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"Dekker, H"
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Metformin Induces Apoptosis and Cell Cycle Arrest Mediated by Oxidative Stress, AMPK and FOXO3a in MCF-7 Breast Cancer Cells
by
Lees, Simon J.
,
Dekker, Robert F. H.
,
Eichler, Rosangela
in
Activation
,
AKT protein
,
AMP-Activated Protein Kinases - genetics
2014
Recent studies have demonstrated that the anti-diabetic drug, metformin, can exhibit direct antitumoral effects, or can indirectly decrease tumor proliferation by improving insulin sensitivity. Despite these recent advances, the underlying molecular mechanisms involved in decreasing tumor formation are not well understood. In this study, we examined the antiproliferative role and mechanism of action of metformin in MCF-7 cancer cells treated with 10 mM of metformin for 24, 48, and 72 hours. Using BrdU and the MTT assay, it was found that metformin demonstrated an antiproliferative effect in MCF-7 cells that occurred in a time- and concentration-dependent manner. Flow cytometry was used to analyze markers of cell cycle, apoptosis, necrosis and oxidative stress. Exposure to metformin induced cell cycle arrest in G0-G1 phase and increased cell apoptosis and necrosis, which were associated with increased oxidative stress. Gene and protein expression were determined in MCF-7 cells by real time RT-PCR and western blotting, respectively. In MCF-7 cells metformin decreased the activation of IRβ, Akt and ERK1/2, increased p-AMPK, FOXO3a, p27, Bax and cleaved caspase-3, and decreased phosphorylation of p70S6K and Bcl-2 protein expression. Co-treatment with metformin and H2O2 increased oxidative stress which was associated with reduced cell number. In the presence of metformin, treating with SOD and catalase improved cell viability. Treatment with metformin resulted in an increase in p-p38 MAPK, catalase, MnSOD and Cu/Zn SOD protein expression. These results show that metformin has an antiproliferative effect associated with cell cycle arrest and apoptosis, which is mediated by oxidative stress, as well as AMPK and FOXO3a activation. Our study further reinforces the potential benefit of metformin in cancer treatment and provides novel mechanistic insight into its antiproliferative role.
Journal Article
Bacillus anthracis in South Africa, 1975–2013 : are some lineages vanishing?
by
Hassim, Ayesha
,
Glover, Barbara A.
,
van Schalkwyk, Louis Ockert
in
Analysis
,
Animal Genetics and Genomics
,
Anthrax
2024
The anthrax-causing bacterium Bacillus anthracis comprises the genetic clades A, B, and C. In the northern most part (Pafuri) of Kruger National Park (KNP), South Africa, both the common A and rare B strains clades occur. The B clade strains were reported to be dominant in Pafuri before 1991, while A clade strains occurred towards the central parts of KNP. The prevalence of B clade strains is currently much lower as only A clade strains have been isolated from 1992 onwards in KNP. In this study 319 B. anthracis strains were characterized with 31-loci multiplelocus variable-number tandem repeat analysis (MLVA-31). B clade strains from soil (n=9) and a Tragelaphus strepsiceros carcass (n=1) were further characterised by whole genome sequencing and compared to publicly available genomes. The KNP strains clustered in the B clade before 1991 into two dominant genotypes. South African strains cluster into a dominant genotype A.Br.005/006 consisting of KNP as well as the other anthrax endemic region, Northern Cape Province (NCP), South Africa. A few A.Br.001/002 strains from both endemic areas were also identified. Subclade A.Br.101 belonging to the A.Br.Aust94 lineage was reported in the NCP. The B-clade strains seems to be vanishing, while outbreaks in South Africa are caused mainly by the A.Br.005/006 genotypes as well as a few minor clades such as A.Br.001/002 and A.Br.101 present in NCP. This work confirmed the existence of the rare and vanishing B-clade strains that group in B.Br.001 branch with KrugerB and A0991 KNP strains.
Journal Article
Ultra-processed food and incident type 2 diabetes: studying the underlying consumption patterns to unravel the health effects of this heterogeneous food category in the prospective Lifelines cohort
by
Dekker, Louise H.
,
Duan, Ming-Jie
,
Vinke, Petra C.
in
Beverages
,
Biomedicine
,
Care and treatment
2022
Background
The overall consumption of ultra-processed food (UPF) has previously been associated with type 2 diabetes. However, due to the substantial heterogeneity of this food category, in terms of their nutritional composition and product type, it remains unclear whether previous results apply to all underlying consumption patterns of UPF.
Methods
Of 70,421 participants (35–70 years, 58.6% women) from the Lifelines cohort study, dietary intake was assessed with a food frequency questionnaire. UPF was identified according to the NOVA classification. Principal component analysis (PCA) was performed to derive UPF consumption patterns. The associations of UPF and adherence to UPF consumption patterns with incidence of type 2 diabetes were studied with logistic regression analyses adjusted for age, sex, diet quality, energy intake, alcohol intake, physical activity, TV watching time, smoking status, and educational level.
Results
During a median follow-up of 41 months, a 10% increment in UPF consumption was associated with a 25% higher risk of developing type 2 diabetes (1128 cases; OR 1.25 [95% CI 1.16, 1.34]). PCA revealed four habitual UPF consumption patterns. A pattern high in cold savory snacks (OR 1.16 [95% CI 1.09, 1.22]) and a pattern high in warm savory snacks (OR 1.15 [95% CI 1.08, 1.21]) were associated with an increased risk of incident type 2 diabetes; a pattern high in traditional Dutch cuisine was not associated with type 2 diabetes incidence (OR 1.05 [95% CI 0.97, 1.14]), while a pattern high in sweet snacks and pastries was inversely associated with type 2 diabetes incidence (OR 0.82 [95% CI 0.76, 0.89]).
Conclusions
The heterogeneity of UPF as a general food category is reflected by the discrepancy in associations between four distinct UPF consumption patterns and incident type 2 diabetes. For better public health prevention, research is encouraged to further clarify how different UPF consumption patterns are related to type 2 diabetes.
Journal Article
Origin of the electrophoretic force on DNA in solid-state nanopores
by
Dekker, Nynke H.
,
van Dorp, Stijn
,
Lemay, Serge G.
in
Atomic
,
Classical and Continuum Physics
,
Complex Systems
2009
When a single strand of DNA is threaded through a nanopore, a direct test of the effect of pore size indicates that a hydrodynamic model for the process should include the coupled Poisson–Boltzmann and Stokes equations.
Despite gel electrophoresis being one of the main workhorses of molecular biology, the physics of polyelectrolyte electrophoresis in a strongly confined environment remains poorly understood. Theory indicates that forces in electrophoresis result from interplay between ionic screening and hydrodynamics
1
,
2
, but these ideas could so far be addressed only indirectly by experiments based on macroscopic porous gels. Here, we provide a first direct experimental test by measuring the electrophoretic force on a single DNA molecule threading through a solid-state nanopore
3
as a function of pore size. The stall force gradually decreases on increasing the nanopore diameter from 6 to 90 nm, inconsistent with expectations from simple electrostatics and strikingly demonstrating the influence of the hydrodynamic environment. We model this process by applying the coupled Poisson–Boltzmann and Stokes equations in the nanopore geometry
4
,
5
and find good agreement with the experimental results.
Journal Article
Warriors and Peacekeepers: Testing a Biosocial Implicit Leadership Hypothesis of Intergroup Relations Using Masculine and Feminine Faces
2012
This paper examines the impact of facial cues on leadership emergence. Using evolutionary social psychology, we expand upon implicit and contingent theories of leadership and propose that different types of intergroup relations elicit different implicit cognitive leadership prototypes. It is argued that a biologically based hormonal connection between behavior and corresponding facial characteristics interacts with evolutionarily consistent social dynamics to influence leadership emergence. We predict that masculine-looking leaders are selected during intergroup conflict (war) and feminine-looking leaders during intergroup cooperation (peace). Across two experiments we show that a general categorization of leader versus nonleader is an initial implicit requirement for emergence, and at a context-specific level facial cues of masculinity and femininity contingently affect war versus peace leadership emergence in the predicted direction. In addition, we replicate our findings in Experiment 1 across culture using Western and East Asian samples. In Experiment 2, we also show that masculine-feminine facial cues are better predictors of leadership than male-female cues. Collectively, our results indicate a multi-level classification of context-specific leadership based on visual cues imbedded in the human face and challenge traditional distinctions of male and female leadership.
Journal Article
Automated cell counting for Trypan blue-stained cell cultures using machine learning
by
van der Pol, Leo A.
,
Dekker, Nynke H.
,
Kuijpers, Louis
in
Animals
,
Biology and Life Sciences
,
Cell Count - methods
2023
Cell counting is a vital practice in the maintenance and manipulation of cell cultures. It is a crucial aspect of assessing cell viability and determining proliferation rates, which are integral to maintaining the health and functionality of a culture. Additionally, it is critical for establishing the time of infection in bioreactors and monitoring cell culture response to targeted infection over time. However, when cell counting is performed manually, the time involved can become substantial, particularly when multiple cultures need to be handled in parallel. Automated cell counters, which enable significant time reduction, are commercially available but remain relatively expensive. Here, we present a machine learning (ML) model based on YOLOv4 that is able to perform cell counts with a high accuracy (>95%) for Trypan blue-stained insect cells. Images of two distinctly different cell lines, Trichoplusia ni (High Five TM ; Hi5 cells) and Spodoptera frugiperda (Sf9), were used for training, validation, and testing of the model. The ML model yielded F 1 scores of 0.97 and 0.96 for alive and dead cells, respectively, which represents a substantially improved performance over that of other cell counters. Furthermore, the ML model is versatile, as an F 1 score of 0.96 was also obtained on images of Trypan blue-stained human embryonic kidney (HEK) cells that the model had not been trained on. Our implementation of the ML model comes with a straightforward user interface and can image in batches, which makes it highly suitable for the evaluation of multiple parallel cultures (e.g. in Design of Experiments). Overall, this approach for accurate classification of cells provides a fast, bias-free alternative to manual counting.
Journal Article
Encapsulation and dispersion of Lactobacillus acidophilus in a chocolate coating as a strategy for maintaining cell viability in cereal bars
by
da Silva Pereira Ronning, Eduardo
,
Lasta, Everton Luiz
,
Dekker, Robert F. H.
in
631/326
,
631/61
,
Alginates
2021
Flour from
Pereskia aculeata
leaf and green banana were used as ingredients in the formulation of a cereal bar with added
Lactobacillus acidophilus
LA02-ID-1688. Encapsulation in a calcium-alginate hydrogel reinforced with magnesium hydroxide was used as a strategy to protect the probiotic cells under gastrointestinal conditions and to prolong shelf-life. The results are relevant especially for maintaining cell viability during shelf-life; a challenge for the food industry in relation to dry probiotic products. Encapsulation promoted the protection of probiotic cells in simulated gastric and intestinal conditions, allowing the maintenance of high viable cell counts (> 10 log CFU, colony forming unit). Encapsulation also contributed to cellular protection under extreme temperature conditions, with reductions of cell viability of < 1 logarithmic cycle when the capsules were subjected to 55ºC/10 min. Even at 75ºC/10 min, encapsulation protected the probiotic cells 3-times greater than the free-cells. The food bar proved to be rich in dietary fiber (19 g 100 g
−1
), lipids (12.63 g 100 g
−1
) and showed an appreciable protein content (5.44 g 100 g
−1
). A high viable probiotic cell count on storage over 120 days (12.54 log CFU) was observed, maintaining a probiotic survival rate > 90% and viability levels sufficient to promote health benefits.
Journal Article
In-vitro biological evaluation of 3,3′,5,5′-tetramethoxy-biphenyl-4,4′-diol and molecular docking studies on trypanothione reductase and Gp63 from Leishmania amazonensis demonstrated anti-leishmania potential
by
Dekker, Robert F. H.
,
Miranda-Sapla, Milena M.
,
Bispo, Marcelle L. F.
in
631/114
,
631/154
,
631/326
2023
Available treatments for leishmaniasis have been widely used since the 1940s but come at a high cost, variable efficacy, high toxicity, and adverse side-effects. 3,3′,5,5′-Tetramethoxy-biphenyl-4,4′-diol (TMBP) was synthesized through laccase-catalysis of 2,6-dimethoxyphenol and displayed antioxidant and anticancer activity, and is considered a potential drug candidate. Thus, this study aimed to evaluate the anti-leishmanial effect of TMBP against promastigote and amastigote forms of
Leishmania (L.) amazonensis
and investigated the mechanisms involved in parasite death. TMBP treatment inhibited the proliferation (IC
50
0.62–0.86 µM) and induced the death of promastigote forms by generating reactive oxygen species and mitochondrial dysfunction. In intracellular amastigotes, TMBP reduced the percentage of infected macrophages, being 62.7 times more selective to the parasite (CC
50
53.93 µM). TMBP did not hemolyze sheep erythrocytes; indicative of low cytotoxicity. Additionally, molecular docking analysis on two enzyme targets of
L. amazonensis
: trypanothione reductase (TR) and leishmanolysin (Gp63), suggested that the hydroxyl group could be a pharmacophoric group due to its binding affinity by hydrogen bonds with residues at the active site of both enzymes. TMBP was more selective to the Gp63 target than TR. This is the first report that TMBP is a promising compound to act as an anti-leishmanial agent.
Journal Article
Fungal Exocellular (1-6)-β-d-glucan: Carboxymethylation, Characterization, and Antioxidant Activity
by
M. Barbosa-Dekker, Aneli
,
Theis, Thais Vanessa
,
A. Cunha, Mário A.
in
Acids
,
Biopolymers
,
Caustic soda
2019
Exocellular (1→6)-β-d-glucan (lasiodiplodan) produced by the fungus Lasiodiplodia theobromae MMPI was derivatized by carboxymethylation using different concentrations of a derivatizing agent. Lasiodiplodan was derivatized by carboxymethylation in an attempt to increase its solubility and enhance its biological activities. Carboxymethylglucans with degrees of substitution (DS) of 0.32, 0.47, 0.51, 0.58, and 0.68 were produced and characterized. FTIR analysis showed a band of strong intensity at 1600 cm−1 and an absorption band at 1421 cm−1, resulting from asymmetric and symmetrical stretching vibrations, respectively, of the carboxymethyl group COO- in the carboxymethylated samples. Thermal analysis showed that native lasiodiplodan (LN) and carboxymethylated derivatives (LC) exhibited thermal stability up to 200–210 °C. X-ray diffractometry demonstrated that both native and carboxymethylated lasiodiplodan presented predominantly an amorphous nature. Scanning electron microscopy revealed that carboxymethylation promoted morphological changes in the biopolymer and increased porosity, and alveolar structures were observed along the surface. The introduction of carboxymethyl groups in the macromolecule promoted increased solubility and potentiated the hydroxyl radical-scavenging activity, suggesting a correlation between degree of substitution and antioxidant activity.
Journal Article
Noise in solid-state nanopores
by
Dekker, C
,
Smeets, R.M.M
,
Keyser, U.F
in
Algorithms
,
Biological Sciences
,
Biological Transport
2008
We study ionic current fluctuations in solid-state nanopores over a wide frequency range and present a complete description of the noise characteristics. At low frequencies (f [less, similar] 100 Hz) we observe 1/f-type of noise. We analyze this low-frequency noise at different salt concentrations and find that the noise power remarkably scales linearly with the inverse number of charge carriers, in agreement with Hooge's relation. We find a Hooge parameter α = (1.1 ± 0.1) x 10⁻⁴. In the high-frequency regime (f [greater, similar] 1 kHz), we can model the increase in current power spectral density with frequency through a calculation of the Johnson noise. Finally, we use these results to compute the signal-to-noise ratio for DNA translocation for different salt concentrations and nanopore diameters, yielding the parameters for optimal detection efficiency.
Journal Article