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Over the past decade, major efforts have been made to systematically survey the characteristics or phenotypes associated with genetic variation in a variety of model systems. These so-called phenomics projects involve the measurement of ‘phenomes’, or the set of phenotypic information that describes an organism or cell, in various genetic contexts or states, and in response to external factors, such as environmental signals. Our understanding of the phenome of an organism depends on the availability of reagents that enable systematic evaluation of the spectrum of possible phenotypic variation and the types of measurements that can be taken. Here, we highlight phenomics studies that use the budding yeast, a pioneer model organism for functional genomics research. We focus on genetic perturbation screens designed to explore genetic interactions, using a variety of phenotypic read-outs, from cell growth to subcellular morphology.

Author(s): Nielsen-Saines, Karin; Mitchell, Kate; Kerin, Tara; Fournier, Jasmine; Kozina, Leslie; Andrews, Brenda; Cortado, Ruth; Bolan, Robert; Flynn, Risa; Rotheram, Mary Jane; Abdalian, Sue Ellen; Bryson, Yvonne; Adolescent Medicine Trials Network (ATN) CARES Team; Mobilizing Minds Research Group | Abstract: BackgroundEarly treatment studies have shown that prompt treatment of HIV with combination antiretroviral therapy (cART) can limit the size of latent viral reservoirs, thereby providing clinical and public health benefits. Studies have demonstrated that adolescents have a greater capacity for immune reconstitution than adults. Nevertheless, adolescents who acquired HIV through sexual transmission have not been included in early treatment studies because of challenges in identification and adherence to cART.ObjectiveThis study aimed to identify and promptly treat with cART youth aged 12 to 24 years in Los Angeles and New Orleans who have acute, recent, or established HIV infection, as determined by Fiebig stages 1 to 6 determined by viral RNA polymerase chain reaction, p24 antigen presence, and HIV-1 antigen Western blot. The protocol recommends treatment on the day of diagnosis when feasible. Surveillance and dedicated behavioral strategies are used to retain them in care and optimize adherence. Through serial follow-up, HIV biomarkers and response to antiretroviral therapy (ART) are assessed. The study aims to assess viral dynamics, decay and persistence of viral reservoirs over time, and correlate these data with the duration of viral suppression.MethodsA total of 72 youth (36 acutely infected and 36 treatment naive controls) are enrolled across clinical sites using a current community-based strategy and direct referrals. Youth are prescribed ART according to the standard of care HIV-1 management guidelines and followed for a period of 2 years. Assessments are conducted at specific time points throughout these 2 years of follow-up for monitoring of adherence to ART, viral load, magnitude of HIV reservoirs, and presence of coinfections.ResultsThe study began enrolling youth in July 2017 across study sites in Los Angeles and New Orleans. As of September 30, 2018, a total of 37 youth were enrolled, 12 with recently acquired, 16 with established HIV infection as determined by Fiebig staging, and 9 pending determination of Fiebig status. Recruitment and enrollment are ongoing.ConclusionsWe hypothesize that the size of the HIV reservoir and immune activation markers will be different across groups treated with cART, that is, those with acute or recent HIV infection and those with established infection. Adolescents treated early who are virally suppressed will have diminished HIV reservoirs than those with established infection. These youth may be potential candidates for a possible HIV vaccine and additional HIV remission intervention trials. Our study will inform future studies of viral remission strategies.International registered report identifier (irrid)DERR1-10.2196/10807.

Objective: The aim of this study was to determine whether an endometrial thickness less than 5 mm on transvaginal ultrasound (TVUS) is sufficient to exclude benign endometrial lesions in postmenopausal women with bleeding and to determine a cutoff value below which benign endometrial pathology could be ruled out. Methods: Electronic medical records of consecutive postmenopausal women presenting with vaginal bleeding suspicious for benign pathology were reviewed between September 2002 and December 2007. All women underwent TVUS with endometrial stripe measurement followed by saline infusion sonography (SIS). Accuracy of endometrial echo thickness for detecting intracavitary masses was compared with the reference standard of SIS. A receiver operating characteristic curve was constructed to calculate whether other cutoff values would be more accurate than 5 mm in detecting benign endometrial masses. Results: A total of 1,097 women were referred during the study period; 135 met the inclusion criteria and underwent TVUS followed by SIS. The endometrial echo was less than 5 mm in 43% and 5 mm or greater in 57%. The overall prevalence of polyps or fibroids was 50%. Using an endometrial echo cutoff less than 5 mm, sensitivity was 76% (95% CI, 65-85), specificity was 63% (95% CI, 51-73), positive predictive value was 67%, and negative predictive value was 72%. The area under the receiver operating characteristic curve for detection of benign masses was 0.79 (95% CI, 0.72-0.87). We were unable to determine a cutoff value below which benign endometrial pathology could be excluded. Conclusions: With an endometrial thickness cutoff of 5 mm a considerable amount of benign endometrial pathology in postmenopausal women with bleeding is missed, and SIS or hysteroscopy may be warranted.

The budding yeast is a simple and genetically tractable eukaryotic organism. It remains a leading system for functional genomic work and has been the focus of many pioneering efforts, including the systematic construction and analysis of gene deletion mutants. Over the past decade, many large-scale studies have made use of the deletion and other mutant collections to assay genetic interactions, chemical sensitivities, and other phenotypes, contributing enormously to our understanding of gene function. The deletion mutant collection has also been used in cell biological surveys to identify genes that control cell and organelle morphology. One valuable approach for systematic definition of gene function and biological pathways involves global assessment of the localization patterns of the proteins they encode and how these patterns are altered in response to environmental or genetic perturbation. However, proteome-wide, cell biological screens are extremely challenging, from both a technical and computational perspective. The yeast GFP collection, an elegant and unique strain set, is ideal for studying both protein localization and abundance across the proteome ( http://yeastgfp.yeastgenome.org/ ). In this chapter, we outline how the yeast GFP collection has been used to date and discuss approaches for conducting future surveys of the proteome.

A genetic interaction occurs when the combination of two mutations leads to an unexpected phenotype. Screens for synthetic genetic interactions have been used extensively to identify genes whose products are functionally related. In particular, synthetic lethal genetic interactions often identify genes that buffer one another or impinge on the same essential pathway. For the yeast Saccharomyces cerevisiae, we developed a method termed synthetic genetic array (SGA) analysis, which offers an efficient approach for the systematic construction of double mutants and enables a global analysis of synthetic genetic interactions. In a typical SGA screen, a query mutation is crossed to an ordered array of ~5000 viable gene deletion mutants (representing ~80% of all yeast genes) such that meiotic progeny harboring both mutations can be scored for fitness defects. This approach can be extended to all ~6000 genes through the use of yeast arrays containing mutants carrying conditional or hypomorphic alleles of essential genes. Estimating the fitness for the two single mutants and their corresponding double mutant enables a quantitative measurement of genetic interactions, distinguishing negative (synthetic lethal) and positive (within pathway and suppression) interactions. The profile of genetic interactions represents a rich phenotypic signature for each gene and clustering genetic interaction profiles group genes into functionally relevant pathways and complexes. This array-based approach automates yeast genetic analysis in general and can be easily adapted for a number of different genetic screens or combined with high-content screening systems to quantify the activity of specific reporters in genome-wide sets of single or more complex multiple mutant backgrounds. Comparison of genetic and chemical-genetic interaction profiles offers the potential to link bioactive compounds to their targets. Finally, we also developed an SGA system for the fission yeast Schizosaccharomyces pombe, providing another model system for comparative analysis of genetic networks and testing the conservation of genetic networks over millions of years of evolution.

In Saccharomyces cerevisiae, at least 17 DNA replication genes are coordinately expressed at the G1/S boundary during the cell cycle. All of these genes have the DNA sequence element ACGCGT in their 5' upstream regulatory regions. This sequence has been shown to be essential for periodic expression of the POL1, CDC9, and TMP1 genes. The cyclin (CLN1 and CLN2) and HO genes are another subset of genes that are expressed with the same timing as the DNA replication genes. Their periodic expression requires the participation of two well-characterized transcriptional activators: the SWI4 and SWI6 gene products. In this study, we present evidence that SWI6 contributes to the regulation of DNA replication genes as well. Surprisingly, a preferential requirement for SWI6 over SWI4 is observed in our studies of ACGCGT-dependent reporter gene expression in vivo. This selectivity has not been observed for the other G1/S genes. Correlating with the in vivo results, protein-DNA complexes formed in vitro on multimeric ACGCGT elements are either abolished or reduced in swi6 delta deletion mutants.

Background Large-scale studies have revealed networks of various biological interaction types, such as protein-protein interaction, genetic interaction, transcriptional regulation, sequence homology, and expression correlation. Recurring patterns of interconnection, or 'network motifs', have revealed biological insights for networks containing either one or two types of interaction. Results To study more complex relationships involving multiple biological interaction types, we assembled an integrated Saccharomyces cerevisiae network in which nodes represent genes (or their protein products) and differently colored links represent the aforementioned five biological interaction types. We examined three- and four-node interconnection patterns containing multiple interaction types and found many enriched multi-color network motifs. Furthermore, we showed that most of the motifs form 'network themes' – classes of higher-order recurring interconnection patterns that encompass multiple occurrences of network motifs. Network themes can be tied to specific biological phenomena and may represent more fundamental network design principles. Examples of network themes include a pair of protein complexes with many inter-complex genetic interactions – the 'compensatory complexes' theme. Thematic maps – networks rendered in terms of such themes – can simplify an otherwise confusing tangle of biological relationships. We show this by mapping the S. cerevisiae network in terms of two specific network themes. Conclusion Significantly enriched motifs in an integrated S. cerevisiae interaction network are often signatures of network themes, higher-order network structures that correspond to biological phenomena. Representing networks in terms of network themes provides a useful simplification of complex biological relationships.

Budding yeast monitor shape and the assembly of cytoskeletal structures and convey this information to regulators of cell division, but the molecular mechanisms responsible for monitoring and interpreting spatial information about the cytoskeleton remain poorly understood. A paper in the September issue of Molecular Cell shows that direct binding of components of the septin cytoskeleton may relieve autoinhibition of a conserved checkpoint kinase, creating a simple molecular device for sensing septin cytoskeleton organization.

Because of concerns expressed by the U.S. Congress and the environmental community, the Department of the Interior began a program in late 1985 to identify the nature and extent of water-quality problems induced by irrigation that might exist in the western States. Surface water, bottom sediment, and biota were collected from March through September 1995 along the lower Colorado River and in agricultural drains at nine sites in the Yuma Valley, Arizona, and analyzed for selected inorganic and organic constituents. Analyses of water, bottom sediment, and biota were completed to determine if irrigation return flow has caused, or has the potential to cause, harmful effects on human health, fish, and wildlife in the study area. Concentrations of dissolved solids in surface-water samples collected in March generally did not vary substantially from surface-water samples collected in June. Concentrations of dissolved solids ranged from 712 to 3,000 milligrams per liter and exceeded the U.S. Environmental Protection Agency secondary maximum contaminant level of 500 milligrams per liter for drinking water. Concentrations of chloride in 9 of 18 water samples and concentrations of sulfate in 16 of 18 water samples exceeded the U.S. Environmental Protection Agency secondary maximum contaminant level of 250 milligrams per liter for drinking water. Calcium and sodium were the dominant cations, and chloride and sulfate were the dominant anions. The maximum selenium concentration of 8 micrograms per liter exceeded the U.S. Environmental Protection Agency aquatic-life chronic criterion of 5 micrograms per liter. Concentrations of lead in 7 of 18 water samples and concentrations of mercury in 4 of 18 water samples exceeded the aquatic-life chronic criteria of 3.2 and 0.012 micrograms per liter, respectively. Concentrations of antimony, beryllium, cadmium, and silver in the water samples were below analytical reporting limits. Arsenic was detected in 3 of 9 bottom-sediment samples, and concentrations ranged from 11 to 16 micrograms per gram. Concentrations of aluminum, beryllium, boron, copper, lead, and zinc were highest in samples from Main Drain at southerly international boundary near San Luis, Arizona. Selenium was detected in all bottom-sediment samples, and concentrations ranged from 0.1 to 0.7 micrograms per gram. Concentrations of cadmium, europium, holmium, mercury, molybdenum, silver, tantalum, tin, and uranium were below analytical reporting limits in the bottom-sediment samples. Concentrations of trace elements in bottom-sediment samples were 'U.S. Geological Survey, 520 N. Park Avenue, Suite 221, Tucson, AZ 85719-5035. 2U.S. Fish and Wildlife Service, 2321 West Royal Palm Road, Suite 103, Phoenix, AZ 85021-4951.

Experience on our clinical service suggested that the real-time ultrasonically measured fetal biparietal diameter (BPD) might not accurately estimate gestational age in the preterm pregnancy complicated by premature rupture of membranes (PROM). Of 2510 consecutive pregnancies for which the BPD could be obtained on ultrasound examination at or beyond 26 weeks gestation, 122 were complicated by PROM. For pregnancies with and without PROM, the relationship, if any, between BPD and gestational age at the time of examination was determined by regression analysis and the resulting equations compared by F test. The regression equations were found to be significantly different (F = 17.2, P less than 0.01); the BPD was found to underestimate the true gestational age in the presence of PROM. To model the situation in which the pregnancy is recognizably very premature, the BPD/gestational age relationship was evaluated at less than or equal to 30 weeks. In these pregnancies the correlation of gestational age with BPD was not statistically significant in the presence of PROM. These results indicate that in the presence of PROM, the BPD may not be a reliable estimator of the gestational age of the fetus. In the presence of PROM, gestational age dependent management decisions would be better based on clinical and ultrasound criteria rather than the ultrasonically determined BPD.