Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum.

Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically diverse as plants or animals. To understand budding yeast evolution, we analyzed the genomes of 332 yeast species, including 220 newly sequenced ones, which represent nearly one-third of all known budding yeast diversity. Here, we establish a robust genus-level phylogeny comprising 12 major clades, infer the timescale of diversification from the Devonian period to the present, quantify horizontal gene transfer (HGT), and reconstruct the evolution of 45 metabolic traits and the metabolic toolkit of the budding yeast common ancestor (BYCA). We infer that BYCA was metabolically complex and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. More generally, our results argue that reductive evolution is a major mode of evolutionary diversification.

Assessment of a community pharmacist remote monitoring service in patients using continuous glucose monitors.

BACKGROUND: Diabetes is the eighth leading cause of death and has a substantial impact on the U.S. health care system. Recent changes to major insurance formularies allow for increased access to continuous glucose monitors (CGMs). Community pharmacists routinely assist and educate patients about diabetes care, including usage of CGM. OBJECTIVES: The purpose of this study was to evaluate the clinical impact of a community pharmacist remote CGM monitoring service on patients' glycemic metrics. Patient completion of comprehensive diabetes standards of care and pharmacist interventions and recommendations were assessed as secondary objectives. METHODS: This study was a prospective, feasibility study conducted at two pharmacies within 1 regional division of a large community pharmacy chain between November 2022 and June 2023. A pharmacist conducted patient enrollment visits and remotely monitored CGM glycemic metrics via cloud-based platforms per the study protocol. CGM glycemic metrics were evaluated for each patient 3 months pre- and post-study enrollment, including time above range (TAR), time in range (TIR), time below range, glucose management indicator, average glucose, CGM utilization rate, and glucose variability. Metrics were evaluated for statistical significance using the Wilcoxon signed-rank test and descriptive statistics. RESULTS: Pharmacists enrolled 36 patients in this study with 20 patients completing the full 3-month study period per protocol. There was a statistically significant improvement in three of eight glycemic metrics (very high TAR, TIR, and average glucose). Specifically, TIR had the largest improvement from 61.8% pre-enrollment to 69.9% (P < 0.006) postenrollment. All other pertinent glycemic metrics displayed improvements but were not statistically significant. CONCLUSION: The results demonstrate clinically and statistically significant improvements in several glycemic metrics for patients who participated in the community pharmacist-led remote CGM monitoring service, which may result in improved diabetes control and fewer long-term diabetes-related health complications.

Pathogenic budding yeasts isolated outside of clinical settings.

Budding yeasts are distributed across a wide range of habitats, including as human commensals. However, under some conditions, these commensals can cause superficial, invasive, and even lethal infections. Despite their importance to human health, little is known about the ecology of these opportunistic pathogens, aside from their associations with mammals and clinical environments. During a survey of approximately 1000 non-clinical samples across the United States of America, we isolated 54 strains of budding yeast species considered opportunistic pathogens, including Candida albicans and Candida (Nakaseomyces) glabrata. We found that, as a group, pathogenic yeasts were positively associated with fruits and soil environments, whereas the species Pichia kudriavzevii (syn. Candida krusei syn. Issatchenkia orientalis) had a significant association with plants. Of the four species that cause 95% of candidiasis, we found a positive association with soil. These results suggest that pathogenic yeast ecology is more complex and diverse than is currently appreciated and raises the possibility that these additional environments could be a point of contact for human infections.

Radial keratotomy and cataract surgery: A quest for emmetropia.

A 75-year-old man with an ocular history of 8-cut radial keratotomy (RK) in both eyes presented for cataract surgery evaluation. He was previously correctable in spectacles in years prior despite his irregular corneas to 20/25 in the right eye and 20/30 in the left eye. He recently noticed a change in his overall visual function with significant nighttime glare and difficulty reading despite spectacle correction. Of note, he was unable to tolerate contact lenses and was resistant to refitting despite additional encouragement. Cataract surgery was delayed for many years, given he was correctable in spectacles and the concern of uncovering a highly aberrated cornea after removing his cataracts (Figures 1 and 2JOURNAL/jcrs/04.03/02158034-202308000-00021/figure1/v/2023-07-21T030437Z/r/image-tiffJOURNAL/jcrs/04.03/02158034-202308000-00021/figure2/v/2023-07-21T030437Z/r/image-tiff). Of note, the patient was interested in returning to the spectacle independence he enjoyed in the past. Ocular examination revealed a corrected distance visual acuity (CDVA) of 20/30 in the right eye and 20/60 in the left eye, with a manifest refraction of +4.50 -0.50 × 177 in the right eye and +5.75 -1.75 × 14 in the left eye. Glare testing was 20/50 in the right eye and 20/100 in the left eye, with retinal acuity meter testing of 20/25 in each eye. Pupils, confrontation visual fields, and intraocular pressures were normal. Pertinent slitlamp examination revealed corneal findings of 8-cut RK with nasal-gaping arcuate incisions in both eyes and lens findings of 2+ nuclear sclerosis with 2+ cortical changes in the right eye and 3+ nuclear sclerosis with 3+ cortical changes in the left eye. Cup-to-disc ratios of the optic nerves measured 0.5 with temporal sloping in the right eye and 0.6 with temporal sloping in the left eye. The dilated fundus examination was unremarkable. What intraocular lens (IOL) options would you offer this patient and how would you counsel regarding realistic expectations? What additional diagnostic testing would be helpful in your assessment? How would you calculate the IOLs?

Evaluating longitudinal relationships between parental monitoring and substance use in a multi-year, intensive longitudinal study of 670 adolescent twins.

Introduction: Parental monitoring is a key intervention target for adolescent substance use, however this practice is largely supported by causally uninformative cross-sectional or sparse-longitudinal observational research designs. Methods: We therefore evaluated relationships between adolescent substance use (assessed weekly) and parental monitoring (assessed every two months) in 670 adolescent twins for two years. This allowed us to assess how individual-level parental monitoring and substance use trajectories were related and, via the twin design, to quantify genetic and environmental contributions to these relationships. Furthermore, we attempted to devise additional measures of parental monitoring by collecting quasi-continuous GPS locations and calculating a) time spent at home between midnight and 5am and b) time spent at school between 8am-3pm. Results: ACE-decomposed latent growth models found alcohol and cannabis use increased with age while parental monitoring, time at home, and time at school decreased. Baseline alcohol and cannabis use were correlated (r = .65) and associated with baseline parental monitoring (r = -.24 to -.29) but not with baseline GPS measures (r = -.06 to -.16). Longitudinally, changes in substance use and parental monitoring were not significantly correlated. Geospatial measures were largely unrelated to parental monitoring, though changes in cannabis use and time at home were highly correlated (r = -.53 to -.90), with genetic correlations suggesting their relationship was substantially genetically mediated. Due to power constraints, ACE estimates and biometric correlations were imprecisely estimated. Most of the substance use and parental monitoring phenotypes were substantially heritable, but genetic correlations between them were not significantly different from 0. Discussion: Overall, we found developmental changes in each phenotype, baseline correlations between substance use and parental monitoring, co-occurring changes and mutual genetic influences for time at home and cannabis use, and substantial genetic influences on many substance use and parental monitoring phenotypes. However, our geospatial variables were mostly unrelated to parental monitoring, suggesting they poorly measured this construct. Furthermore, though we did not detect evidence of genetic confounding, changes in parental monitoring and substance use were not significantly correlated, suggesting that, at least in community samples of mid-to-late adolescents, the two may not be causally related.

Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms.

BACKGROUND: Lignocellulosic conversion residue (LCR) is the material remaining after deconstructed lignocellulosic biomass is subjected to microbial fermentation and treated to remove the biofuel. Technoeconomic analyses of biofuel refineries have shown that further microbial processing of this LCR into other bioproducts may help offset the costs of biofuel generation. Identifying organisms able to metabolize LCR is an important first step for harnessing the full chemical and economic potential of this material. In this study, we investigated the aerobic LCR utilization capabilities of 71 Streptomyces and 163 yeast species that could be engineered to produce valuable bioproducts. The LCR utilization by these individual microbes was compared to that of an aerobic mixed microbial consortium derived from a wastewater treatment plant as representative of a consortium with the highest potential for degrading the LCR components and a source of genetic material for future engineering efforts. RESULTS: We analyzed several batches of a model LCR by chemical oxygen demand (COD) and chromatography-based assays and determined that the major components of LCR were oligomeric and monomeric sugars and other organic compounds. Many of the Streptomyces and yeast species tested were able to grow in LCR, with some individual microbes capable of utilizing over 40% of the soluble COD. For comparison, the maximum total soluble COD utilized by the mixed microbial consortium was about 70%. This represents an upper limit on how much of the LCR could be valorized by engineered Streptomyces or yeasts into bioproducts. To investigate the utilization of specific components in LCR and have a defined media for future experiments, we developed a synthetic conversion residue (SynCR) to mimic our model LCR and used it to show lignocellulose-derived inhibitors (LDIs) had little effect on the ability of the Streptomyces species to metabolize SynCR. CONCLUSIONS: We found that LCR is rich in carbon sources for microbial utilization and has vitamins, minerals, amino acids and other trace metabolites necessary to support growth. Testing diverse collections of Streptomyces and yeast species confirmed that these microorganisms were capable of growth on LCR and revealed a phylogenetic correlation between those able to best utilize LCR. Identification and quantification of the components of LCR enabled us to develop a synthetic LCR (SynCR) that will be a useful tool for examining how individual components of LCR contribute to microbial growth and as a substrate for future engineering efforts to use these microorganisms to generate valuable bioproducts.

PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation.

The role of PPM1D mutations in de novo gliomagenesis has not been systematically explored. Here we analyze whole genome sequences of 170 pediatric high-grade gliomas and find that truncating mutations in PPM1D that increase the stability of its phosphatase are clonal driver events in 11% of Diffuse Midline Gliomas (DMGs) and are enriched in primary pontine tumors. Through the development of DMG mouse models, we show that PPM1D mutations potentiate gliomagenesis and that PPM1D phosphatase activity is required for in vivo oncogenesis. Finally, we apply integrative phosphoproteomic and functional genomics assays and find that oncogenic effects of PPM1D truncation converge on regulators of cell cycle, DNA damage response, and p53 pathways, revealing therapeutic vulnerabilities including MDM2 inhibition.

Mapping the Opioid Epidemic in Rhode Island: Where Are We Missing Resources?

Opioid overdose deaths have been rising steadily over the past decade in Rhode Island (RI), and although deaths have decreased slightly over the past year, there were 314 deaths in 2018 and there have been 208 deaths in the first 9 months of 2019.1 The objective of this spatial study is to identify the RI regions with the greatest need for opioid emergency response and rehabilitation resources. Using geographic information systems (GIS), we identify areas in RI with high overdose rates and that are far from emergency departments, and areas with high rates of treatment admissions that are far away from Centers of Excellence (COEs) which provide effective medication-assisted treatment (MAT). Ultimately, we identified Burrillville, Coventry, Bristol, and Portsmouth as towns needing more emergency resources and Western Hopkinton, Western Richmond, and Western Scituate as areas needing more high-quality rehabilitation resources. These findings should inform future decisions when considering new locations for COEs or emergency resources to respond to the Rhode Island opioid epidemic.

"No matter what has been done wrong can always be redone right": spirituality in the lives of imprisoned battered women.

In this article, the authors explore the religious and spiritual experiences and beliefs of incarcerated battered women who killed abusive intimate partners or (step)fathers. Through in-depth interviews with 12 imprisoned battered women, the authors examine the role that religion and spirituality played in the women's lives before and during their incarceration. Regardless of their religious upbringing, most had what they described as spiritual experiences during their time in prison. For them, participation in the support group for battered women and their spiritual experiences "freed them" by giving them a way to reconstruct and reinterpret their victimization, perpetration of violence, and subsequent incarceration.

Improving access to vision screening in urban Philadelphia elementary schools.

BACKGROUND: The Wills Eye Vision Screening Program for Children is a community-based vision screening program for children in urban Philadelphia elementary schools that aims to provide vision screening, remedy refractive error by providing glasses, and refer children with suspected nonrefractive eye disease for eye care. METHODS: Children in grades K-5 from 45 Philadelphia elementary schools were screened for distance and near visual acuity, stereopsis, and color vision from January 2014 to June 2015. Children who failed were assessed by an on-site optometrist. Two pairs of eyeglasses were provided at no cost. Children with suspected, nonrefractive disease were referred to Wills Eye Hospital Pediatric Ophthalmology and contacted by a social worker to schedule an appointment. RESULTS: Over 84 days, 10,726 children were screened for vision problems at 45 schools. A total of 1,321 children (12%) had refractive error and 1,015 children (77%) returned the consent form and received two pairs of glasses. Of the 509 children (5%) referred to Wills Eye, 177 returned consent forms and were not being followed by an ophthalmologist. Of these, 127 children (72%) completed an eye examination at Wills. CONCLUSIONS: The program described herein can provide comprehensive vision screening, with eyeglasses and/or referrals, to children within an underserved community.

Is there a magnitude effect in tipping?

The present study examined nearly 1,000 tips recorded for two taxicabs, two hair salons, and two restaurants. In each of the six cases, amount of tip increased linearly as a function of the amount of the bill. Contrary to standard microeconomic theory, there was a magnitude effect in that as the amount of the bill increased, the percent tip tended to decrease. The present results extend the findings of Chapman and Winquist (1998), obtained using hypothetical scenarios, to real-world tipping behavior. Chapman and Winquist argued that a magnitude effect in tipping reflects the shape of the utility function for money. We suggest, however, that the magnitude effect may be the mathematical consequence of replotting the fundamental relationship between tip and bill amounts in terms of percent tip, given that the observed linear relation between tip and bill amounts has a positive intercept. We suggest further that the positive intercept arises because a tip represents a judgment as to what constitutes a fair or equitable wage, and part of what constitutes a fair wage is independent of the amount of the bill, reflecting compensation for simply being there when needed. The present account implies that different explanations may be needed for magnitude effects observed in different domains.

The Trichomonas vaginalis hydrogenosome proteome is highly reduced relative to mitochondria, yet complex compared with mitosomes.

The human pathogen Trichomonas vaginalis lacks conventional mitochondria and instead contains divergent mitochondrial-related organelles. These double-membrane bound organelles, called hydrogenosomes, produce molecular hydrogen. Phylogenetic and biochemical analyses of hydrogenosomes indicate a common origin with mitochondria; however identification of hydrogenosomal proteins and studies on its metabolism have been limited. Here we provide a detailed proteomic analysis of the T. vaginalis hydrogenosome. The proteome of purified hydrogenosomes consists of 569 proteins, a number substantially lower than the 1,000-1,500 proteins reported for fungal and animal mitochondrial proteomes, yet considerably higher than proteins assigned to mitosomes. Pathways common to and distinct from both mitochondria and mitosomes were revealed by the hydrogenosome proteome. Proteins known to function in amino acid and energy metabolism, Fe-S cluster assembly, flavin-mediated catalysis, oxygen stress response, membrane translocation, chaperonin functions, proteolytic processing and ATP hydrolysis account for ∼30% of the hydrogenosome proteome. Of the 569 proteins in the hydrogenosome proteome, many appear to be associated with the external surface of hydrogenosomes, including large numbers of GTPases and ribosomal proteins. Glycolytic proteins were also found to be associated with the hydrogenosome proteome, similar to that previously observed for mitochondrial proteomes. Approximately 18% of the hydrogenosomal proteome is composed of hypothetical proteins of unknown function, predictive of multiple activities and properties yet to be uncovered for these highly adapted organelles.

Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis.

We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.

Detection and mutation of a luxS-encoded autoinducer in Proteus mirabilis.

Quorum sensing regulates the expression of virulence factors in a wide variety of pathogenic bacteria. This study has shown that Proteus mirabilis harbours a homologue of luxS, a gene required for the synthesis of the quorum sensing autoinducer 2 (AI-2). AI-2 activity is expressed during and is correlated with the initiation of swarming migration on agar surfaces. The P. mirabilis luxS locus was cloned and a LuxS(-) strain constructed by allelic-exchange mutagenesis. While lacking AI-2 activity, a null mutation in luxS, however, did not affect swimming or swarming motility, swarmer cell differentiation, or virulence in a mouse model of ascending urinary tract infection.

Trichomonas vaginalis Hmp35, a putative pore-forming hydrogenosomal membrane protein, can form a complex in yeast mitochondria.

An abundant integral membrane protein, Hmp35, has been isolated from hydrogenosomes of Trichomonas vaginalis. This protein has no known homologue and exists as a stable 300-kDa complex, termed HMP35, in membranes of the hydrogenosome. By using blue native gel electrophoresis, we found the HMP35 complex to be stable in 2 m NaCl and up to 5 m urea. The endogenous Hmp35 protein was largely protease-resistant. The protein has a predominantly beta-sheet structure and predicted transmembrane domains that may form a pore. Interestingly, the protein has a high number of cysteine residues, some of which are arranged in motifs that resemble the RING finger, suggesting that they could be coordinating zinc or another divalent cation. Our data show that Hmp35 forms one intramolecular but no intermolecular disulfide bonds. We have isolated the HMP35 complex by expressing a His-tagged Hmp35 protein in vivo followed by purification with nickel-agarose beads. The purified 300-kDa complex consists of mostly Hmp35 with lesser amounts of 12-, 25-27-, and 32-kDa proteins. The stoichiometry of proteins in the complex indicates that Hmp35 exists as an oligomer. Hmp35 can be targeted heterologously into yeast mitochondria, despite the lack of homology with any yeast protein, demonstrating the compatibility of mitochondrial and hydrogenosomal protein translocation machineries.