Correlation between transcript profiles and fitness of deletion mutants in anaerobic chemostat cultures of Saccharomyces cerevisiae

The applicability of transcriptomics for functional genome analysis rests on the assumption that global information on gene function can be inferred from transcriptional regulation patterns. This study investigated whether Saccharomyces cerevisiae genes that show a consistently higher transcript level under anaerobic than aerobic conditions do indeed contribute to fitness in the absence of oxygen. Tagged deletion mutants were constructed in 27 S. cerevisiae genes that showed a strong and consistent transcriptional upregulation under anaerobic conditions, irrespective of the nature of the growth-limiting nutrient (glucose, ammonia, sulfate or phosphate). Competitive anaerobic chemostat cultivation showed that only five out of the 27 mutants (eug1Δ, izh2Δ, plb2Δ, ylr413wΔ and yor012wΔ) conferred a significant disadvantage relative to a tagged reference strain. The implications of this study are that: (i) transcriptome analysis has a very limited predictive value for the contribution of individual genes to fitness under specific environmental conditions, and (ii) competitive chemostat cultivation of tagged deletion strains offers an efficient approach to select relevant leads for functional analysis studies

Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A

<p>Abstract</p> <p>Background</p> <p>The yeast <it>Saccharomyces cerevisiae </it>is able to adjust to external oxygen availability by utilizing both respirative and fermentative metabolic modes. Adjusting the metabolic mode involves alteration of the intracellular metabolic fluxes that are determined by the cell's multilevel regulatory network. Oxygen is a major determinant of the physiology of <it>S. cerevisiae </it>but understanding of the oxygen dependence of intracellular flux distributions is still scarce.</p> <p>Results</p> <p>Metabolic flux distributions of <it>S. cerevisiae </it>CEN.PK113-1A growing in glucose-limited chemostat cultures at a dilution rate of 0.1 h^-1with 20.9%, 2.8%, 1.0%, 0.5% or 0.0% O₂in the inlet gas were quantified by ¹³C-MFA. Metabolic flux ratios from fractional [U-¹³C]glucose labelling experiments were used to solve the underdetermined MFA system of central carbon metabolism of <it>S. cerevisiae</it>.</p> <p>While ethanol production was observed already in 2.8% oxygen, only minor differences in the flux distribution were observed, compared to fully aerobic conditions. However, in 1.0% and 0.5% oxygen the respiratory rate was severely restricted, resulting in progressively reduced fluxes through the TCA cycle and the direction of major fluxes to the fermentative pathway. A redistribution of fluxes was observed in all branching points of central carbon metabolism. Yet only when oxygen provision was reduced to 0.5%, was the biomass yield exceeded by the yields of ethanol and CO₂. Respirative ATP generation provided 59% of the ATP demand in fully aerobic conditions and still a substantial 25% in 0.5% oxygenation. An extensive redistribution of fluxes was observed in anaerobic conditions compared to all the aerobic conditions. Positive correlation between the transcriptional levels of metabolic enzymes and the corresponding fluxes in the different oxygenation conditions was found only in the respirative pathway.</p> <p>Conclusion</p> <p>¹³C-constrained MFA enabled quantitative determination of intracellular fluxes in conditions of different redox challenges without including redox cofactors in metabolite mass balances. A redistribution of fluxes was observed not only for respirative, respiro-fermentative and fermentative metabolisms, but also for cells grown with 2.8%, 1.0% and 0.5% oxygen. Although the cellular metabolism was respiro-fermentative in each of these low oxygen conditions, the actual amount of oxygen available resulted in different contributions through respirative and fermentative pathways.</p

Anaerobiosis revisited: growth of Saccharomyces cerevisiae under extremely low oxygen availability

The budding yeast Saccharomyces cerevisiae plays an important role in biotechnological applications, ranging from fuel ethanol to recombinant protein production. It is also a model organism for studies on cell physiology and genetic regulation. Its ability to grow under anaerobic conditions is of interest in many industrial applications. Unlike industrial bioreactors with their low surface area relative to volume, ensuring a complete anaerobic atmosphere during microbial cultivations in the laboratory is rather difficult. Tiny amounts of O2 that enter the system can vastly influence product yields and microbial physiology. A common procedure in the laboratory is to sparge the culture vessel with ultrapure N2 gas; together with the use of butyl rubber stoppers and norprene tubing, O2 diffusion into the system can be strongly minimized. With insights from some studies conducted in our laboratory, we explore the question ‘how anaerobic is anaerobiosis?’. We briefly discuss the role of O2 in non-respiratory pathways in S. cerevisiae and provide a systematic survey of the attempts made thus far to cultivate yeast under anaerobic conditions. We conclude that very few data exist on the physiology of S. cerevisiae under anaerobiosis in the absence of the anaerobic growth factors ergosterol and unsaturated fatty acids. Anaerobicity should be treated as a relative condition since complete anaerobiosis is hardly achievable in the laboratory. Ideally, researchers should provide all the details of their anaerobic set-up, to ensure reproducibility of results among different laboratories. A correction to this article is available online at http://eprints.whiterose.ac.uk/131930/ https://doi.org/10.1007/s00253-018-9036-

Op zoek naar synergie tussen praktijk en theorie: Aankomende en startende leerkrachten opleiden en begeleiden met het oog op preventie en aanpak van ongewenst gedrag

Veel startende leerkrachten in het basisonderwijs voelen zich niet goed in staat om adequaat in te spelen op ongewenst gedrag van leerlingen, hetgeen kan resulteren in gevoelens van onmacht, onzekerheid en incompetentie. Deze handelingsverlegenheid raakt een wezenlijke kern van hun professionaliteit, omdat het realiseren van een prettig en veilig klasklimaat een noodzakelijke voorwaarde is voor het verzorgen van kwalitatief goed onderwijs. Dat roept de vraag op hoe startende leerkrachten kunnen worden voorbereid op het voorkomen van en leren omgaan met ongewenst gedrag. Door middel van diepte-interviews met startende leerkrachten en ervaren praktijkbegeleiders, is inzicht verkregen in de ontwikkeling van leerkrachtcompetenties met betrekking tot de preventie en aanpak van ongewenst gedrag. Daarnaast zijn excellente leerkrachten gevraagd naar hun ervaringen en aanbevelingen. Op grond van de resultaten worden aanbevelingen gedaan voor de pabo-opleiding en de begeleiding van startende leerkrachten. Zo is het tijdens de verschillende fasen van de opleiding niet alleen essentieel om theoretische kennis aan te brengen over verschijningsvormen en oorzaken van ongewenst gedrag, maar ook om de samenhang te benadrukken tussen andere aspecten van goed onderwijs, waaronder klassenmanagement, pedagogische klimaat en groepsvorming. Daarnaast is het werken met persoonlijke ervaringen van studenten van belang voor een betekenisvolle vertaling en toepassing van theorie naar praktijk en duiding van praktijk met behulp van theorie. Ook praktijkbegeleiders zouden hun pedagogisch-didactische adviezen meer expliciet kunnen koppelen aan het aangeboden theoretische kader binnen de opleiding. Opleiden ‘op het instituut’ en ‘in de praktijk’ versterken elkaar op deze wijze en dragen bij aan het opbouwen van een persoonlijk handelingsrepertoire van startende leerkrachten

Clinical assessment of emotions in patients with cancer: Diagnostic accuracy compared with two reference standards

Contains fulltext : 220750.pdf (Publisher’s version ) (Open Access)BACKGROUND: Previous research has suggested that clinical assessment of emotions in patients with cancer is suboptimal. However, it is a possibility that well-trained and experienced doctors and nurses do recognize emotions but that they do not evaluate all emotions as necessitating professional mental health care. This implies that the sensitivity of clinical assessment should be tested against the need for professional mental health care as reference standard, instead of emotional distress. We hypothesized that the observed sensitivity of clinical assessment of emotions would be higher when tested against need for professional mental health care as reference standard, compared with emotional distress as reference standard. PATIENTS AND METHODS: A consecutive series of patients starting with chemotherapy were recruited during their routine clinical care, at a department of medical oncology. Clinical assessment of emotions by medical oncologists and nurses was derived from the patient file. Emotional distress and need for professional mental health care were assessed using the Distress Thermometer and Problem List. RESULTS: Clinical assessment resulted in notes on emotions in 42.2% of the patient files with 36.2% of patients experiencing emotional distress and 10.8% expressing a need for professional mental health care (N = 185). As expected, the sensitivity of clinical assessment of emotions was higher with the reference standard "need for professional mental health care" compared with "emotional distress" (P < .001). For specificity, equivalent results were obtained with the two reference standards (P = .63). CONCLUSIONS: Clinical assessment of emotions in patients with cancer may be more accurate than previously concluded

Meeting report: Towards better risk stratification, prevention and therapy of invasive GBS disease, ESPID research meeting May 2022

The European Society of Pediatric Infectious Diseases (ESPID) hosted the third Group B Streptococcus (GBS) Research Session in Athens on 11th May 2022, providing researchers and clinicians from around the world an opportunity to share and discuss recent advances in GBS pathophysiology, molecular and genetic epidemiology and how these new insights can help in improving prevention and control of early- and late-onset GBS disease. The meeting provided a state-of-the-art overview of the existing GBS prevention strategies and their limitations, and an opportunity to share the latest research findings. The first presentation provided an overview of current GBS prevention and treatment strategies. In the second presentation, the genomic and antimicrobial resistance profiles of invasive and colonizing GBS strains were presented. The third presentation explained the association of intrapartum antibiotic prophylaxis (IAP) with the development of late-onset disease (LOD) and the interplay of host innate immunity and GBS. The fourth presentation evaluated the role of genomics in understanding horizontal GBS transmission. The fifth presentation focused on the zoonotic links for certain GBS lineages and the last presentation described the protective role of breastmilk. Talks were followed with interactive discussions and concluded with recommendations on what is needed to further GBS clinical research; these included: (i) the development of better risk stratification methods by combining GBS virulence factors, serological biomarkers and clinical risk factors; (ii) further studies on the interplay of perinatal antimicrobials, disturbances in the development of host immunity and late-onset GBS disease; (iii) routine submission of GBS isolates to reference laboratories to help in detecting potential clusters by using genomic sequencing; (iv) collaboration in animal and human GBS studies to detect and prevent the emergence of new pathogenic sequence types; and (v) harnessing the plethora of immune factors in the breastmilk to develop adjunct therapies

Clinical assessment of emotions in patients with cancer: Diagnostic accuracy compared with two reference standards

Background: Previous research has suggested that clinical assessment of emotions in patients with cancer is suboptimal. However, it is a possibility that well-trained and experienced doctors and nurses do recognize emotions but that they do not evaluate all emotions as necessitating professional mental health care. This implies that the sensitivity of clinical assessment should be tested against the need for professional mental health care as reference standard, instead of emotional distress. We hypothesized that the observed sensitivity of clinical assessment of emotions would be higher when tested against need for professional mental health care as reference standard, compared with emotional distress as reference standard. Patients and Methods: A consecutive series of patients starting with chemotherapy were recruited during their routine clinical care, at a department of medical oncology. Clinical assessment of emotions by medical oncologists and nurses was derived from the patient file. Emotional distress and need for professional mental health care were assessed using the Distress Thermometer and Problem List. Results: Clinical assessment resulted in notes on emotions in 42.2% of the patient files with 36.2% of patients experiencing emotional distress and 10.8% expressing a need for professional mental health care (N = 185). As expected, the sensitivity of clinical assessment of emotions was higher with the reference standard “need for professional mental health care” compared with “emotional distress” (P '.001). For specificity, equivalent results were obtained with the two reference standards (P =.63). Conclusions: Clinical assessment of emotions in patients with cancer may be more accurate than previously concluded