yEvo: A modular eukaryotic genetics and evolution research experience for high school students

The resources for carrying out and analyzing microbial evolution experiments have become more accessible, making it possible to expand these studies beyond the research laboratory and into the classroom. We developed five connected, standards-aligned yeast evolution laboratory modules, called "yEvo," for high school students. The modules enable students to take agency in answering open-ended research questions. In Module 1, students evolve baker's yeast to tolerate an antifungal drug, and in subsequent modules, investigate how evolved yeasts adapted to this stressful condition at both the phenotype and genotype levels. We used pre- and post-surveys from 72 students at two different schools and post-interviews with students and teachers to assess our program goals and guide module improvement over 3 years. We measured changes in student conceptions, confidence in scientific practices, and interest in STEM careers. Students who participated in yEvo showed improvements in understanding of activity-specific concepts and reported increased confidence in designing a valid biology experiment. Student experimental data replicated literature findings and has led to new insights into antifungal resistance. The modules and provided materials, alongside "proof of concept" evaluation metrics, will serve as a model for other university researchers and K - 16 classrooms interested in engaging in open-ended research questions using yeast as a model system.

Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae

It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae. A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S. cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S. cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite genome encoding an RNA-dependent RNA polymerase (RdRP) and a coat protein (CP). Phylogenetic analysis of ScPVs identified three species of ScPV, which are most closely related to viruses of the genus Cryspovirus from the mammalian pathogenic protozoan Cryptosporidium parvum. Molecular modeling of the ScPV RdRP revealed a conserved tertiary structure and catalytic site organization when compared to the RdRPs of the Picornaviridae. The ScPV CP is the smallest so far identified in the Partitiviridae and has structural homology with the CP of other partitiviruses but likely lacks a protrusion domain that is a conspicuous feature of other partitivirus particles. ScPVs were stably maintained during laboratory growth and were successfully transferred to haploid progeny after sporulation, which provides future opportunities to study partitivirus-host interactions using the powerful genetic tools available for the model organism S. cerevisiae.

yEvo: Experimental evolution in high school classrooms selects for novel mutations that impact clotrimazole resistance in S. cerevisiae

Antifungal resistance in pathogenic fungi is a growing global health concern. Nonpathogenic laboratory strains of Saccharomyces cerevisiae are an important model for studying mechanisms of antifungal resistance that are relevant to understanding the same processes in pathogenic fungi. We have developed a series of laboratory modules in which high school students used experimental evolution to study antifungal resistance by isolating azole-resistant S. cerevisiae mutants and examining the genetic basis of resistance. We have sequenced 99 clones from these experiments and found that all possessed mutations previously shown to impact azole resistance, validating our approach. We additionally found recurrent mutations in an mRNA degradation pathway and an uncharacterized mitochondrial protein (Csf1) that have possible mechanistic connections to azole resistance. The scale of replication in this initiative allowed us to identify candidate epistatic interactions, as evidenced by pairs of mutations that occur in the same clone more frequently than expected by chance (positive epistasis) or less frequently (negative epistasis). We validated one of these pairs, a negative epistatic interaction between gain-of-function mutations in the multidrug resistance transcription factors Pdr1 and Pdr3. This high school–university collaboration can serve as a model for involving members of the broader public in the scientific process to make meaningful discoveries in biomedical research.

The Species-Specific Acquisition and Diversification of a K1-like Family of Killer Toxins in Budding Yeasts of the Saccharomycotina

Killer toxins are extracellular antifungal proteins that are produced by a wide variety of fungi, including Saccharomyces yeasts. Although many Saccharomyces killer toxins have been previously identified, their evolutionary origins remain uncertain given that many of these genes have been mobilized by double-stranded RNA (dsRNA) viruses. A survey of yeasts from the Saccharomyces genus has identified a novel killer toxin with a unique spectrum of activity produced by Saccharomyces paradoxus. The expression of this killer toxin is associated with the presence of a dsRNA totivirus and a satellite dsRNA. Genetic sequencing of the satellite dsRNA confirmed that it encodes a killer toxin with homology to the canonical ionophoric K1 toxin from Saccharomyces cerevisiae and has been named K1-like (K1L). Genomic homologs of K1L were identified in six non-Saccharomyces yeast species of the Saccharomycotina subphylum, predominantly in subtelomeric regions of the genome. When ectopically expressed in S. cerevisiae from cloned cDNAs, both K1L and its homologs can inhibit the growth of competing yeast species, confirming the discovery of a family of biologically active K1-like killer toxins. The sporadic distribution of these genes supports their acquisition by horizontal gene transfer followed by diversification. The phylogenetic relationship between K1L and its genomic homologs suggests a common ancestry and gene flow via dsRNAs and DNAs across taxonomic divisions. This appears to enable the acquisition of a diverse arsenal of killer toxins by different yeast species for potential use in niche competition.

Testing Critical Slowing Down as a Bifurcation Indicator in a Low-Dissipation Dynamical System

We study a two-dimensional low-dissipation nonautonomous dynamical system, with a control parameter that is swept linearly in time across a transcritical bifurcation. We investigate the relaxation time of a perturbation applied to a variable of the system and we show that critical slowing down may occur at a parameter value well above the bifurcation point. We test experimentally the occurrence of critical slowing down by applying a perturbation to the accessible control parameter and we find that this perturbation leaves the system behavior unaltered, thus providing no useful information on the occurrence of critical slowing down. The theoretical analysis reveals the reasons why these tests fail in predicting an incoming bifurcation.

Synthesis and dispersion of Ni(OH)2 platelet-like nanoparticles in water

Synthesis of nanometric platelet-like Ni(OH)2 particles is described. The role of several experimental parameters on the particle size is investigated. A colloidal dispersion of particles is produced by adsorbing ionizable organic ligands (trisodium citrate) on the particle surface. The stability of this colloidal dispersion and the particle charge density are determined for different citrate ions concentrations.

Central vein catheter-related thrombosis in intensive care patients: incidence, risks factors, and relationship with catheter-related sepsis

OBJECTIVE

To evaluate the incidence and risk factors for catheter-related central vein thrombosis in ICU patients.

DESIGN

Observational prospective multicenter study.

SETTING

An 8-bed surgical ICU, a 10-bed surgical cardiovascular ICU, and a 10-bed medical-surgical ICU.

PATIENTS

During an 18-month period, 265 internaljugular or subclavian catheters were included. Veins were explored by duplex scanning performed just before or < 24 h after catheter removal. Suspected risk factors of catheter-related central vein thrombosis were recorded.

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

Fifty-seven catheters were excluded from the analysis. Therefore 208 catheters were analyzed. Mean age of patients was 64+/-15 years, simplified acute physiologic score was 12+/-5, organ system failure score at insertion was 1+/-1, and mean duration of catheterization was 9+/-5 days. A catheter-related internal jugular or subclavian vein thrombosis occurred in 33% of the cases (42% [95% confidence interval (CI), 34 to 49%] and 10% [95% CI, 3 to 18%], respectively). Thrombosis was limited in 8%, large in 22%, and occlusive in 3% of the cases. Internal jugular route (relative risk [RR], 4.13; 95% CI, 1.72 to 9.95), therapeutic heparinization (RR 0.47; 95% CI, 0.23 to 0.99), and age >64 years (RR, 2.44; 95% CI, 2.05 to 3.19) were independently associated with catheter-related thrombosis. Moreover, the risk of catheter-related sepsis was 2.62-fold higher when thrombosis occurred (p=0.011).

CONCLUSIONS

Catheter-related central vein thrombosis is a frequent complication of central venous catheterization in ICU patients and is closely associated with catheter-related sepsis.

Root growth potential, seedling morphology and bud dormancy correlate with survival of loblolly pine seedlings planted in December in Alabama

First-year survival of December-planted loblolly pine seedlings sampled from 20 nurseries ranged from 36 to 86%. Various characteristics of the seedlings including root growth potential (RGP), shoot/root ratio, root weight and stem length were correlated with survival. A regression model using the number of new roots >/= 0.5 cm and the shoot/root ratio accounted for 80% of the variation in first-year survival. Alone, the number of new roots >/= 0.5 cm accounted for 76% of the variation in survival. Foliar nutrients were not correlated with survival. Seedlings with a high proportion of quiescent buds at planting had a higher RGP and better survival than seedlings with dormant (endodormant) buds. The data suggest that seedlings with dormant buds should not be planted on sites where rapid new root growth is needed for survival.

Lipid composition and activity of a lytic factor isolated from Plasmodium berghei

A fraction was obtained from Plasmodium berghei which induced hemolysis of the erythrocytes of mice and hamsters. This fraction, called lytic factor (LF), was found to be composed of a large amount of lipid material. An examination of the lipids showed the major lipids to be monoglycerides, diglycerides, triglycerides, fatty acids, long-chain alcohol, sterol, sterol ester, sterol glycoside, and two cerebrosides. The most abundant component found in the LF was sterol ester, followed in order by cerebrosides, sterol, and sterol glycoside. Lytic activity was found to be lost when samples were boiled for 5 min. An examination of the lipid composition of LF before and after boiling showed changes which may be useful in studies on the mechanism of activity of this factor. The fatty acid composition of the total lipid fraction of LF was examined by gas-liquid chromatography. The major fractions were 18:1 and 16:0 in unheated LF and 16:0 in the heated LF.

Biochemical characterization of anaerobic bacteria by an impregnated disk method

An impregnated disk method was used to characterize 20 clinical isolates of anaerobic bacteria by utilization of substrate. The procedure was easy to perform, reliable, and economical.