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"Scherer, Nicole"
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Posttranslational Control of PlsB Is Sufficient To Coordinate Membrane Synthesis with Growth in Escherichia coli
by
Büke, Ferhat
,
van den Broek, Niels J. F.
,
Yang, Flora
in
Allosteric properties
,
Biomass
,
Coenzyme A
2020
How do bacterial cells grow without breaking their membranes? Although the biochemistry of fatty acid and membrane synthesis is well known, how membrane synthesis is balanced with growth and metabolism has remained unclear. This is partly due to the many control points that have been discovered within the membrane synthesis pathways. By precisely establishing the contributions of individual pathway enzymes, our results simplify the model of membrane biogenesis in the model bacterial species Escherichia coli . Specifically, we found that allosteric control of a single enzyme, PlsB, is sufficient to balance growth with membrane synthesis and to ensure that growing E. coli cells produce sufficient membrane. Identifying the signals that activate and deactivate PlsB will resolve the issue of how membrane synthesis is synchronized with growth. Every cell must produce enough membrane to contain itself. However, the mechanisms by which the rate of membrane synthesis is coupled with the rate of cell growth remain unresolved. By comparing substrate and enzyme concentrations of the fatty acid and phospholipid synthesis pathways of Escherichia coli across a 3-fold range of carbon-limited growth rates, we show that the rate of membrane phospholipid synthesis during steady-state growth is determined principally through allosteric control of a single enzyme, PlsB. Due to feedback regulation of the fatty acid pathway, PlsB activity also indirectly controls synthesis of lipopolysaccharide, a major component of the outer membrane synthesized from a fatty acid synthesis intermediate. Surprisingly, concentrations of the enzyme that catalyzes the committed step of lipopolysaccharide synthesis (LpxC) do not differ across steady-state growth conditions, suggesting that steady-state lipopolysaccharide synthesis is modulated primarily via indirect control by PlsB. In contrast to steady-state regulation, we found that responses to environmental perturbations are triggered directly via changes in acetyl coenzyme A (acetyl-CoA) concentrations, which enable rapid adaptation. Adaptations are further modulated by ppGpp, which regulates PlsB activity during slow growth and growth arrest. The strong reliance of the membrane synthesis pathway upon posttranslational regulation ensures both the reliability and the responsiveness of membrane synthesis. IMPORTANCE How do bacterial cells grow without breaking their membranes? Although the biochemistry of fatty acid and membrane synthesis is well known, how membrane synthesis is balanced with growth and metabolism has remained unclear. This is partly due to the many control points that have been discovered within the membrane synthesis pathways. By precisely establishing the contributions of individual pathway enzymes, our results simplify the model of membrane biogenesis in the model bacterial species Escherichia coli . Specifically, we found that allosteric control of a single enzyme, PlsB, is sufficient to balance growth with membrane synthesis and to ensure that growing E. coli cells produce sufficient membrane. Identifying the signals that activate and deactivate PlsB will resolve the issue of how membrane synthesis is synchronized with growth.
Journal Article
BRCA1, BRCA2, and TP53 germline and somatic variants and clinicopathological characteristics of Brazilian patients with epithelial ovarian cancer
by
Matta, Bruna Palma
,
Barros Moreira, Fábio Carvalho
,
Boroni, Mariana
in
Biopsy
,
Brazil - epidemiology
,
BRCA1
2024
Background Approximately 3/4 of ovarian cancers are diagnosed in advanced stages, with the high‐grade epithelial ovarian carcinoma (EOC) accounting for 90% of the cases. EOC present high genomic instability and somatic loss‐of‐function variants in genes associated with homologous recombination mutational repair pathway (HR), such as BRCA1 and BRCA2, and in TP53. The identification of germline variants in HR genes in EOC is relevant for treatment of platinum resistant tumors and relapsed tumors with therapies based in synthetic lethality such as PARP inhibitors. Patients with somatic variants in HR genes may also benefit from these therapies. In this work was analyzed the frequency of somatic variants in BRCA1, BRCA2, and TP53 in an EOC cohort of Brazilian patients, estimating the proportion of variants in tumoral tissue and their association with progression‐free survival and overall survival. Methods The study was conducted with paired blood/tumor samples from 56 patients. Germline and tumoral sequences of BRCA1, BRCA2, and TP53 were obtained by massive parallel sequencing. The HaplotypeCaller method was used for calling germline variants, and somatic variants were called with Mutect2. Results A total of 26 germline variants were found, and seven patients presented germline pathogenic or likely pathogenic variants in BRCA1 or BRCA2. The analysis of tumoral tissue identified 52 somatic variants in 41 patients, being 43 somatic variants affecting or likely affecting protein functionality. Survival analyses showed that tumor staging was associated with overall survival (OS), while the presence of somatic mutation in TP53 was not associated with OS or progression‐free survival. Conclusion Frequency of pathogenic or likely pathogenic germline variants in BRCA1 and BRCA2 (12.5%) was lower in comparison with other studies. TP53 was the most altered gene in tumors, with 62.5% presenting likely non‐functional or non‐functional somatic variants, while eight 14.2% presented likely non‐functional or non‐functional somatic variants in BRCA1 or BRCA2.
Journal Article
Genes Controlled by DNA Methylation Are Involved in Wilms Tumor Progression
by
Guerra, João Victor da Silva
,
Faria, Paulo
,
Montalvão de Azevedo, Rafaela
in
Bayesian analysis
,
cancer progression
,
Chemotherapy
2019
To identify underlying mechanisms involved with metastasis formation in Wilms tumors (WTs), we performed comprehensive DNA methylation and gene expression analyses of matched normal kidney (NK), WT blastemal component, and metastatic tissues (MT) from patients treated under SIOP 2001 protocol. A linear Bayesian framework model identified 497 differentially methylated positions (DMPs) between groups that discriminated NK from WT, but MT samples were divided in two groups. Accordingly, methylation variance grouped NK and three MT samples tightly together and all WT with four MT samples that showed high variability. WT were hypomethylated compared to NK, and MT had a hypermethylated pattern compared to both groups. The methylation patterns were in agreement with methylases and demethylases expression. Methylation data pointed to the existence of two groups of metastases. While hierarchical clustering analysis based on the expression of all 2569 differentially expressed genes (DEGs) discriminated WT and MT from all NK samples, the hierarchical clustering based on the expression of 44 genes with a differentially methylated region (DMR) located in their promoter region revealed two groups: one containing all NKs and three MTs and one containing all WT and four MTs. Methylation changes might be controlling expression of genes associated with WT progression. The 44 genes are candidates to be further explored as a signature for metastasis formation in WT.
Journal Article
SKIRTING THE ISSUE
2017
Military have endured one confusing uniform policy change after another. In 2013, the issue making headlines was hats, called covers in the military. It was decided that the traditional dress uniform covers-previously designed differently for men and women--should be more standard. The newly designed women's cover looked a lot like the men's cover. The upswept sides and curves designed in the mid-20th century were replaced by a standard duck-bill brim airline pilot or police officer hat. Newspaper articles that covered the uniform changes included some very cautious quotes from high-ranking officers, stating explicitly that they were not trying to put women in men's uniforms. They pointed to extensive fit testing and tailoring to make these new uniforms, both hats and choker blouses, fit better than even the old women's uniforms. There was not, however, any discussion of tailoring women's uniforms to fit men.
Trade Publication Article
Post-translational control is sufficient to coordinate membrane synthesis with growth in Escherichia coli
by
Noga, Marek J
,
Niels Jf Van Den Broek
,
Scherer, Nicole
in
Adaptation
,
Allosteric properties
,
E coli
2019
Every cell must produce enough membrane to contain itself. However, the mechanisms by which cells couple the rate of membrane synthesis with the rate of growth remain unresolved. By measuring precursors, intermediates, and enzymes of the fatty acid and phospholipid synthesis pathways of Escherichia coli, we show that while fatty acid and membrane synthesis capacities are maintained at a constant level across a 3-fold range of growth rates, the steady-state rate of phospholipid synthesis is principally mediated by allosteric control of a single enzyme, PlsB. Surprisingly, metabolic modelling indicates that PlsB activity also strongly influences flux into the synthesis pathway of lipopolysaccharide, the second-most abundant membrane component. In contrast to steady-state regulation, we find that responses to environmental perturbations are triggered directly via changes in acetyl-CoA concentrations, enabling rapid adaptation. Adaptations are further modulated by ppGpp, which regulates PlsB activity during slow growth and growth arrest. The strong reliance upon post-translational regulation for flux control ensures both robustness and responsiveness of membrane synthesis.
Post-translational control of PlsB is sufficient to coordinate membrane synthesis with growth in Escherichia coli
2020
Every cell must produce enough membrane to contain itself. However, the mechanisms by which the rate of membrane synthesis is coupled with the rate of cell growth remain unresolved. By comparing substrate and enzyme concentrations of the fatty acid and phospholipid synthesis pathways of Escherichia coli across a 3-fold range of carbon-limited growth rates, we show that the rate of membrane phospholipid synthesis during steady-state growth is determined principally through allosteric control of a single enzyme, PlsB. Due to feedback regulation of the fatty acid pathway, PlsB activity also indirectly controls synthesis of lipopolysaccharide, a major component of the outer membrane synthesized from a fatty acid synthesis intermediate. Surprisingly, concentrations of the enzyme that catalyses the committed step of lipopolysaccharide synthesis (LpxC) do not vary across steady-state growth conditions, suggesting that steady-state lipopolysaccharide synthesis is modulated primarily via indirect control by PlsB. In contrast to steady-state regulation, we find that responses to environmental perturbations are triggered directly via changes in acetyl-CoA concentrations, which enables rapid adaptation. Adaptations are further modulated by ppGpp, which regulates PlsB activity during slow growth and growth arrest. The strong reliance of the membrane synthesis pathway upon post-translational regulation ensures both reliability and responsiveness of membrane synthesis.
How do bacteria cells grow without breaking their membranes? Although the biochemistry of fatty acid and membrane synthesis is well-known, how membrane synthesis is balanced with growth and metabolism has remained unclear. This is partly due to the many control points that have been discovered within the membrane synthesis pathways. By precisely establishing the contributions of individual pathway enzymes, our results simplify the model of membrane biogenesis in the model bacteria species Escherichia coli. Specifically, we find that allosteric control of a single enzyme, PlsB, is sufficient to balance growth with membrane synthesis and to ensure that growing E. coli produces sufficient membrane. Identifying the signals that activate and deactivate PlsB will answer the question of how membrane synthesis is synchronized with growth.
Effects of early trauma on metacognitive functioning in psychosis
2010
Background: Empirical evidence suggests a relationship between early trauma and psychosis. However, the underlying mechanisms for this relationship remain unclear. Research into metacognitive functioning in psychosis indicates higher levels of metacognitive dysfunctional beliefs within this patient group. The potential effects of early trauma on metacognitive functioning in psychosis has to date been scarcely researched. Reflective functioning (RF) is believed to be affected by early trauma and leading to psychopathology, particularly borderline personality disorder. However, to date no studies have investigated the effects of early trauma on RF within psychosis. Objectives: The primary aim of this study was to establish core links between the effects of early trauma and metacognitive and reflective functioning in psychosis. A secondary aim was to test the clinical applicability of a brief, newly developed attachment-based measure for RF. Furthermore, the study aimed to explore potential overlaps between the concepts of metacognition and reflective functioning. Method: A quantitative methodology was employed, using a combination of semi-structured interviews and self-report questionnaire, and group comparisons were conducted. Twenty-seven patients with psychosis or bipolar disorder were recruited. Participants were grouped into early trauma versus no early trauma; trauma versus no trauma; and in-patient versus out-patient, and exploratory analyses were completed. Results: No significant effects were found for early trauma but for trauma in general, indicating higher level of dysfunctional beliefs in patients with trauma (early plus adult trauma) history. No significant effect between groups were found for RF. Inpatients, however, showed significantly lower levels of RF when compared with outpatients, and outpatients significantly higher levels of cognitive self-focus(thinking about thoughts). Moreover, a modest positive correlation was found between both measures. Discussion: The findings of the present study suggest core links between the effects of trauma on metacognitive functioning in psychosis. This highlights the importance of routine trauma assessment with psychotic patients. The limitations of the metacognitive model within psychosis are discussed. Further research is implicated to investigate any potential effects of early trauma on RF in psychosis. Low level of RF in in-patients highlights the importance to integrate therapeutic techniques to improve RF functioning in this patient group since high RF is associated with resilience and better therapy outcome. The correlation between metacognition and RF measure indicates construct-validity for the RF measure. The differences between both concepts are considered. Furthermore, the limitations of this study and clinical utility are discussed along with suggestions for future research.
Dissertation
DEFINE & DESIGN: THE BOOKSTORE MODEL OF CUSTOMER SERVICE
by
Janoski, Jay
,
Bucci, Marissa
,
Scherer, Nicole
in
Bookstores
,
Customer service
,
Customer services
2020
As former and current booksellers, it's no surprise to us when patrons approach library staff with questions like these. New users often conflate libraries with the way retail stores operate. In this situation a service provider has a choice-become exasperated while taking the time to explain that this is a library and doesn't work that way, or just answer the question.
Magazine Article
Feeding type and development drive the ingestion of microplastics by freshwater invertebrates
by
Brennholt, Nicole
,
Reifferscheid, Georg
,
Scherer, Christian
in
631/158
,
704/172
,
Amphipoda - drug effects
2017
Microscopic plastic items (microplastics) are ubiquitously present in aquatic ecosystems. With decreasing size their availability and potential to accumulate throughout food webs increase. However, little is known on the uptake of microplastics by freshwater invertebrates. To address this, we exposed species with different feeding strategies to 1, 10 and 90 µm fluorescent polystyrene spheres (3–3 000 particles mL
−1
). Additionally, we investigated how developmental stages and a co-exposure to natural particles (e.g., food) modulate microplastic ingestion. All species ingested microplastics in a concentration-dependent manner with
Daphnia magna
consuming up to 6 180 particles h
−1
, followed by
Chironomus riparius
(226 particles h
−1
),
Physella acuta
(118 particles h
−1
),
Gammarus pulex
(10 particles h
−1
) and
Lumbriculus variegatus
(8 particles h
−1
).
D. magna
did not ingest 90 µm microplastics whereas the other species preferred larger microplastics over 1 µm in size. In
C. riparius
and
D. magna
, size preference depended on the life stage with larger specimens ingesting more and larger microplastics. The presence of natural particles generally reduced the microplastics uptake. Our results demonstrate that freshwater invertebrates have the capacity to ingest microplastics. However, the quantity of uptake depends on their feeding type and morphology as well as on the availability of microplastics.
Journal Article