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The process of icing and the resulting layered ice masses, called aufeis, are caused by the freezing of overflow originating from groundwater or surface water. Aufeis can directly impact infrastructure and property, most commonly through winter ice formation and spring flooding within, against, and on the surface of hydraulic structures and transportation infrastructure. They also represent a safety concern for drivers. This geohazard often needs to be managed proactively and efficiently to mitigate associated risks. This paper provides an overview of the consequences of aufeis in northwestern Canada. A total of 50 existing and novel icing and aufeis mitigation approaches are described and classified. The context of applicability for each approach is identified, considering the source of water, the type of infrastructure, and its role in the formation of aufeis. Finally, future research avenues to support the development or improvement of aufeis risk reduction techniques are presented. [ABSTRACT FROM AUTHOR]

The process of icing involves the freezing of overflow layers, on ground or within streams, and results in ice bodies called "aufeis" that are common in most northern landscapes. Knowledge about aufeis is still limited despite the cold region engineering challenge they represent. Understanding the causes of overflow events leading to aufeis development represents a key for the prediction, mitigation, and management of this geohazard and can also support the planning and design of infrastructure in the North. This paper introduces a practical classification for the diverse range of overflow processes that generate aufeis, including under-represented processes, such as the instability of winter streamflow. Importantly, it distinguishes flow conveyance from water supply overflow processes and describes the temporal aspect of icing intensity. Finally, research topics are proposed to improve our understanding of aufeis, including their predictability, the impact of climate change on their occurrence and extent, and stream morphology–aufeis interaction. [ABSTRACT FROM AUTHOR]

As the climate changes, ice characteristics and river-ice processes are altered, sometimes in unexpected ways. A warmer climate will obviously result in less ice globally, and in a general northward shift in the limits of seasonal river-ice occurrence. However, in several watersheds, the frequency of midwinter breakup events and the intensity of breakup ice jams may also change. In addition, climate change will alter other river-ice processes such as ice formation, freeze-up jams, and hanging dams. This is of concern during the design and construction of infrastructure as well as during the planning and implementation of flood-damage-reduction measures in and along rivers with seasonal ice covers. Changes in river-ice regimes will also alter the ecology of many lotic systems. The paper reviews the potential effects of a changing climate on river-ice properties and processes, and provides a discussion of future outcomes and their significance, as well as a suggested direction for future cold-regions river research. [ABSTRACT FROM AUTHOR]

In budding yeast, fermentation is the most important pathway for energy production. Under low-glucose conditions, ethanol is used for synthesis of this sugar requiring a shift to respiration. This process is controlled by the transcriptional regulators Cat8, Sip4, Rds2 and Ert1. We characterized Gsm1 (glucose starvation modulator 1), a paralog of Rds2 and Ert1. Genome-wide analysis showed that Gsm1 has a DNA binding profile highly similar to Rds2. Binding of Gsm1 and Rds2 is interdependent at the gluconeogenic gene FBP1. However, Rds2 is required for Gsm1 to bind at other promoters but not the reverse. Gsm1 and Rds2 also bind to DNA independently of each other. Western blot analysis revealed that Rds2 controls expression of Gsm1. In addition, we showed that the DNA binding domains of Gsm1 and Rds2 bind cooperatively in vitro to the FBP1 promoter. In contrast, at the HAP4 gene, Ert1 cooperates with Rds2 for DNA binding. Mutational analysis suggests that Gsm1/Rds2 and Ert1/Rds2 bind to short common DNA stretches, revealing a novel mode of binding for this class of factors. Two-point mutations in a HAP4 site convert it to a Gsm1 binding site. Thus, Rds2 controls binding of Gsm1 at many promoters by two different mechanisms: regulation of Gsm1 levels and increased DNA binding by formation of heterodimers., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Introduction: Optimal analgesia for circumcision is still debated. The dorsal penile nerve block has been shown to be superior to topical and caudal analgesia. Recently, the ultrasound-guided pudendal nerve block (group pudendal) has been popularized. This randomized, blinded clinical trial compared group pudendal with ultrasound-guided dorsal penile nerve block (group penile) under general anesthesia for pediatric circumcision., Methods: Prepubertal males aged 1-12 years undergoing elective circumcision were randomized to either group. The primary outcome was postoperative face, legs, activity, cry, consolability (FLACC) scores. Our secondary outcomes included parent's postoperative pain measure, analgesic consumption during the first 24 hours, surgeon's and parent's satisfaction, time to perform the block, hemodynamic changes intraoperatively and total time in postanesthesia care unit and until discharge., Results: A total of 155 patients were included for analysis (77 in group pudendal and 78 in group penile). Mean age was 7.3 years old. FLACC scores were not statistically different between groups (p=0.19-0.97). Surgeon satisfaction was higher with group pudendal (90.8% vs 56.6% optimal, p<0.01). Intraoperative hemodynamic changes (>20% rise of heart rate or blood pressure) were higher in group pudendal (33.8% vs 9.0%, p<0.01) as was intraoperative fentanyl use (1.3 vs 1.0 μg/kg, p<0.01). Other secondary outcomes were not statistically different., Discussion: Both ultrasound-guided blocks, performed under general anesthesia, provide equivalent postoperative analgesia for pediatric circumcision as evidenced by low pain scores and opioid consumption. Surgeon satisfaction was higher in the pudendal group., Trial Registration Number: NCT03914365., Competing Interests: Competing interests: No authors have any competing interests or disclosure with regard to this study., (© American Society of Regional Anesthesia & Pain Medicine 2023. No commercial re-use. See rights and permissions. Published by BMJ.)

Super-resolution fluorescence microscopy methods enable the characterization of nanostructures in living and fixed biological tissues. However, they require the adjustment of multiple imaging parameters while attempting to satisfy conflicting objectives, such as maximizing spatial and temporal resolution while minimizing light exposure. To overcome the limitations imposed by these trade-offs, post-acquisition algorithmic approaches have been proposed for resolution enhancement and image-quality improvement. Here we introduce the task-assisted generative adversarial network (TA-GAN), which incorporates an auxiliary task (for example, segmentation, localization) closely related to the observed biological nanostructure characterization. We evaluate how the TA-GAN improves generative accuracy over unassisted methods, using images acquired with different modalities such as confocal, bright-field, stimulated emission depletion and structured illumination microscopy. The TA-GAN is incorporated directly into the acquisition pipeline of the microscope to predict the nanometric content of the field of view without requiring the acquisition of a super-resolved image. This information is used to automatically select the imaging modality and regions of interest, optimizing the acquisition sequence by reducing light exposure. Data-driven microscopy methods like the TA-GAN will enable the observation of dynamic molecular processes with spatial and temporal resolutions that surpass the limits currently imposed by the trade-offs constraining super-resolution microscopy., Competing Interests: Competing interestsThe authors declare no competing interests., (© The Author(s) 2023.)

Introduction: During the first regional COVID-19 lockdown in March 2020, we conducted a study aimed at evaluating completeness of telemedicine consultation in urology. Of 1679 consultations, 67% were considered completely managed by phone. The aim of the present study was to assess patients' experience and satisfaction with telemedicine and to compare them with urologists' perceptions about quality and completeness of the telemedicine consultation., Methods: We contacted a randomly selected sample of patients (n=356) from our previous study to enquire about their experience. We used a home patient experience questionnaire, inspired by the Patient Experiences Questionnaire for Out-of-Hours Care (PEQOHC) and the Consumer Assessment Health Profile Survey (CAHPS)., Results: Of 356 patients contacted, 315 agreed to complete the questionnaire. Urological consultations were for non-oncological (104), oncological (121), cancer suspicion (41), and pediatric (49) indications. Mean patient satisfaction score after telemedicine consultation was 8.8/10 (median 9/10) and 86.3% of patients rated the quality of the consultation as either excellent (54.6%) or very good (31.7%). Consultations regarding cancer suspicion had the lowest score (8.3/10). Overall, 46.7% of all patients would have preferred an in-person visit outside of the pandemic situation. Among patients whose consultations were rated suboptimal by urologists, almost a third more (31.2%) would have preferred an in-person visit (p=0.03)., Conclusions: Despite high reported patient satisfaction rates with telemedicine, it is noteworthy that nearly half of the patients would have preferred an in-person visit. Post-pandemic, it will be important to incorporate telemedicine as an alternative, while retaining and offering in-person visits.

Background: The durability of immune responses to COVID-19 vaccines among older people living with HIV (PWH) is clinically important., Methods: We aimed to assess vaccine-induced humoral immunity and durability in older PWH (≥ 55 years, n = 26) over 6 months (post-initial BNT162b2 series). A secondary and exploratory objective was to assess T-cell response and BNT162b2 booster reactogenicity, respectively. Our Visit 1 (3 weeks post-initial BNT162b2 dose) SARS-CoV-2 humoral immunity results are previously reported; these subjects were recruited for Visit 2 [2 weeks (+ 1 week window) post-second vaccination] and Visit 3 [6 months (± 2 week window) post-initial vaccination] in a single-center longitudinal observational study. Twelve participants had paired Visit 2/3 SARS-CoV-2 Anti-Spike IgG data. At Visit 3, SARS-CoV-2 Anti-Spike IgG testing occurred, and 5 subjects underwent T-cell immune response evaluation. Thereafter, subjects were offered BNT162b2 booster (concurrent day outside our study) per US FDA/CDC guidance; reactogenicity was assessed. The primary study outcome was presence of detectable Visit 3 SARS-CoV-2 Anti-Spike-1-RBD IgG levels. Secondary and exploratory outcomes were T-cell immune response and BNT162b2 booster reactogenicity, respectively. Wilcoxon signed-rank tests analyzed median SARS-CoV-2 Anti-Spike IgG 6-month trends., Results: At Visit 3, 26 subjects underwent primary analysis with demographics noted: Median age 61 years; male n = 16 (62%), female n = 10 (38%); Black n = 13 (50%), White n = 13 (50%). Most subjects (n = 20, 77%) had suppressed HIV viremia on antiretroviral therapy, majority (n = 24, 92%) with CD4 > 200 cells/µL. At Visit 3, 26/26 (100%) had detectable Anti-Spike-1-RBD (≥ 0.8 U/mL). Among 12 subjects presenting to Visit 2/3, median SARS-CoV-2 Anti-Spike 1-RBD was 2087 U/mL at Visit 2, falling to 581.5 U/mL at Visit 3 (p = 0.0923), with a median 3.305-fold decrease over 6 months. Among subjects (n = 5) with 6-month T-cell responses measured, all had detectable cytokine-secreting anti-spike CD4 responses; 3 had detectable CD4 + Activation induced marker (AIM) + cells. Two had detectable cytokine-secreting CD8 responses, but all had positive CD8 + AIM + cells., Conclusions: Among older PWH, SARS-CoV-2 Anti-Spike IgG and virus-specific T-cell responses are present 6 months post-primary BNT162b2 vaccination, and although waning, suggest retention of some degree of long-term protective immunity., (© 2022. The Author(s).)

Introduction: Recent literature emphasizes how overprescription and lack of guidelines contribute to wide variation in opioid prescribing practices and opioid-related harms. We conducted a prospective, observational study to evaluate opioid prescriptions among uro-oncologic patients discharged following elective in-patient surgery., Methods: Patients who underwent four surgeries were included: open retropubic radical prostatectomy, robot-assisted radical prostatectomy, laparoscopic radical nephrectomy, and laparoscopic partial nephrectomy. The primary outcome was the dose of opioids used after discharge (in oral morphine equivalents [MEq]). Secondary outcomes included: opioid requirements for 80% of the patients, management of unused opioids, opioid use three months postoperative, opioid prescription refills, and guidance about opioid disposal., Results: Sixty patients were included for analysis. Patients used a mean of 30 MEq (95% confidence interval 17.8-42.2) at home and 80% of the patients used 50 MEq or less. A mean of 40.4 MEq per patient was overprescribed. Fifty percent of the patients kept the remaining opioids at home, with only 20.0% returning them to their pharmacy. After three months, 5.0% of the patients were using opioids at least occasionally. Three patients needed a new opioid prescription. Forty percent reported having received information regarding management of unused opioids., Conclusions: We found 60% of opioids prescribed were unused, with half of our patients keeping these unused tablets at home. Our results suggest appropriate opioid prescription amounts needed for urological cancer surgery, with 80% of the patients using 50 MEq or less of morphine equivalents.

Objectives: Effective and safe COVID-19 vaccines have been developed and have resulted in decreased incidence and severity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and can decrease secondary transmission. However, there are concerns about dampened immune responses to COVID-19 vaccination among immunocompromised patients, including people living with HIV (PLWH), which may blunt the vaccine's efficacy and durability of protection. This study aimed to assess the qualitative SARS-CoV-2 vaccine immunogenicity among PLWH after vaccination., Methods: We conducted targeted COVID-19 vaccination (all received BNT162b2 vaccine) of PLWH (aged ≥ 55 years per state guidelines) at Yale New Haven Health System and established a longitudinal survey to assess their qualitative antibody responses at 3 weeks after the first vaccination (and prior to receipt of the second dose of the COVID-19 vaccine) (visit 1) and at 2-3 weeks after the second vaccination (visit 2) but excluded patients with prior COVID-19 infection. Our goal was to assess vaccine-induced immunity in the population we studied. Qualitative immunogenicity testing was performed using Healgen COVID-19 anti-Spike IgG/IgM rapid testing. Poisson regression with robust standard errors was used to determine factors associated with a positive IgG response., Results: At visit 1, 45 of 78 subjects (57.7%) tested positive for SARS-CoV-2 anti-Spike IgG after the first dose of COVID-19 vaccine. Thirty-nine subjects returned for visit 2. Of these, 38 had positive IgG (97.5%), including 20 of 21 subjects (95.2%) with an initial negative anti-Spike IgG. Our bivariate analysis suggested that participants on an antiretroviral regimen containing integrase strand transfer inhibitors [relative risk (RR) = 1.81, 95% confidence interval (CI): 0.92-3.56, p = 0.085] were more likely to seroconvert after the first dose of the COVID-19 vaccine, while those with a CD4 count < 500 cells/μL (RR = 0.59, 95% CI: 0.33-1.05, p = 0.071), and those diagnosed with cancer or another immunosuppressive condition (RR = 0.49, 95% CI: 0.18-1.28, p = 0.15) may have been less likely to seroconvert after the first dose of the COVID-19 vaccine. The direction of these associations was similar in the multivariate model, although none of these findings reached statistical significance (RR integrase inhibitor  = 1.71, 95% CI: 0.90-3.25, p = 0.10; RR CD4 count  = 0.68, 95% CI: 0.39-1.19, p = 0.18; RR cancer or another immunosuppressive condition  = 0.50, 95% CI: 0.19-1.33, p = 0.16). With regard to immunogenicity, we were able to record very high rates of new seroconversion following the second dose of the COVID-19 vaccine., Conclusions: Our study suggests that completing a two-dose series of BNT162b2 vaccine is critical for PLWH given suboptimal seroconversion rates after the first dose and subsequent improved seroconversion rates after the second dose., (© 2021 The Authors. HIV Medicine published by John Wiley & Sons Ltd on behalf of British HIV Association.)

Reporter genes are useful tools to study gene transcription in various organisms. For example, the lacZ gene encoding β-galactosidase has been extensively used as a reporter in bacteria, budding yeast, fruit fly, mouse etc. However, use of this gene in the human fungal pathogen Candida albicans has been limited, probably due to low β-galactosidase activity. Here, we describe a reporter derived from the Vibrio cholerae lacZ gene in which codons have been optimized for expression in C. albicans. The constitutively active ACT1 promoter was fused to this synthetic lacZ reporter and integrated in the C. albicans genome. High β-galactosidase activity in liquid assays was observed for this reporter as well as coloration on X-gal plates. When the lacZ reporter expression was driven by the MET3 promoter, β-galactosidase activity in liquid assays and coloration on X-gal plates was higher in the absence of methionine, thus recapitulating the regulation of the native MET3 gene. This synthetic lacZ gene extends the toolbox of C. albicans reagents by providing a useful reporter for analysis of promoter activity in this organism of medical importance., (© The Author(s) 2021. Published by Oxford University Press on behalf of FEMS.)

The Ski2-Ski3-Ski8 (SKI) complex assists the RNA exosome during the 3' to 5' degradation of cytoplasmic transcripts. Previous reports showed that the SKI complex is involved in the 3' to 5' degradation of mRNAs, including 3' untranslated regions (UTRs) and devoid of ribosomes. Paradoxically, we recently showed that the SKI complex directly interacts with ribosomes during the co-translational mRNA decay and that this interaction is necessary for its RNA degradation promoting activity. Here, we characterised a new SKI-associated factor, Ska1, that associates with a subpopulation of the SKI complex. We showed that Ska1 is specifically involved in the degradation of long 3'UTR-containing mRNAs, poorly translated mRNAs as well as other RNA regions not associated with ribosomes, such as cytoplasmic lncRNAs. We further show that the overexpression of SKA1 antagonises the SKI-ribosome association. We propose that the Ska1-SKI complex assists the cytoplasmic exosome in the absence of direct association of the SKI complex with ribosomes., (© 2019 The Authors.)

In the yeast Saccharomyces cerevisiae, fermentation is the major pathway for energy production, even under aerobic conditions. However, when glucose becomes scarce, ethanol produced during fermentation is used as a carbon source, requiring a shift to respiration. This adaptation results in massive reprogramming of gene expression. Increased expression of genes for gluconeogenesis and the glyoxylate cycle is observed upon a shift to ethanol and, conversely, expression of some fermentation genes is reduced. The zinc cluster proteins Cat8, Sip4, and Rds2, as well as Adr1, have been shown to mediate this reprogramming of gene expression. In this study, we have characterized the gene YBR239C encoding a putative zinc cluster protein and it was named ERT1 (ethanol regulated transcription factor 1). ChIP-chip analysis showed that Ert1 binds to a limited number of targets in the presence of glucose. The strongest enrichment was observed at the promoter of PCK1 encoding an important gluconeogenic enzyme. With ethanol as the carbon source, enrichment was observed with many additional genes involved in gluconeogenesis and mitochondrial function. Use of lacZ reporters and quantitative RT-PCR analyses demonstrated that Ert1 regulates expression of its target genes in a manner that is highly redundant with other regulators of gluconeogenesis. Interestingly, in the presence of ethanol, Ert1 is a repressor of PDC1 encoding an important enzyme for fermentation. We also show that Ert1 binds directly to the PCK1 and PDC1 promoters. In summary, Ert1 is a novel factor involved in the regulation of gluconeogenesis as well as a key fermentation gene., (Copyright © 2014 by the Genetics Society of America.)

Candida glabrata is the second most important human fungal pathogen. Despite its formal name, C. glabrata is in fact more closely related to the nonpathogenic budding yeast Saccharomyces cerevisiae. However, less is known about the biology of this pathogen. Zinc cluster proteins form a large family of transcriptional regulators involved in the regulation of numerous processes such as the control of the metabolism of sugars, amino acids, fatty acids, as well as drug resistance. The C. glabrata genome encodes 41 known or putative zinc cluster proteins, and the majority of them are uncharacterized. We have generated a panel of strains carrying individual deletions of zinc cluster genes. Using a novel approach relying on tetracycline for conditional expression in C. glabrata at the translational level, we show that only two zinc cluster genes are essential. We have performed phenotypic analysis of nonessential zinc cluster genes. Our results show that two deletion strains are thermosensitive whereas two strains are sensitive to caffeine, an inhibitor of the target of rapamycin pathway. Increased salt tolerance has been observed for eight deletion strains, whereas one strain showed reduced tolerance to salt. We have also identified a number of strains with increased susceptibility to the antifungal drugs fluconazole and ketoconazole. Interestingly, one deletion strain showed decreased susceptibility to the antifungal micafungin. In summary, we have assigned phenotypes to more than half of the zinc cluster genes in C. glabrata. Our study provides a resource that will be useful to better understand the biological role of these transcription factors., (Copyright © 2014 Klimova et al.)

Rapidly increasing bacterial resistance to existing therapies creates an urgent need for the development of new antibacterials. Tirapazamine (TPZ, 3-amino-1,2,4-benzotriazine 1,4 dioxide) is a prodrug undergoing clinical trials for various types of cancers. In this study, we showed that TPZ has antibacterial activity, particularly at low oxygen levels. With Escherichia coli, TPZ was bactericidal under both aerobic and anaerobic conditions. Escherichia coli mutants deficient in homologous recombination were hypersusceptible to TPZ, suggesting that drug toxicity may be due to DNA damage. Moreover, E. coli strains deleted for genes encoding putative reductases were resistant to TPZ, implying that these enzymes are responsible for conversion of the prodrug to a toxic compound. Fluoroquinolone-resistant E. coli strains were as susceptible to TPZ as a wild-type strain. Methicillin-resistant Staphylococcus aureus strains were also susceptible to TPZ (MIC = 0.5 μg mL(-1) ), as were pathogenic strains of Clostridium difficile (MIC = 7.5 ng mL(-1) ). TPZ may merit additional study as a broad-spectrum antibacterial, particularly for anaerobes., (© 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.)

Background: The Amoebozoa constitute one of the primary divisions of eukaryotes, encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii (Ac) the first representative from a solitary free-living amoebozoan., Results: Ac encodes 15,455 compact intron-rich genes, a significant number of which are predicted to have arisen through inter-kingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Ac appears to have incorporated them into established transcriptional programs. Ac manifests a complex signaling and cell communication repertoire, including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An important environmental host of a diverse range of bacteria and viruses, Ac utilizes a diverse repertoire of predicted pattern recognition receptors, many with predicted orthologous functions in the innate immune systems of higher organisms., Conclusions: Our analysis highlights the important role of LGT in the biology of Ac and in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall, the availability of an Ac genome should aid in deciphering the biology of the Amoebozoa and facilitate functional genomic studies in this important model organism and environmental host.

Upon glucose depletion, a massive reprogramming of gene expression occurs in the yeast Saccharomyces cerevisiae for the use of alternate carbon sources such as the nonfermentable compounds ethanol and glycerol. This process is mediated by the master kinase Snf1 that controls the activity of various targets including the transcriptional regulators Cat8, Sip4 and Adr1. We have recently identified Rds2 as an additional player in this pathway. Here, we have performed genome-wide location analysis of Rds2 in cells grown in the presence of glycerol. We show that Rds2 binds to promoters of genes involved in gluconeogenesis, the glyoxylate shunt, and the TCA cycle as well as some genes encoding mitochondrial components or some involved in the stress response. Interestingly, we also detected Rds2 at the promoters of SIP4, ADR1 and HAP4 which encodes the limiting subunit of the Hap2/3/4/5 complex, a regulator of respiration. Strikingly, we observed an important overlap between the targets of Rds2 and Adr1. Finally, we provide a model to account for the complex interplay among these transcriptional regulators., (Copyright © 2012 Elsevier Inc. All rights reserved.)

The Candida albicans MYO5 gene encodes myosin I, a protein required for the formation of germ tubes and true hyphae. Because the polarized growth of opaque-phase cells in response to pheromone results in mating projections that can resemble germ tubes, we examined the role of Myo5p in this process. We localized green fluorescent protein (GFP)-tagged Myo5p in opaque-phase cells of C. albicans during both bud and shmoo formation. In vegetatively growing opaque cells, Myo5p is found at sites of bud emergence and bud growth, while in pheromone-stimulated cells, Myo5p localizes at the growing tips of shmoos. Intriguingly, cells homozygous for MTLa in which the MYO5 gene was deleted failed to switch efficiently from the white phase to the opaque phase, although ectopic expression of WOR1 from the MET3 promoter can convert myo5 mutants into mating-competent opaque cells. However, when WOR1 expression was shut off, the myo5-defective cells rapidly lost both their opaque phenotype and mating competence, suggesting that Myo5p is involved in the maintenance of the opaque state. When MYO5 is expressed conditionally in opaque cells, the opaque phenotype, as well as the mating ability of the cells, becomes unstable under repressive conditions, and quantitative real-time PCR demonstrated that the shutoff of MYO5 expression correlates with a dramatic reduction in WOR1 expression. It appears that while myosin I is not directly required for mating in C. albicans, it is involved in WOR1 expression and the white-opaque transition and thus is indirectly implicated in mating.

In Saccharomyces cerevisiae, optimal utilization of various compounds as a nitrogen source is mediated by a complex transcriptional network. The zinc cluster protein Dal81 is a general activator of nitrogen metabolic genes, including those for γ-aminobutyrate (GABA). In contrast, Uga3 (another zinc cluster protein) is an activator restricted to the control of genes involved in utilization of GABA. Uga3 binds to DNA elements found in the promoters of target genes and increases their expression in the presence of GABA. Dal81 appears to act as a coactivator since the DNA-binding activity of this factor is dispensable but its mode of action is not known. In this study, we have mapped a regulatory, as well as an activating, region for Uga3. A LexA-Uga3 chimeric protein activates a lexA reporter in a GABA- and Dal81-dependent manner. Activation by Uga3 requires the SAGA complex as well as Gal11, a component of mediator. ChIP analysis revealed that Uga3 is weakly bound to target promoters. The presence of GABA enhances binding of Uga3 and allows recruitment of Dal81 and Gal11 to target genes. Recruitment of Gal11 is prevented in the absence of Dal81. Importantly, Dal81 by itself is a potent activator when tethered to DNA and its activity depends on SAGA and Gal11 but not Uga3. Overexpression of Uga3 bypasses the requirement for Dal81 but not for SAGA or Gal11. Thus, under artificial conditions, both Dal81 and Uga3 can activate transcription independently of each other. However, under physiological conditions, both factors cooperate by targeting common coactivators.

Saccharomyces cerevisiae preferentially uses glucose as a carbon source, but following its depletion, it can utilize a wide variety of other carbons including nonfermentable compounds such as ethanol. A shift to a nonfermentable carbon source results in massive reprogramming of gene expression including genes involved in gluconeogenesis, the glyoxylate cycle, and the tricarboxylic acid cycle. This review is aimed at describing the recent progress made toward understanding the mechanism of transcriptional regulation of genes responsible for utilization of nonfermentable carbon sources. A central player for the use of nonfermentable carbons is the Snf1 kinase, which becomes activated under low glucose levels. Snf1 phosphorylates various targets including the transcriptional repressor Mig1, resulting in its inactivation allowing derepression of gene expression. For example, the expression of CAT8, encoding a member of the zinc cluster family of transcriptional regulators, is then no longer repressed by Mig1. Cat8 becomes activated through phosphorylation by Snf1, allowing upregulation of the zinc cluster gene SIP4. These regulators control the expression of various genes including those involved in gluconeogenesis. Recent data show that another zinc cluster protein, Rds2, plays a key role in regulating genes involved in gluconeogenesis and the glyoxylate pathway. Finally, the role of additional regulators such as Adr1, Ert1, Oaf1, and Pip2 is also discussed.

In Saccharomyces cerevisiae, RDS2 encodes a zinc cluster transcription factor with unknown function. Here, we unravel a key function of Rds2 in gluconeogenesis using chromatin immunoprecipitation-chip technology. While we observed that Rds2 binds to only a few promoters in glucose-containing medium, it binds many additional genes when the medium is shifted to ethanol, a nonfermentable carbon source. Interestingly, many of these genes are involved in gluconeogenesis, the tricarboxylic acid cycle, and the glyoxylate cycle. Importantly, we show that Rds2 has a dual function: it directly activates the expression of gluconeogenic structural genes while it represses the expression of negative regulators of this pathway. We also show that the purified DNA binding domain of Rds2 binds in vitro to carbon source response elements found in the promoters of target genes. Finally, we show that upon a shift to ethanol, Rds2 activation is correlated with its hyperphosphorylation by the Snf1 kinase. In summary, we have characterized Rds2 as a novel major regulator of gluconeogenesis.

In Saccharomyces cerevisiae, zinc cluster protein Pdr1 can form homodimers as well as heterodimers with Pdr3 and Stb5, suggesting that different combinations of these proteins may regulate the expression of different genes. To gain insight into the interplay among these regulators, we performed genome-wide location analysis (chromatin immunoprecipitation with hybridization to DNA microarrays) and gene expression profiling. Unexpectedly, we observed that Stb5 shares only a few target genes with Pdr1 or Pdr3 in rich medium. Interestingly, upon oxidative stress, Stb5 binds and regulates the expression of most genes of the pentose phosphate pathway as well as of genes involved in the production of NADPH, a metabolite required for oxidative stress resistance. Importantly, deletion of STB5 results in sensitivity to diamide and hydrogen peroxide. Our data suggest that Stb5 acts both as an activator and as a repressor in the presence of oxidative stress. Furthermore, we show that Stb5 activation is not mediated by known regulators of the oxidative stress response. Integrity of the pentose phosphate pathway is required for the activation of Stb5 target genes but is not necessary for the increased DNA binding of Stb5 in the presence of diamide. These data suggest that Stb5 is a key player in the control of NADPH production for resistance to oxidative stress.

The trace element zinc is required for proper functioning of a large number of proteins, including various enzymes. However, most zinc-containing proteins are transcription factors capable of binding DNA and are named zinc finger proteins. They form one of the largest families of transcriptional regulators and are categorized into various classes according to zinc-binding motifs. This review focuses on one class of zinc finger proteins called zinc cluster (or binuclear) proteins. Members of this family are exclusively fungal and possess the well-conserved motif CysX(2)CysX(6)CysX(5-12)CysX(2)CysX(6-8)Cys. The cysteine residues bind to two zinc atoms, which coordinate folding of the domain involved in DNA recognition. The first- and best-studied zinc cluster protein is Gal4p, a transcriptional activator of genes involved in the catabolism of galactose in the budding yeast Saccharomyces cerevisiae. Since the discovery of Gal4p, many other zinc cluster proteins have been characterized; they function in a wide range of processes, including primary and secondary metabolism and meiosis. Other roles include regulation of genes involved in the stress response as well as pleiotropic drug resistance, as demonstrated in budding yeast and in human fungal pathogens. With the number of characterized zinc cluster proteins growing rapidly, it is becoming more and more apparent that they are important regulators of fungal physiology.

Availability of the complete sequence of the Candida albicans genome allows for global gene analysis. We designed a gene deletion method to facilitate such studies. First, we constructed C. albicans strains that are both Deltaura3 and Deltatrp1. Second, we designed a system that relies on in vitro recombination, using the Gateway((R)) technology, for efficient generation of deletion cassettes. They are generated in two steps: (a) upstream and downstream DNA fragments of the chromosomal region to be deleted are amplified by PCR and introduced into two separate entry vectors; (b) the second step involves a quadruple recombination event including the two entry vectors, a plasmid bearing a marker of interest and a destination vector, in order to generate a plasmid containing the deletion cassette. The deletion plasmid contains very rare restriction sites for convenient excision of the knockout cassette. Selection in C. albicans can be performed with one of the following markers: the C. albicans URA3 gene, a modified S. cerevisiae TRP1 gene or the mycophenolic acid resistance (MPA(R)) gene. Upon integration into the genome, these markers can be removed by the use of 5-fluoroorotic acid (URA3), 5-fluoroanthranilic acid (TRP1) or the FLP recombinase (MPA(R)). Using this approach, we show that removal of the C. albicans orf19.1035 gene results in sensitivity to the weak acid sorbate, while its overexpression increases resistance to this compound. We named it WAR1, in analogy to its S. cerevisiae orthologue., (Copyright 2006 John Wiley & Sons, Ltd.)

Tirapazamine (TPZ) is an anticancer drug that targets topoisomerase II. TPZ is preferentially active under hypoxic conditions. The drug itself is not harmful to cells; rather, it is reduced to a toxic radical species by an NADPH cytochrome P450 oxidoreductase. Under aerobic conditions, the toxic compound reacts with oxygen to revert back to TPZ and a much less toxic radical species. We have used yeast (Saccharomyces cerevisiae) as a model to better understand the mechanism of action of TPZ. Overexpression of NCP1, encoding the yeast ortholog of the human P450 oxidoreductase, results in greatly increased sensitivity to TPZ. Likewise, overexpression of TOP2 (encoding topoisomerase II) leads to hypersensitivity to TPZ, suggesting that topoisomerase II is also a target of TPZ in yeast. Thus, our data show that yeast mimics human cells in terms of TPZ sensitivity. We have performed robot-aided screens for altered sensitivity to TPZ using a collection of approximately 4600 haploid yeast deletion strains. We have identified 117 and 73 genes whose deletion results in increased or decreased resistance to TPZ, respectively. For example, cells lacking various DNA repair genes are hypersensitive to TPZ. In contrast, deletion of genes encoding some amino acid permeases results in cells that are resistant to TPZ. This suggests that permeases may be involved in intracellular uptake of TPZ. Our discoveries in yeast may lead to a better understanding of TPZ biology in humans.

Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications., Competing Interests: Competing interests. BRB is an employee of both Incyte and University of California at San Francisco (UCSF). Incyte played no role in this work, and the resources used were all from UCSF.

The human pathogen Candida albicans is responsible for a large proportion of infections in immunocompromised individuals, and the emergence of drug-resistant strains is of medical concern. Resistance to antifungal azole compounds is often due to an increase in drug efflux or an alteration of the pathway for synthesis of ergosterol, an important plasma membrane component in fungi. However, little is known about the transcription factors that mediate drug resistance. In Saccharomyces cerevisiae, two highly related transcriptional activators, Upc2p and Ecm22p, positively regulate the expression of genes involved in ergosterol synthesis (ERG genes). We have identified a homologue in C. albicans of the S. cerevisiae UPC2/ECM22 genes and named it UPC2. Deletion of this gene impaired growth under anaerobic conditions and rendered cells highly susceptible to the antifungal drugs ketoconazole and fluconazole. Conversely, overexpression of Upc2p increased resistance to ketoconazole, fluconazole, and fluphenazine. Azole-induced expression of the ERG genes was abolished in a Delta upc2 strain, while basal levels of these mRNAs remained unchanged. Importantly, the purified DNA binding domain of Upc2p bound in vitro to putative sterol response elements in the ERG2 promoter, suggesting that Upc2p increases the expression of the ERG genes by directly binding to their promoters. These results provide an important link between changes in the ergosterol biosynthetic pathway and azole resistance in this opportunistic fungal species.