention to items sharing these properties. Recent work indicates that information about properties of non-targets (i.e., negative cues) can also guide search. In the present study, we examine whether negative cues lead to different search behavior compared to positive cues. We asked observers to search for a target defined by a certain shape singleton (broken line among solid lines). Each line was embedded in a colored disk. In “positive cue” blocks, participants were informed about possible colors of the target item. In “negative cue” blocks, the participants were informed about colors that could not contain the target. Search displays were designed such that with both the positive and negative cues, the same number of items could potentially contain the broken line (“relevant items”). Thus, both cues were equally informative. We measured response times and eye movements. Participants exhibited longer response times when provided with negative cues compared to positive cues. Although negative cues did guide the eyes to relevant items, there were marked differences in eye movements. Negative cues resulted in smaller proportions of fixations on relevant items, longer duration of fixations and in higher rates of fixations per item as compared to positive cues. The effectiveness of both cue types, as measured by fixations on relevant items, increased over the course of each search. In sum, a negative color cue can guide attention to relevant items, but it is less efficient than a positive cue of the same informational value.     

Effects of Nuclear and Cytoplasmic Genes Altering Chlorophyll Loss on Gas Exchange during Monocarpic Senescence in Soybean

Several genes can alter the yellowing processes that normallyoccur during pod development and monocarpic senescence in soybean.CytG and d₁ + d₂ cause the leaves and seeds to stay green atmaturity. G blocks yellowing of the seed coat but not the leavesor embryos. By contrast, another gene, y₃, causes earlier yellowingof the leaves. This paper examines the effects of these geneson photosynthesis and some related parameters of the senescencesyndrome in near-isogenic backgrounds (cv. Clark). Neither cytGnor d₁ d₂ delays the decline in photosynthetic rate during monocarpicsenescence relative to Clark; while Gd₁ d₂ does. Again, y₃ causesan earlier decrease. Similarly, neither cytG nor d₁ d₂ altersthe decline in stomatal conductance and transpiration, whichoccurs at the end of podfill; however, Gd₁ d₂ delays it andy₃ advances it. Neither cytG nor d₁ d₂ prevents the rise inintercellular CO₂ during podfill, while Gd₁ d₂ does, and y₃promotesit. These changes in intercellular CO₂ may reciprocally reflectthe status (maintenance for Gd₁ d₂ and early loss for y₃) ofthe photosynthetic enzymes. Gd₁ d₂, d₁ d₂ and cytG do not appreciablyaffect leaf blade abscission; however, y₃ prevents it. Gd₁ d₂increases the dry weight seed yield, and y₃ decreases it. Gd₁d₂ inhibits several components in the senescence process, whilecytG seems to affect mainly chlorophyll loss and y₃ may actmore broadly than just accelerating senescence. Clearly, thestay-green trait can be caused by more than one genetic locus,and it may or may not maintain photosynthesis. ³Present address: Instituto de Fisologia Vegetal, Facultad deAgronomia, c.c. 31, 1900-La Plata, Argentina (Received May 18, 1990; Accepted September 4, 1990)