Comparative Genome-Wide Screening Identifies a Conserved Doxorubicin Repair Network That Is Diploid Specific in Saccharomyces cerevisiae

The chemotherapeutic doxorubicin (DOX) induces DNA double-strand break (DSB) damage. In order to identify conserved genes that mediate DOX resistance, we screened the Saccharomyces cerevisiae diploid deletion collection and identified 376 deletion strains in which exposure to DOX was lethal or severely reduced growth fitness. This diploid screen identified 5-fold more DOX resistance genes than a comparable screen using the isogenic haploid derivative. Since DSB damage is repaired primarily by homologous recombination in yeast, and haploid cells lack an available DNA homolog in G1 and early S phase, this suggests that our diploid screen may have detected the loss of repair functions in G1 or early S phase prior to complete DNA replication. To test this, we compared the relative DOX sensitivity of 30 diploid deletion mutants identified under our screening conditions to their isogenic haploid counterpart, most of which (n = 26) were not detected in the haploid screen. For six mutants (bem1Δ, ctf4Δ, ctk1Δ, hfi1Δ,nup133Δ, tho2Δ) DOX-induced lethality was absent or greatly reduced in the haploid as compared to the isogenic diploid derivative. Moreover, unlike WT, all six diploid mutants displayed severe G1/S phase cell cycle progression defects when exposed to DOX and some were significantly enhanced (ctk1Δ and hfi1Δ) or deficient (tho2Δ) for recombination. Using these and other “THO2-like” hypo-recombinogenic, diploid-specific DOX sensitive mutants (mft1Δ, thp1Δ, thp2Δ) we utilized known genetic/proteomic interactions to construct an interactive functional genomic network which predicted additional DOX resistance genes not detected in the primary screen. Most (76%) of the DOX resistance genes detected in this diploid yeast screen are evolutionarily conserved suggesting the human orthologs are candidates for mediating DOX resistance by impacting on checkpoint and recombination functions in G1 and/or early S phases.     

Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins

SH3 domains are peptide recognition modules that mediate the assembly of diverse biological complexes. We scanned billions of phage-displayed peptides to map the binding specificities of the SH3 domain family in the budding yeast, Saccharomyces cerevisiae. Although most of the SH3 domains fall into the canonical classes I and II, each domain utilizes distinct features of its cognate ligands to achieve binding selectivity. Furthermore, we uncovered several SH3 domains with specificity profiles that clearly deviate from the two canonical classes. In conjunction with phage display, we used yeast two-hybrid and peptide array screening to independently identify SH3 domain binding partners. The results from the three complementary techniques were integrated using a Bayesian algorithm to generate a high-confidence yeast SH3 domain interaction map. The interaction map was enriched for proteins involved in endocytosis, revealing a set of SH3-mediated interactions that underlie formation of protein complexes essential to this biological pathway. We used the SH3 domain interaction network to predict the dynamic localization of several previously uncharacterized endocytic proteins, and our analysis suggests a novel role for the SH3 domains of Lsb3p and Lsb4p as hubs that recruit and assemble several endocytic complexes.     

Partitioning the non-consumptive effects of predators on prey with complex life histories

Non-consumptive effects (NCEs) of predators on prey can be as strong as consumptive effects (CEs) and may be driven by numerous mechanisms, including predator characteristics. Previous work has highlighted the importance of predator characteristics in predicting NCEs, but has not addressed how complex life histories of prey could mediate predator NCEs. We conducted a meta-analysis to compare the effects of predator gape limitation (gape limited or not) and hunting mode (active or sit-and-pursue) on the activity, larval period, and size at metamorphosis of larval aquatic amphibians and invertebrates. Larval prey tended to reduce their activity and require more time to reach metamorphosis in the presence of all predator functional groups, but the responses did not differ from zero. Prey metamorphosed at smaller size in response to non-gape-limited, active predators, but counter to expectations, prey metamorphosed larger when confronted by non-gape-limited, sit-and-pursue predators. These results indicate NCEs on larval prey life history can be strongly influenced by predator functional characteristics. More broadly, our results suggest that understanding predator NCEs would benefit from greater consideration of how prey life history attributes mediate population and community-level outcomes.     

A Noninvasive Method For In situ Determination of Mating Success in Female American Lobsters (Homarus americanus)

Despite being one of the most productive fisheries in the Northwest Atlantic, much remains unknown about the natural reproductive dynamics of American lobsters. Recent work in exploited crustacean populations (crabs and lobsters) suggests that there are circumstances where mature females are unable to achieve their full reproductive potential due to sperm limitation. To examine this possibility in different regions of the American lobster fishery, a reliable and noninvasive method was developed for sampling large numbers of female lobsters at sea. This method involves inserting a blunt-tipped needle into the female''s seminal receptacle to determine the presence or absence of a sperm plug and to withdraw a sample that can be examined for the presence of sperm. A series of control studies were conducted at the dock and in the laboratory to test the reliability of this technique. These efforts entailed sampling 294 female lobsters to confirm that the presence of a sperm plug was a reliable indicator of sperm within the receptacle and thus, mating. This paper details the methodology and the results obtained from a subset of the total females sampled. Of the 230 female lobsters sampled from George''s Bank and Cape Ann, MA (size range = 71-145 mm in carapace length), 90.3% were positive for sperm. Potential explanations for the absence of sperm in some females include: immaturity (lack of physiological maturity), breakdown of the sperm plug after being used to fertilize a clutch of eggs, and lack of mating activity. The surveys indicate that this technique for examining the mating success of female lobsters is a reliable proxy that can be used in the field to document reproductive activity in natural populations.     

Species, Demes, and the Omega Taxonomy: Gilmour and The NewSystematics

The word ``deme' was coined by the botanists J.S.L. Gilmour and J.W.Gregor in 1939, following the pattern of J.S. Huxley's ``cline'. Its purposewas not only to rationalize the plethora of terms describing chromosomaland genetic variation, but also to reduce hostility between traditionaltaxonomists and researchers on evolution, who sometimes scorned eachother's understanding of species. A multi-layered system of compoundterms based on deme was published by Gilmour and J. Heslop-Harrison in1954 but not widely used. Deme was adopted with a modified meaning byzoologists leading the evolutionary synthesis – Huxley, Simpson, Wright,and Mayr. Connections are shown between Gilmour's ideas around definingthe deme, his role in founding the Systematics Association, and his chapter``Taxonomy and Philosophy' in the book The New Systematics. Thishistorical episode raises questions about the role of carefully-definedwords in scientific practice.     

Rhythms of locomotion expressed by Limulus polyphemus, the American horseshoe crab: I. Synchronization by artificial tides

Limulus polyphemus, the American horseshoe crab, has an endogenous clock that drives circatidal rhythms of locomotor activity. In this study, we examined the ability of artificial tides to entrain the locomotor rhythms of Limulus in the laboratory. In experiments one and two, the activity of 16 individuals of L. polyphemus was monitored with activity boxes and "running wheels." When the crabs were exposed to artificial tides created by changes in water depth, circatidal rhythms were observed in animals exposed to 12.4-h "tidal" cycles of either water depth changes (8 of 8 animals) or inundation (7 of 8 animals). In experiment three, an additional 8 animals were exposed to water depth changes under cyclic conditions of light and dark and then monitored for 10 days with no imposed artificial tides. Most animals (5) clearly synchronized their activity to the imposed artificial tidal cycles, and 3 of these animals showed clear evidence of entrainment after the artificial tides were terminated. Overall, these results demonstrate that the endogenous tidal clock that influences locomotion in Limulus can be entrained by imposed artificial tides. In the laboratory, these tidal cues override the influence of light/dark cycles. In their natural habitat, where both tidal and photoperiod inputs are typically always present, their activity rhythms are likely to be much more complex.     

NEWER METHODS FOR SELECTION OF PATIENTS FOR LUMBAR SYMPATHECTOMY

The degree of vasodilatation achieved by various diagnostic methods (arterial occlusion, ganglionic block established by certain agents, lumbar sympathetic block, spinal anesthesia, and indirect heating) was studied by means of the pneumo-plethysmogram as well as through readings of skin temperature and skin resistance. The data obtained were interpreted as to their value in determining the type of patient with vascular disease for whom lumbar sympathectomy would be of noticeable benefit. Arterial occlusion proved itself a rapid and simple method which in most patients produced satisfactory results. As a rule, lumbar sympathectomy was effective in patients who preoperatively had shown a positive response upon release of arterial occlusion. A negative response, that is, absence of significant increase in blood flow, does not necessarily indicate organic disease, and cannot be taken to mean that lumbar sympathectomy would always be ineffective. Ganglionic block, using 2.6 dimethyl piperidinium bromide or tetraethylammonium ion, was generally less reliable in indicating the probable results of sympathectomy than lumbar sympathetic block or indirect heating. Lumbar sympathetic block with procaine was followed by a greater increase in skin temperature and blood flow than spinal anesthesia, and permitted far more accurate conclusions as to the probable outcome of sympathectomy. Subsequent to indirect heating the plethysmogram showed characteristic differences depending on the degree of vascular disease present. From the effect of this simple, safe and painless method upon the relative blood flow to the toe it becomes possible to arrive at a comparatively accurate estimate of the clinical benefit to be expected from lumbar sympathectomy.     

POLLEN LOADS AND PROGENY VIGOR IN CUCURBITA PEPO: THE NEXT GENERATION

Previous research on the Black Beauty bush cv. of zucchini has documented a strong positive relationship between the size of the pollen load and the vigor (performance) of the progeny. Here we report the results of three studies designed to test the hypothesis that the previously observed differences in progeny vigor are heritable. Two studies examined the transmission of the pollen load effect to subsequent generations through the ovules (female role). The third study determined if there is genetic variation for pollen performance and if the pollen load effect could be transmitted to a subsequent generation through the pollen (male role). In each of these studies the vigor of the progeny from the subsequent generation was evaluated in the greenhouse and/or the field. The results of these studies reveal (1) that the ability to sire seeds does respond to selection imposed by high pollen loads, (2) that only 23 of the 35 total traits that we measured in the three studies of transmission to subsequent generations changed in the direction predicted by the pollen competition hypothesis, (3) that only 5 of the 35 traits were significantly affected by the size of the pollen load that produced the previous generation (but all 5 were in the direction predicted by the pollen competition hypothesis), and (4) that only one study produced an overall significant difference (MANOVA) attributable to the size of the pollen load that produced the previous generation (but it too was in the direction predicted by the pollen competition hypothesis). From these experiments we conclude that pollen competition appears to play a real but minor role in the production of differences in vigor between progeny arising from low versus high pollen loads. In Black Beauty bush cv. of zucchini, maternal effects, pollen-pistil interactions, or nonrandom patterns of seed abortion must play important roles as well.     

Circalunidian clocks control tidal rhythms of locomotion in the American horseshoe crab,Limulus polyphemus

While many intertidal animals exhibit circatidal rhythms, the nature of the underlying endogenous clocks that control these rhythms has been controversial. In this study American horseshoe crabs, Limulus polyphemus, were used to test the circalunidian hypothesis by exposing them to four different tidal regimes. Overall, the results obtained support the circalunidian hypothesis: each of the twice-daily rhythms of activity appears to be controlled by a separate clock, each with an endogenous period of approximately 24.8 h. First, spontaneous “skipping” of one of the daily bouts was observed under several different conditions. Second, the presence of two bouts of activity/day, with different periods, was observed. Lastly, we were able to separately synchronize bouts of activity to two artificial tidal regimes with different periods. These results, taken together, argue in favor of two separate circalunidian clocks in Limulus, each of which controls one of the two bouts of their daily tidal activity rhythms.