Targeting and retention enhancement of quantum dots decorated with amino acids in an invertebrate model organism

Background: The goals of laboratory experiences include developing knowledge base, research skills, and scientific communication abilities. Objective: The aim was to assess an inquiry-based laboratory activity using the model organism Caenorhabditis elegans in relation to learning goals. Method: Students in a Biopsychology laboratory course worked in groups to test the effect of various drugs (e.g., nicotine, ethanol, fluoxetine, and melatonin) on C. elegans behavior. The activity included literature review, experimental design, and a final lab report. A cumulative final exam included a synaptic communication question related to the content of the activity. Results: Students showed better retention of laboratory-related content compared to other topics from the course, as demonstrated through performance on the final exam and were able to replicate previous research demonstrating effects of drug on locomotion. However, students did not improve writing ability compared to performance on a previous American Psychological Association style lab report. Conclusion: This study demonstrates that using a student-designed, multi-week laboratory assignment in an undergraduate Biopsychology course supports the growth of psychology knowledge and the development of research skills. Teaching Implications: Instructors should consider using the described laboratory activity for biopsychology or behavioral neuroscience classes or consider similarly designed laboratory formats for other courses in Psychology.

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GC-TOF/MS-based metabolomics analysis to investigate the changes driven by N-Acetylcysteine in the plant-pathogen Xanthomonas citri subsp. citri

Scientific Reports ◽

10.1038/s41598-021-95113-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Simone Cristina Picchi ◽

Mariana de Souza e Silva ◽

Luiz Leonardo Saldanha ◽

Henrique Ferreira ◽

Marco Aurélio Takita ◽

...

Keyword(s):

Amino Acids ◽

Cell Proliferation ◽

Plant Pathogen ◽

Model Organism ◽

Citrus Canker ◽

Bacterial Cells ◽

Xanthomonas Citri ◽

Canker Disease ◽

Potential Use

AbstractN-Acetylcysteine (NAC) is an antioxidant, anti-adhesive, and antimicrobial compound. Even though there is much information regarding the role of NAC as an antioxidant and anti-adhesive agent, little is known about its antimicrobial activity. In order to assess its mode of action in bacterial cells, we investigated the metabolic responses triggered by NAC at neutral pH. As a model organism, we chose the Gram-negative plant pathogen Xanthomonas citri subsp. citri (X. citri), the causal agent of citrus canker disease, due to the potential use of NAC as a sustainable molecule against phytopathogens dissemination in citrus cultivated areas. In presence of NAC, cell proliferation was affected after 4 h, but damages to the cell membrane were observed only after 24 h. Targeted metabolite profiling analysis using GC–MS/TOF unravelled that NAC seems to be metabolized by the cells affecting cysteine metabolism. Intriguingly, glutamine, a marker for nitrogen status, was not detected among the cells treated with NAC. The absence of glutamine was followed by a decrease in the levels of the majority of the proteinogenic amino acids, suggesting that the reduced availability of amino acids affect protein synthesis and consequently cell proliferation.

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Basal-Level Effects of (p)ppGpp in the Absence of Branched-Chain Amino Acids in Actinobacillus pleuropneumoniae

Journal of Bacteriology ◽

10.1128/jb.00640-19 ◽

2020 ◽

Vol 202 (8) ◽

Author(s):

Gang Li ◽

Qian Zhao ◽

Tian Luan ◽

Yangbo Hu ◽

Yueling Zhang ◽

...

Keyword(s):

Escherichia Coli ◽

Amino Acids ◽

De Novo ◽

Model Organism ◽

Stringent Response ◽

Actinobacillus Pleuropneumoniae ◽

Branched Chain Amino Acids ◽

Content Type ◽

Phenotypic Differences ◽

Branched Chain

ABSTRACT The (p)ppGpp-mediated stringent response (SR) is a highly conserved regulatory mechanism in bacterial pathogens, enabling adaptation to adverse environments, and is linked to pathogenesis. Actinobacillus pleuropneumoniae can cause damage to the lungs of pigs, its only known natural host. Pig lungs are known to have a low concentration of free branched-chain amino acids (BCAAs) compared to the level in plasma. We had investigated the role for (p)ppGpp in viability and biofilm formation of A. pleuropneumoniae. Now, we sought to determine whether (p)ppGpp was a trigger signal for the SR in A. pleuropneumoniae in the absence of BCAAs. Combining transcriptome and phenotypic analyses of the wild type (WT) and an relA spoT double mutant [which does not produce (p)ppGpp], we found that (p)ppGpp could repress de novo purine biosynthesis and activate antioxidant pathways. There was a positive correlation between GTP and endogenous hydrogen peroxide content. Furthermore, the growth, viability, morphology, and virulence were altered by the inability to produce (p)ppGpp. Genes involved in the biosynthesis of BCAAs were constitutively upregulated, regardless of the existence of BCAAs, without accumulation of (p)ppGpp beyond a basal level. Collectively, our study shows that the absence of BCAAs was not a sufficient signal to trigger the SR in A. pleuropneumoniae. (p)ppGpp-mediated regulation in A. pleuropneumoniae is different from that described for the model organism Escherichia coli. Further work will establish whether the (p)ppGpp-dependent SR mechanism in A. pleuropneumoniae is conserved among other veterinary pathogens, especially those in the Pasteurellaceae family. IMPORTANCE (p)ppGpp is a key player in reprogramming transcriptomes to respond to nutritional challenges. Here, we present transcriptional and phenotypic differences of A. pleuropneumoniae grown in different chemically defined media in the absence of (p)ppGpp. We show that the deprivation of branched-chain amino acids (BCAAs) does not elicit a change in the basal-level (p)ppGpp, but this level is sufficient to regulate the expression of BCAA biosynthesis. The mechanism found in A. pleuropneumoniae is different from that of the model organism Escherichia coli but similar to that found in some Gram-positive bacteria. This study not only broadens the research scope of (p)ppGpp but also further validates the complexity and multiplicity of (p)ppGpp regulation in microorganisms that occupy different biological niches.

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Quantum Dots—Assisted 2D Fluorescence for Pattern Based Sensing of Amino Acids, Oligopeptides and Neurotransmitters

Sensors ◽

10.3390/s19173655 ◽

2019 ◽

Vol 19 (17) ◽

pp. 3655 ◽

Cited By ~ 1

Author(s):

Marcin Zabadaj ◽

Patrycja Ciosek-Skibińska

Keyword(s):

Amino Acids ◽

Quantum Dots ◽

Emission Spectra ◽

Specific Interactions ◽

High Quantum Yield ◽

Huge Amount ◽

Broad Absorption ◽

Amount Of Information ◽

Decay Times ◽

Proof Of Principle

Quantum dots (QDs) are very attractive nanomaterials for analytical chemistry, due to high photostability, large surface area featuring numerous ways of bioconjugation with biomolecules, usually high quantum yield and long decay times. Their broad absorption spectra and narrow, sharp emission spectra of size-tunable fluorescence make them ideal tools for pattern-based sensing. However, almost always they are applied for specific sensing with zero-dimensional (0D) signal reporting (only peak heights or peak shifts are considered), without taking advantage of greater amount of information hidden in 1D signal (emission spectra), or huge amount of information hidden in 2D fluorescence maps (Excitation-Emission Matrixes, EEMs). Therefore, in this work we propose opposite strategy—non-specific interactions of QDs, which are usually avoided and regarded as their disadvantage, were exploited here for 2D fluorescence fingerprinting. Analyte-specific multivariate fluorescence response of QDs is decoded with the use of Partial Least Squares—Discriminant Analysis. Even though only one type of QDs is studied, the proposed pattern-based method enables to obtain satisfactory accuracy for all studied compounds—various neurotransmitters, amino-acids and oligopeptides. This is a proof of principle of the possibility of the identification of various bioanalytes by such fluorescence fingerprinting with the use of QDs.

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Embryonic chimerism does not induce tolerance in an invertebrate model organism

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0608696104 ◽

2007 ◽

Vol 104 (11) ◽

pp. 4559-4564 ◽

Cited By ~ 13

Author(s):

M. Poudyal ◽

S. Rosa ◽

A. E. Powell ◽

M. Moreno ◽

S. L. Dellaporta ◽

...

Keyword(s):

Model Organism ◽

Invertebrate Model

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Photoluminescent sensing for acidic amino acids based on the disruption of graphene quantum dots/europium ions aggregates

Biosensors and Bioelectronics ◽

10.1016/j.bios.2014.10.043 ◽

2015 ◽

Vol 65 ◽

pp. 204-210 ◽

Cited By ~ 31

Author(s):

Qi Zhang ◽

Chan Song ◽

Ting Zhao ◽

Hai-Wei Fu ◽

Hui-Zhen Wang ◽

...

Keyword(s):

Amino Acids ◽

Quantum Dots ◽

Graphene Quantum Dots ◽

Acidic Amino Acids

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Anaerobic Growth of Corynebacterium glutamicum via Mixed-Acid Fermentation

Applied and Environmental Microbiology ◽

10.1128/aem.02413-15 ◽

2015 ◽

Vol 81 (21) ◽

pp. 7496-7508 ◽

Cited By ~ 23

Author(s):

Andrea Michel ◽

Abigail Koch-Koerfges ◽

Karin Krumbach ◽

Melanie Brocker ◽

Michael Bott

Keyword(s):

Amino Acids ◽

Corynebacterium Glutamicum ◽

Tricarboxylic Acid Cycle ◽

Model Organism ◽

Anaerobic Growth ◽

Efficient Production ◽

Ph Homeostasis ◽

Anaerobic Conditions ◽

Acid Fermentation ◽

Content Type

ABSTRACTCorynebacterium glutamicum, a model organism in microbial biotechnology, is known to metabolize glucose under oxygen-deprived conditions tol-lactate, succinate, and acetate without significant growth. This property is exploited for efficient production of lactate and succinate. Our detailed analysis revealed that marginal growth takes place under anaerobic conditions with glucose, fructose, sucrose, or ribose as a carbon and energy source but not with gluconate, pyruvate, lactate, propionate, or acetate. Supplementation of glucose minimal medium with tryptone strongly enhanced growth up to a final optical density at 600 nm (OD600) of 12, whereas tryptone alone did not allow growth. Amino acids with a high ATP demand for biosynthesis and amino acids of the glutamate family were particularly important for growth stimulation, indicating ATP limitation and a restricted carbon flux into the oxidative tricarboxylic acid cycle toward 2-oxoglutarate. Anaerobic cultivation in a bioreactor with constant nitrogen flushing disclosed that CO2is required to achieve maximal growth and that the pH tolerance is reduced compared to that under aerobic conditions, reflecting a decreased capability for pH homeostasis. Continued growth under anaerobic conditions indicated the absence of an oxygen-requiring reaction that is essential for biomass formation. The results provide an improved understanding of the physiology ofC. glutamicumunder anaerobic conditions.

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