odelay-large-scale-method-for-multi-parameter-quantification-yeast

ODELAY: A Large-scale Method for Multi-parameter Quantification of Yeast Growth

Growth phenotypes of microorganisms are a strong indicator of their underlying genetic fitness and can be segregated into 3 growth regimes: lag-phase, ...

Institute for Systems Biology

When the surfaces of Ag nanowires were coated with thin sheaths of Pd/Ag alloys, they exhibited hydrogen absorption/desorption behaviors and capacities similar to those of pure Pd powders or nanotubes. The stronger mechanical strengths of these cable-like nanostructures also allowed them to undergo more absorption/desorption cycles with no morphological changes. These nanostructures can be used as a good model system to study the interaction between hydrogen and metal alloys with relatively low concentrations of Pd (<10%) with respect to structural, thermodynamic, and kinetic features.

Ag nanowires coated with Ag/Pd alloy sheaths and their use as substrates for reversible absorption and desorption of hydrogen.

Platinum nanowires of approximately 100 nm in length and approximately 5 nm in diameter have been synthesized by reducing H(2)PtCl(6) with ethylene glycol in the presence of poly(vinyl pyrrolidone) (PVP) and a trace amount of Fe(3+) or Fe(2+). The wires were generated at the final stage of the synthesis, which involved the formation of several intermediate species. The Fe(3+) or Fe(2+) ions had dual functions in the synthesis: they induced aggregation of Pt nanoparticles into larger structures that served as the nucleation sites, and they greatly reduced the reaction rate and supersaturation level to induce anisotropic growth. The reaction mechanism was studied by X-ray photoelectron spectroscopy (XPS) and UV-vis spectral analysis. The Pt nanowires could be readily separated from the surfaces of the agglomerates by sonication and obtained as pure samples by centrifugation.

Single-crystal nanowires of platinum can be synthesized by controlling the reaction rate of a polyol process.

We have successfully incorporated iron oxide nanoparticles into monodispersed amorphous selenium (a-Se) colloids by regulating the reaction temperature during the synthesis of a-Se. The surfaces of these a-Se colloids could be coated with conformal and smooth shells made of Pt and SiO2. The Se cores could then be removed by etching with hydrazine. The spherical morphology and superparamagnetism were maintained in all these synthetic steps. The presence of Pt and SiO2 on the outer surfaces of these colloidal particles allows one to control their surface functionalities through the formation of alkanethiolate and siloxane monolayers, respectively.

Amorphous Se: a new platform for synthesizing superparamagnetic colloids with controllable surfaces.

Polyol synthesis of platinum nanostructures: control of morphology through the manipulation of reduction kinetics.

The clinical outcomes of human infections by Plasmodium falciparum remain highly unpredictable. A complete understanding of the complex interactions between host cells and the parasite will require in vitro experimental models that simultaneously capture diverse host-parasite interactions relevant to pathogenesis. Here we show that advanced microfluidic devices concurrently model (a) adhesion of infected red blood cells to host cell ligands, (b) rheological responses to changing dimensions of capillaries with shapes and sizes similar to small blood vessels, and (c) phagocytosis of infected erythrocytes by macrophages. All of this is accomplished under physiologically relevant flow conditions for up to 20 h. Using select examples, we demonstrate how this enabling technology can be applied in novel, integrated ways to dissect interactions between host cell ligands and parasitized erythrocytes in synthetic capillaries. The devices are cheap and portable and require small sample volumes; thus, they have the potential to be widely used in research laboratories and at field sites with access to fresh patient samples.

Microfluidic modeling of cell-cell interactions in malaria pathogenesis.

Malaria is a major poverty-related human infectious disease of the world. Over a billion individuals are under threat and several million die from malaria every year. The nature of disease, especially fatal disease, has been the subject of many studies. The consensus is that parasite-induced cytoadherance of red blood cells precipitates capillary blockage and inflammatory responses in affected organs. Reduced deformability of infected erythrocytes may also contribute to disease. What is not very clear is why people with significant parasite burdens display large variations in disease outcomes. Technologies which allow a detailed description of the cytoadherance properties of infected erythrocytes in individual patients, and which allow a complete description of the flow capabilities of red blood cell populations in that patient, would be very useful. Here we review the recent introduction of microfluidic technology to study malaria pathogenesis, including the fabrication processes. The devices are cheap, versatile, portable and require very small patient samples. With greater use in research laboratories and field sites, we eventually expect microfluidic methods to play important roles in malaria diagnosis, as well as prognosis.

Microfluidic approaches to malaria pathogenesis.

Splenic filtration of infected red blood cells (RBCs) may contribute to innate immunity and variable outcomes of malaria infections. We show that filterability of individual RBCs is well predicted by the minimum cylindrical diameter (MCD) which is calculated from a RBC's surface area and volume. The MCD describes the smallest diameter tube or smallest pore that a cell may fit through without increasing its surface area. A microfluidic device was developed to measure the MCD from thousands of individual infected RBCs (IRBCs) and uninfected RBCs (URBCs). Average MCD changes during the blood-stage cycle of Plasmodium falciparum were tracked for the cytoadherent strain ITG and the knobless strain Dd2. The MCD values for IRBCs and URBCs raise several new intriguing insights into how the spleen may remove IRBCs: some early-stage ring-IRBCs, and not just late-stage schizont-IRBCs, may be highly susceptible to filtration. In addition, knobby parasites may limit surface area expansions and thus confer high MCDs on IRBCs. Finally, URBCs, in culture with IRBCs, show higher surface area loss which makes them more susceptible to filtration than naive URBCs. These findings raise important basic questions about the variable pathology of malaria infections and metabolic process that affect volume and surface area of IRBCs.

Deformability limits of Plasmodium falciparum-infected red blood cells.

The cellular events leading to severe and complicated malaria in some Plasmodium falciparum infections are poorly understood. Additional tools are required to better understand the pathogenesis of this disease. In this technical report, we describe a microfluidic culture system and image processing algorithms that were developed to observe cytoadhesion interactions of P. falciparum parasitized erythrocytes rolling on primary brain microvascularendothelial cells. We isolated and cultured human primary microvascular brain endothelial cells in a closed loop microfluidic culture system where a peristaltic pump and media reservoirs were integrated onto a microscope stage insert. We developed image processing methods to enhance contrast of rolling parasitized erythrocytes on endothelial cells and to estimate the local wall shear stress. The velocity of parasitized erythrocytes rolling on primary brain microvascularendothelial cells was then measured under physiologically relevant wall shear stresses. Finally, we deployed this method successfully at a field site in Blantyre, Malawi. The method is a promising new tool for the investigation of the pathogenesis of severe malaria.

A microfluidic system to study cytoadhesion of Plasmodium falciparum infected erythrocytes to primary brain microvascularendothelial cells.

The study of malaria parasites on the Indian subcontinent should help us understand unexpected disease outbreaks and unpredictable disease presentations from Plasmodium falciparum and Plasmodium vivax infections. The Malaria Evolution in South Asia (MESA) research program is one of ten International Centers of Excellence for Malaria Research (ICEMR) sponsored by the US National Institutes of Health. In this second of two reviews, we describe why population structures of Plasmodia in India will be characterized and how we will determine their consequences on disease presentation, outcome and patterns. Specific projects will determine if genetic diversity, possibly driven by parasites with higher genetic plasticity, plays a role in changing epidemiology, pathogenesis, vector competence of parasite populations and whether innate human genetic traits protect Indians from malaria today. Deep local clinical knowledge of malaria in India will be supplemented by basic scientists who bring new research tools. Such tools will include whole genome sequencing and analysis methods; in vitro assays to measure genome plasticity, RBC cytoadhesion, invasion, and deformability; mosquito infectivity assays to evaluate changing parasite-vector compatibilities; and host genetics to understand protective traits in Indian populations. The MESA-ICEMR study sites span diagonally across India and include a mixture of very urban and rural hospitals, each with very different disease patterns and patient populations. Research partnerships include government-associated research institutes, private medical schools, city and state government hospitals, and hospitals with industry ties. Between 2012 and 2017, in addition to developing clinical research and basic science infrastructure at new clinical sites, our training workshops will engage new scientists and clinicians throughout South Asia in the malaria research field.

Malaria evolution in South Asia: knowledge for control and elimination.

Splenic filtration of Plasmodium falciparum-infected red blood cells has been hypothesized to influence malaria pathogenesis. We have developed a minimum cylindrical diameter (MCD) filtration model which estimates physical splenic filtration during malaria infection. The key parameter in the model is the MCD, the smallest tube or cylinder that a red blood cell (RBC) can traverse without lysing. The MCD is defined by a relationship between the RBC surface area and volume. In the MCD filtration model, the MCD filtration function represents the probability of a cell becoming physically removed from circulation. This modelling approach was implemented at a field site in Blantyre, Malawi. We analysed peripheral blood samples from 120 study participants in four clinically defined groups (30 subjects each): cerebral malaria, uncomplicated malaria, aparasitaemic coma and healthy controls. We found statistically significant differences in the surface area and volumes of uninfected RBCs when healthy controls were compared with malaria patients. The estimated filtration rates generated by the MCD model corresponded to previous observations in ex vivo spleen experiments and models of red blood cell loss during acute malaria anaemia.There were no differences in the estimated splenic filtration rates between cerebral malaria and uncomplicated malaria patients. The MCD filtration model estimates that at time of admission, one ring-stage infected RBC is physically filtered by the spleen for each parasite that remains in peripheral circulation. This field study is the first to use microfluidic devices to identify rheological diversity in RBC populations associated with malaria infection and illness in well-characterized groups of children living in a malaria endemic area.

Estimating physical splenic filtration of Plasmodium falciparum-infected red blood cells in malaria patients.

Cytoadhesion of Plasmodium falciparum parasitized red blood cells (pRBCs) has been implicated in the virulence of malaria infection. Cytoadhesive interactions are mediated by the protein family of Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1). The PfEMP1 family is under strong antibody and binding selection, resulting in extensive sequence and size variation of the extracellular domains. Here, we investigated cytoadhesion of pRBCs to CD36, a common receptor of P. falciparum field isolates, under dynamic flow conditions. Isogeneic parasites, predominantly expressing single PfEMP1 variants, were evaluated for binding to recombinant CD36 under dynamic flow conditions using microfluidic devices. We tested if PfEMP1 size (number of extracellular domains) or sequence variation affected the pRBC-CD36 interaction. Our analysis showed that clonal parasite variants varied ∼5-fold in CD36 rolling velocity despite extensive PfEMP1 sequence polymorphism. In addition, adherent pRBCs exhibited a characteristic hysteresis in rolling velocity at microvascular flow rates, which was accompanied by changes in pRBC shape and may represent important adaptations that favor stable binding.

Clonal variants of Plasmodium falciparum exhibit a narrow range of rolling velocities to host receptor CD36 under dynamic flow conditions.

The interplay between cellular and molecular determinants that lead to severe malaria in adults is unexplored. Here, we analyzed parasite virulence factors in an infected adult population in India and investigated whether severe malaria isolates impair endothelial protein C receptor (EPCR), a protein involved in coagulation and endothelial barrier permeability. Severe malaria isolates overexpressed specific members of the Plasmodium falciparum var gene/PfEMP1 (P. falciparum erythrocyte membrane protein 1) family that bind EPCR, including DC8 var genes that have previously been linked to severe pediatric malaria. Machine learning analysis revealed that DC6- and DC8-encoding var transcripts in combination with high parasite biomass were the strongest indicators of patient hospitalization and disease severity. We found that DC8 CIDRα1 domains from severe malaria isolates had substantial differences in EPCR binding affinity and blockade activity for its ligand activated protein C. Additionally, even a low level of inhibition exhibited by domains from two cerebral malaria isolates was sufficient to interfere with activated protein C-barrier protective activities in human brain endothelial cells. Our findings demonstrate an interplay between parasite biomass and specific PfEMP1 adhesion types in the development of adult severe malaria, and indicate that low impairment of EPCR function may contribute to parasite virulence.

Severe adult malaria is associated with specific PfEMP1 adhesion types and high parasite biomass.

Cell growth is a complex phenotype widely used in systems biology to gauge the impact of genetic and environmental perturbations. Due to the magnitude of genome-wide studies, resolution is often sacrificed in favor of throughput, creating a demand for scalable, time-resolved, quantitative methods of growth assessment. We present ODELAY (One-cell Doubling Evaluation by Living Arrays of Yeast), an automated and scalable growth analysis platform. High measurement density and single-cell resolution provide a powerful tool for large-scale multiparameter growth analysis based on the modeling of microcolony expansion on solid media. Pioneered in yeast but applicable to other colony forming organisms, ODELAY extracts the three key growth parameters (lag time, doubling time, and carrying capacity) that define microcolony expansion from single cells, simultaneously permitting the assessment of population heterogeneity. The utility of ODELAY is illustrated using yeast mutants, revealing a spectrum of phenotypes arising from single and combinatorial growth parameter perturbations.

One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY!

Gene regulatory and metabolic network models have been used successfully in many organisms, but inherent differences between them make networks difficult to integrate. Probabilistic Regulation Of Metabolism (PROM) provides a partial solution, but it does not incorporate network inference and underperforms in eukaryotes. We present an Integrated Deduced And Metabolism (IDREAM) method that combines statistically inferred Environment and Gene Regulatory Influence Network (EGRIN) models with the PROM framework to create enhanced metabolic-regulatory network models. We used IDREAM to predict phenotypes and genetic interactions between transcription factors and genes encoding metabolic activities in the eukaryote, Saccharomyces cerevisiae. IDREAM models contain many fewer interactions than PROM and yet produce significantly more accurate growth predictions. IDREAM consistently outperformed PROM using any of three popular yeast metabolic models and across three experimental growth conditions. Importantly, IDREAM's enhanced accuracy makes it possible to identify subtle synthetic growth defects. With experimental validation, these novel genetic interactions involving the pyruvate dehydrogenase complex suggested a new role for fatty acid-responsive factor Oaf1 in regulating acetyl-CoA production in glucose grown cells.

Article	Year
Ag nanowires coated with Ag/Pd alloy sheaths and their use as substrates for reversible absorption and desorption of hydrogen. Journal of the American Chemical Society\| PubMed ID: 15137739	2004
Single-crystal nanowires of platinum can be synthesized by controlling the reaction rate of a polyol process. Journal of the American Chemical Society\| PubMed ID: 15339165	2004
Amorphous Se: a new platform for synthesizing superparamagnetic colloids with controllable surfaces. Journal of the American Chemical Society\| PubMed ID: 15669838	2005
Polyol synthesis of platinum nanostructures: control of morphology through the manipulation of reduction kinetics. Angewandte Chemie (International ed. in English)\| PubMed ID: 15772941	2005
Microfluidic modeling of cell-cell interactions in malaria pathogenesis. PLoS pathogens\| PubMed ID: 17658948	2007
Microfluidic approaches to malaria pathogenesis. Cellular microbiology\| PubMed ID: 18754851	2008
Deformability limits of Plasmodium falciparum-infected red blood cells. Cellular microbiology\| PubMed ID: 19438513	2009
A microfluidic system to study cytoadhesion of Plasmodium falciparum infected erythrocytes to primary brain microvascularendothelial cells. Lab on a chip\| PubMed ID: 21743938	2011
Malaria evolution in South Asia: knowledge for control and elimination. Acta tropica\| PubMed ID: 22266213	2012
Estimating physical splenic filtration of Plasmodium falciparum-infected red blood cells in malaria patients. Cellular microbiology\| PubMed ID: 22892025	2012
Clonal variants of Plasmodium falciparum exhibit a narrow range of rolling velocities to host receptor CD36 under dynamic flow conditions. Eukaryotic cell\| PubMed ID: 24014767	2013
Severe adult malaria is associated with specific PfEMP1 adhesion types and high parasite biomass. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 27185931	2016
One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY! G3 (Bethesda, Md.)\| PubMed ID: 27856698	2017
Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast. PLoS computational biology\| PubMed ID: 28520713	2017

Thurston Herricks

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