This paper explores the design considerations and hurdles encountered by the CHinA National CancEr Screening (CHANCES) Trial and the Tomosynthesis Mammographic Imaging Screening Trial (TMIST), both aimed at advancing cancer screening research. Before population-based cancer screening programs are launched, it is important to have confidence that the potential benefits of the screening process and resulting interventions outweigh harms, an ethical imperative because the people actively invited into the programs are relatively healthy. Large randomized screening trials provide the strongest, direct evidence regarding the balance of benefits and harms. The implementation of cancer screening programs involves a series of steps, with outcomes influenced by factors such as the prevalence of the disease, availability of effective treatment within the health-care system, and acceptance by the target population—all of which may vary considerably from country to country. This paper examines how these factors shaped the design and statistical approach of the CHANCES Trial for lung and colorectal cancers and the TMIST trial for breast cancer. We discuss the rationale, objectives, endpoint definitions, trial designs, and sample size considerations, highlighting both the challenges and opportunities presented in different settings. Ultimately, the goal is to foster collaboration and develop screening strategies that are scientifically robust and practically effective for diverse populations worldwide.

Studying the genetic and molecular characteristics of brewing yeast strains is crucial for understanding their domestication history and adaptations accumulated over time in fermentation environments, and for guiding optimizations to the brewing process itself. Saccharomyces cerevisiae (brewing yeast) is among the most profiled organisms on the planet, yet the temporal molecular changes that underlie industrial fermentation and beer brewing remain understudied. Here, we characterized the genomic makeup of a Saccharomyces cerevisiae ale yeast widely used in the production of Hefeweizen beers, and applied shotgun mass spectrometry to systematically measure the proteomic changes throughout 2 fermentation cycles which were separated by 14 rounds of serial repitching. The resulting brewing yeast proteomics resource includes 64,740 protein abundance measurements. We found that this strain possesses typical genetic characteristics of Saccharomyces cerevisiae ale strains and displayed progressive shifts in molecular processes during fermentation based on protein abundance changes. We observed protein abundance differences between early fermentation batches compared to those separated by 14 rounds of serial repitching. The observed abundance differences occurred mainly in proteins involved in the metabolism of ergosterol and isobutyraldehyde. Our systematic profiling serves as a starting point for deeper characterization of how the yeast proteome changes during commercial fermentations and additionally serves as a resource to guide fermentation protocols, strain handling, and engineering practices in commercial brewing and fermentation environments. Finally, we created a web interface (https://brewing-yeast-proteomics.ccbb.utexas.edu/) to serve as a valuable resource for yeast geneticists, brewers, and biochemists to provide insights into the global trends underlying commercial beer production.

Supplementary Methods from Identification of Novel Gene Amplifications in Breast Cancer and Coexistence of Gene Amplification with an Activating Mutation of PIK3CA

Supplementary Tables 1-5 from Identification of Novel Gene Amplifications in Breast Cancer and Coexistence of Gene Amplification with an Activating Mutation of PIK3CA

Table showing the studies that were excluded from analysis and reasons why.

Supplementary Figure 6 from Identification of Novel Gene Amplifications in Breast Cancer and Coexistence of Gene Amplification with an Activating Mutation of PIK3CA

Supplementary Figure 5 from Identification of Novel Gene Amplifications in Breast Cancer and Coexistence of Gene Amplification with an Activating Mutation of PIK3CA

Clinicopathologic features stratified by treatment arm (RNA-seq analysis population).

Supplementary Figures 1-4 from Identification of Novel Gene Amplifications in Breast Cancer and Coexistence of Gene Amplification with an Activating Mutation of PIK3CA

In Brazil, sucrose-rich broths (cane juice and/or molasses) are used to produce billions of liters of both fuel ethanol and cachaça per year using selected Saccharomyces cerevisiae industrial strains. Considering the important role of feedstock (sugar) prices in the overall process economics, to improve sucrose fermentation the genetic characteristics of a group of eight fuel-ethanol and five cachaça industrial yeasts that tend to dominate the fermentors during the production season were determined by array comparative genomic hybridization. The widespread presence of genes encoding invertase at multiple telomeres has been shown to be a common feature of both baker's and distillers' yeast strains, and is postulated to be an adaptation to sucrose-rich broths. Our results show that only two strains (one fuel-ethanol and one cachaça yeast) have amplification of genes encoding invertase, with high specific activity. The other industrial yeast strains had a single locus (SUC2) in their genome, with different patterns of invertase activity. These results indicate that invertase activity probably does not limit sucrose fermentation during fuel-ethanol and cachaça production by these industrial strains. Using this knowledge, we changed the mode of sucrose metabolism of an industrial strain by avoiding extracellular invertase activity, overexpressing the intracellular invertase, and increasing its transport through the AGT1 permease. This approach allowed the direct consumption of the disaccharide by the cells, without releasing glucose or fructose into the medium, and a 11% higher ethanol production from sucrose by the modified industrial yeast, when compared to its parental strain.

Epidemiological studies of metformin and cancer risk with BMI adjustment

During DNA replication, the newly created sister chromatids are held together until their separation at anaphase. The cohesin complex is in charge of creating and maintaining sister chromatid cohesion (SCC) in all eukaryotes. In Saccharomyces cerevisiae cells, cohesin is composed of two elongated proteins, Smc1 and Smc3, bridged by the kleisin Mcd1/Scc1. The latter also acts as a scaffold for three additional proteins, Scc3/Irr1, Wpl1/Rad61, and Pds5. Although the HEAT-repeat protein Pds5 is essential for cohesion, its precise function is still debated. Deletion of the ELG1 gene, encoding a PCNA unloader, can partially suppress the temperature-sensitive pds5-1 allele, but not a complete deletion of PDS5. We carried out a genetic screen for high-copy-number suppressors and another for spontaneously arising mutants, allowing the survival of a pds5Δ elg1Δ strain. Our results show that cells remain viable in the absence of Pds5 provided that there is both an elevation in the level of Mcd1 (which can be due to mutations in the CLN2 gene, encoding a G1 cyclin), and an increase in the level of SUMO-modified PCNA on chromatin (caused by lack of PCNA unloading in elg1Δ mutants). The elevated SUMO-PCNA levels increase the recruitment of the Srs2 helicase, which evicts Rad51 molecules from the moving fork, creating single-stranded DNA (ssDNA) regions that serve as sites for increased cohesin loading and SCC establishment. Thus, our results delineate a double role for Pds5 in protecting the cohesin ring and interacting with the DNA replication machinery. IMPORTANCE Sister chromatid cohesion is vital for faithful chromosome segregation, chromosome folding into loops, and gene expression. A multisubunit protein complex known as cohesin holds the sister chromatids from S phase until the anaphase stage. In this study, we explore the function of the essential cohesin subunit Pds5 in the regulation of sister chromatid cohesion. We performed two independent genetic screens to bypass the function of the Pds5 protein. We observe that Pds5 protein is a cohesin stabilizer, and elevating the levels of Mcd1 protein along with SUMO-PCNA accumulation on chromatin can compensate for the loss of the PDS5 gene. In addition, Pds5 plays a role in coordinating the DNA replication and sister chromatid cohesion establishment. This work elucidates the function of cohesin subunit Pds5, the G1 cyclin Cln2, and replication factors PCNA, Elg1, and Srs2 in the proper regulation of sister chromatid cohesion.

“Screening” is a search for preclinical, asymptomatic disease, including cancer. Widespread cancer screening has led to large increases in early-stage cancers and pre-cancers. Ubiquitous public messages emphasize the potential benefits to screening for these lesions based on the underlying assumption that treating cancer at early stages before spread to other organs should make it easier to treat and cure, using more tolerable interventions. The intuition is so strong that public campaigns are sometimes launched without conducting definitive trials directly comparing screening to usual care. An effective cancer screening test should not only increase the incidence of early-stage preclinical disease but should also decrease the incidence of advanced and metastatic cancer, as well as a subsequent decrease in cancer-related mortality. Otherwise, screening efforts may be uncovering a reservoir of non-progressive and very slowly progressive lesions that were not destined to cause symptoms or suffering during the person's remaining natural lifespan: a phenomenon known as “overdiagnosis.” We provide here a qualitative review of cancer overdiagnosis and discuss specific examples due to extensive population-based screening, including neuroblastoma, prostate cancer, thyroid cancer, lung cancer, melanoma, and breast cancer. The harms of unnecessary diagnosis and cancer therapy call for a balanced presentation to people considering undergoing screening, even with a test of accepted benefit, with a goal of informed decision-making. We also discuss proposed strategies to mitigate the adverse sequelae of overdiagnosis.

<div>Yeasts are important industrial platforms for the efficient production of</div><div>foods, beverages, commodity chemicals, and biofuels. Although these yeasts usually</div><div>have beneficial native phenotypes, it is often desirable to engineer these cell factories</div><div>to increase yield, titer, and production rates, or even promote the production of new</div><div>molecules. In the present chapter, we describe several classical genetic approaches to</div><div>improve industrial yeast strains (mating, cell and protoplast fusion techniques,</div><div>mutagenesis, genome shuffling, adaptive laboratory evolution, etc.), as well as methods</div><div>to identify the genetic basis of phenotypic traits, including phenotypes controlled by</div><div>quantitative trait loci (QTL), through bulk segregant analysis (BSA) and DNA</div><div>sequencing. We then review modern technologies for industrial yeast strain</div><div>improvement (genomic engineering through homologous recombination, CRISPRCas9,</div><div>synthetic chromosomes, synthetic genomes and SCRaMbLE) both in</div><div>conventional (mostly Saccharomyces strains) as well as non-conventional yeasts.</div><div>Finally, we give several current examples (and ideas for the future) of yeast strains</div><div>genetically modified in the laboratory to produce a range of commercial products and</div><div>biofuels through industrial bioprocesses.</div>

EDITORIAL article Front. Oncol., 24 July 2020Sec. Cancer Genetics Volume 10 - 2020 | https://doi.org/10.3389/fonc.2020.01201

The term “big data” refers broadly to large volumes of data, often gathered from several sources, that are then analyzed, for example, for predictive analytics. Combining and mining genetic data from varied sources including clinical genetic testing, for example, electronic health records, what might be termed as “recreational” genetic testing such as ancestry testing, as well as research studies, provide one type of “big data.” Challenges and cautions in analyzing big data include recognizing the lack of systematic collection of the source data, the variety of assay technologies used, the potential variation in classification and interpretation of genetic variants. While advanced technologies such as microarrays and, more recently, next-generation sequencing, that enable testing an individual's DNA for thousands of genes and variants simultaneously are briefly discussed, attention is focused more closely on challenges to analysis of the massive data generated by these genomic technologies. The main theme of this review is to evaluate challenges associated with big data in general and specifically to bring the sophisticated technology of genetic/genomic testing down to the individual level, keeping in mind the human aspect of the data source and considering where the impact of the data will be translated and applied. Considerations in this “humanizing” process include providing adequate counseling and consent for genetic testing in all settings, as well as understanding the strengths and limitations of assays and their interpretation.

The Saccharomyces Genome Database (SGD; www.yeastgenome.org) maintains the official annotation of all genes in the Saccharomyces cerevisiae reference genome and aims to elucidate the function of these genes and their products by integrating manually curated experimental data. Technological advances have allowed researchers to profile RNA expression and identify transcripts at high resolution. These data can be configured in web-based genome browser applications for display to the general public. Accordingly, SGD has incorporated published transcript isoform data in our instance of JBrowse, a genome visualization platform. This resource will help clarify S. cerevisiae biological processes by furthering studies of transcriptional regulation, untranslated regions, genome engineering, and expression quantification in S. cerevisiae.