This document describes a label-free method for cell counting using paramagnetic bead aggregation. When cells are lysed in a chaotropic solution, the released DNA causes paramagnetic beads to aggregate. The extent of aggregation correlates with the amount of DNA and cell number. This allows direct enumeration of cells from crude samples. The method is demonstrated by monitoring bacterial growth and obtaining white blood cell counts from whole blood samples, showing good agreement with standard methods. Specific cell types like CD4+ T cells can also be enumerated using bead-based immunocapture prior to the aggregation step. The method requires only inexpensive equipment and could provide an accessible alternative to more expensive cell counting techniques.
Method for physiologic phenotype characterization at the single-cell level in...Shashaanka Ashili
Intercellular heterogeneity is a key factor in a variety of core cellular processes including proliferation, stimulus response, carcinogenesis, and drug resistance. However, cell-to-cell variability studies at the single-cell level have been hampered by the lack of enabling experimental techniques. We present a measurement platform that features the capability to quantify oxygen consumption rates of individual, non-interacting and interacting cells
under normoxic and hypoxic conditions. It is based on real-time concentration measurements of metabolites of
interest by means of extracellular optical sensors in cell-isolating microwells of subnanoliter volume. We present the results of a series of measurements of oxygen consumption rates (OCRs) of individual non-interacting and interacting human epithelial cells. We measured the effects of cell-to-cell interactions by using the system’s capability to isolate two and three cells in a single well. The major advantages of the approach are: 1. ratiometric, intensity-based characterization of the metabolic phenotype at the single-cell level, 2. minimal invasiveness due to the distant positioning of sensors, and 3. ability to study the effects of cell-cell interactions on cellular respiration rates.
Polymerase Chain Reaction (PCR)-Based Sex Determination Using Unembalmed Huma...IOSR Journals
The strategy developed for sex determination in skeletal remains is to amplify the highly degraded DNA, by use of primers that span short DNA fragments. To determine sex of unembalmed human cadaveric skeletal fragments from Sokoto, North-western Nigeria, using Polymerase Chain Reaction (PCR). A single blind study of Polymerase Chain Reaction (PCR)-based sex determination using amelogenin gene and alphoid repeats primers on unembalmed human cadaveric skeletal fragments from Sokoto, North-western Nigeria, was undertaken. With amelogenin gene, genetic sex identification was achieved in four samples only. PCR Sensitivity = 40%, Specificity = 100%, Predictive value of positive test = 100%, Predictive value of negative test = 25%, False positive rate = 0%, False negative rate = 150%, Efficiency of test = 50%. Fisher’s exact probability test P = 1. Z-test: z-value = -1.0955, p>0.05; not statistically significant. With alphoid repeats primers, correct genetic sex identification was achieved in all the samples. PCR Sensitivity = 100%, Specificity = 0%, Predictive value of positive test = 100%, Predictive value of negative test = 0%, False positive rate = 0%, False negative rate = 0%, Efficiency of test = 100%. Fisher’s exact probability test P = 1. Z-test: z- and p values were invalid. The study, has demonstrated the applicability of PCR method of sex determination in unembalmed human skeletal fragments from Sokoto, Northwestern Nigeria. With amelogenin gene primers, correct genetic sex identification was achieved in four samples only. With alphoid repeats primers, correct genetic sex identification was achieved in all the samples. Therefore, alphoid repeats is more efficient and more reliable than amelogenin gene, in sex determination from unembalmed human skeletal fragments. This is the first known study determining the sex of unembalmed human skeletal fragments by means of PCR in Nigeria. There is need for further studies in Nigeria to complement the findings of this study.
3D culture in phenotypic screening : advantages, process changes and new tech...HCS Pharma
It was a real pleasure to be in the « High-Content and Phenotypic Screening » meeting in Cambridge. We were invited by our partner Molecular Devices to give a talk during the "User meeting Molecular Devices" about our vision of 3D culture in phenotypic screening and the impact of new technologies. We also presented a poster about "Neurotoxicity assay on 2D and 3D culture using High Content Screening technology".
To evaluate the Interaction of Mn(II), Fe(II), Co(II), Ni(II),Cu(II), Zn(II) And Cd(II) Mixed- Ligand Complexes of
cephalexin mono hydrate (antibiotics) And Furan-2-Carboxylic Acid To The Different DNA Sources. All the metal
complexes were observed to cleave the DNA. A difference in the bands of complexes .The cleavage efficiency of the
complexes compared with that of the control is due to their efficient DNA-binding ability and the other factors like
solubility and bond length between the metal and ligand may also increase the DNA-binding ability. The ligands
(Cephalexin mono hydrate (antibiotics) and Furan-2-Carboxylic acid and there newly synthesized metal complexes
shows good antimicrobial activities and Binding DNA , thus, can be used as a new drug of choice in the field of
pharmacy. And for formulating novel medicinal agents.
Analysis of Single-Cell Sequencing Data by CLC/Ingenuity: Single Cell Analysi...QIAGEN
Single-cell analysis is useful to study genetic heterogeneity between individual cells and can help in result interpretation by looking at the average behavior of a large number of cells. Applications include circulating tumor cells, cells from small biopsies and cells from in vitro fertilized embryos. In this slidedeck, we show how single cell next-generation sequencing data can be analyzed and what challenges needs to be overcome. One of the examples we use is single cell data from two colorectal cancer cell lines.
Method for physiologic phenotype characterization at the single-cell level in...Shashaanka Ashili
Intercellular heterogeneity is a key factor in a variety of core cellular processes including proliferation, stimulus response, carcinogenesis, and drug resistance. However, cell-to-cell variability studies at the single-cell level have been hampered by the lack of enabling experimental techniques. We present a measurement platform that features the capability to quantify oxygen consumption rates of individual, non-interacting and interacting cells
under normoxic and hypoxic conditions. It is based on real-time concentration measurements of metabolites of
interest by means of extracellular optical sensors in cell-isolating microwells of subnanoliter volume. We present the results of a series of measurements of oxygen consumption rates (OCRs) of individual non-interacting and interacting human epithelial cells. We measured the effects of cell-to-cell interactions by using the system’s capability to isolate two and three cells in a single well. The major advantages of the approach are: 1. ratiometric, intensity-based characterization of the metabolic phenotype at the single-cell level, 2. minimal invasiveness due to the distant positioning of sensors, and 3. ability to study the effects of cell-cell interactions on cellular respiration rates.
Polymerase Chain Reaction (PCR)-Based Sex Determination Using Unembalmed Huma...IOSR Journals
The strategy developed for sex determination in skeletal remains is to amplify the highly degraded DNA, by use of primers that span short DNA fragments. To determine sex of unembalmed human cadaveric skeletal fragments from Sokoto, North-western Nigeria, using Polymerase Chain Reaction (PCR). A single blind study of Polymerase Chain Reaction (PCR)-based sex determination using amelogenin gene and alphoid repeats primers on unembalmed human cadaveric skeletal fragments from Sokoto, North-western Nigeria, was undertaken. With amelogenin gene, genetic sex identification was achieved in four samples only. PCR Sensitivity = 40%, Specificity = 100%, Predictive value of positive test = 100%, Predictive value of negative test = 25%, False positive rate = 0%, False negative rate = 150%, Efficiency of test = 50%. Fisher’s exact probability test P = 1. Z-test: z-value = -1.0955, p>0.05; not statistically significant. With alphoid repeats primers, correct genetic sex identification was achieved in all the samples. PCR Sensitivity = 100%, Specificity = 0%, Predictive value of positive test = 100%, Predictive value of negative test = 0%, False positive rate = 0%, False negative rate = 0%, Efficiency of test = 100%. Fisher’s exact probability test P = 1. Z-test: z- and p values were invalid. The study, has demonstrated the applicability of PCR method of sex determination in unembalmed human skeletal fragments from Sokoto, Northwestern Nigeria. With amelogenin gene primers, correct genetic sex identification was achieved in four samples only. With alphoid repeats primers, correct genetic sex identification was achieved in all the samples. Therefore, alphoid repeats is more efficient and more reliable than amelogenin gene, in sex determination from unembalmed human skeletal fragments. This is the first known study determining the sex of unembalmed human skeletal fragments by means of PCR in Nigeria. There is need for further studies in Nigeria to complement the findings of this study.
3D culture in phenotypic screening : advantages, process changes and new tech...HCS Pharma
It was a real pleasure to be in the « High-Content and Phenotypic Screening » meeting in Cambridge. We were invited by our partner Molecular Devices to give a talk during the "User meeting Molecular Devices" about our vision of 3D culture in phenotypic screening and the impact of new technologies. We also presented a poster about "Neurotoxicity assay on 2D and 3D culture using High Content Screening technology".
To evaluate the Interaction of Mn(II), Fe(II), Co(II), Ni(II),Cu(II), Zn(II) And Cd(II) Mixed- Ligand Complexes of
cephalexin mono hydrate (antibiotics) And Furan-2-Carboxylic Acid To The Different DNA Sources. All the metal
complexes were observed to cleave the DNA. A difference in the bands of complexes .The cleavage efficiency of the
complexes compared with that of the control is due to their efficient DNA-binding ability and the other factors like
solubility and bond length between the metal and ligand may also increase the DNA-binding ability. The ligands
(Cephalexin mono hydrate (antibiotics) and Furan-2-Carboxylic acid and there newly synthesized metal complexes
shows good antimicrobial activities and Binding DNA , thus, can be used as a new drug of choice in the field of
pharmacy. And for formulating novel medicinal agents.
Analysis of Single-Cell Sequencing Data by CLC/Ingenuity: Single Cell Analysi...QIAGEN
Single-cell analysis is useful to study genetic heterogeneity between individual cells and can help in result interpretation by looking at the average behavior of a large number of cells. Applications include circulating tumor cells, cells from small biopsies and cells from in vitro fertilized embryos. In this slidedeck, we show how single cell next-generation sequencing data can be analyzed and what challenges needs to be overcome. One of the examples we use is single cell data from two colorectal cancer cell lines.
How to Make Awesome SlideShares: Tips & TricksSlideShare
Turbocharge your online presence with SlideShare. We provide the best tips and tricks for succeeding on SlideShare. Get ideas for what to upload, tips for designing your deck and more.
Content Cytotoxicity Studies of Colorectal Carcinoma Cells Using Printed Impe...journalBEEI
Monitoring the effectiveness of drugs on cancer cells is crucial for chemotherapeutics studies. In-vitro cell-based biosensors can be used as an alternative for characteristic studies of cells’ response to drugs. Cell-based sensors provide real-time measurements and require smaller sample volumes compared to conventional T-flask measurement methods. This paper presents a biosensor that detects in real-time, impedance variations of human colon cancer, HCT-116 cells when treated with anti-cancer agent, 5-Fluorouracil (5-FU). Two different extracellular matrix (ECM); polyaniline and gelatin were tested and evaluated in terms of attachment quality. Polyaniline was found to provide the best attachment for HCT-116 cells and was used for cytotoxicity studies. Cytokinetic behavior indicated that 5-FU inhibited HCT-116 cells at IC50 of 6.8 µg/mL. Trypan blue exclusion method for testing cell viability was used to validate the impedance measurements, where the cancer cell concentrations were reduced to ~35% when treated with 2.5 µg/mL, and 50% when treated with 6.8 µg/mL. The results generated by the microfabricated impedance biosensor are comparable to the Trypan blue method since both gave similar cell growth trend. It can be concluded that the impedance biosensor has potential to be used as an alternative method in drug testing applications.
A statistical framework for multiparameter analysis at the single cell levelShashaanka Ashili
Phenotypic characterization of individual cells provides crucial insights into intercellular heterogeneity and enables access to information that is unavailable from ensemble averaged, bulk cell analyses. Single-cell studies have attracted significant interest in recent years and spurred the development of a variety of commercially available and research-grade technologies. To quantify cell-to-cell variability of cell populations, we have developed an experimental platform for real-time measurements of oxygen consumption (OC) kinetics at the single-cell level. Unique challenges inherent to these single-cell measurements arise, and no existing data analysis
methodology is available to address them. Here we present a data processing and analysis method that addresses challenges encountered with this unique type of data in order to extract biologically relevant information. We applied the method to analyze OC profiles obtained with single cells of two different cell lines derived from metaplastic and dysplastic human Barrett’s esophageal epithelium. In terms of method development, three main challenges were considered for this heterogeneous dynamic system: (i) high levels of noise, (ii) the lack of a priori knowledge of single-cell dynamics, and (iii) the role of intercellular variability within and across cell types.
Several strategies and solutions to address each of these three challenges are presented. The features such as slopes, intercepts, breakpoint or change-point were extracted for every OC profile and compared across individual cells and cell types. The results demonstrated that the extracted features facilitated exposition of subtle differences between individual cells and their responses to
cell–cell interactions. With minor modifications, this method can be used to process and analyze
data from other acquisition and experimental modalities at the single-cell level, providing a valuable statistical framework for single-cell analysis.
1)patterns of genetic variability in human mitochondria show evidenc.pdfdeepakangel
1)patterns of genetic variability in human mitochondria show evidence for recombination have
provoked considerable argument and much correspondence concerning the quality of the data,
the nature of the analyses and the biological realism of mitochondrial recombination. While the
majority of evidence now points towards a lack of effective recombination, at least in humans,
the debate has highlighted how difficult the detection of recombination can be in genomes with
unusual mutation processes and complex demographic histories. A major difficulty is the lack of
consensus about how to measure linkage disequilibrium. I show that measures differ in the way
they treat data that are uninformative about recombination, and that when just those pairwise
comparisons that are informative about recombination are used, there is agreement between
different statistics. In this light, the significant negative correlation between linkage
disequilibrium and distance in at least some of the data sets is a real pattern that requires
explanation
2)The analysis of mitochondrial DNA (mtDNA) has been a potent tool in our understanding of
human evolution, owing to characteristics such as high copy number, apparent lack of
recombination, high substitution rate and maternal mode of inheritance. However, almost all
studies of human evolution based on mtDNA sequencing have been confined to the control
region, which constitutes less than 7% of the mitochondrial genome. These studies are
complicated by the extreme variation in substitution rate between sites, and the consequence of
parallel mutations causing difficulties in the estimation of genetic distance and making
phylogenetic inferences questionable. Most comprehensive studies of the human mitochondrial
molecule have been carried out through restriction-fragment length polymorphism analysis,
providing data that are ill suited to estimations of mutation rate and therefore the timing of
evolutionary events. Here, to improve the information obtained from the mitochondrial molecule
for studies of human evolution, we describe the global mtDNA diversity in humans based on
analyses of the complete mtDNA sequence of 53 humans of diverse origins. Our mtDNA data, in
comparison with those of a parallel study of the Xq13.3 region in the same individuals, provide a
concurrent view on human evolution with respect to the age of modern humans.
3)Nephropathy associated with BK virus has emerged as an important cause of allograft failure
in renal transplant recipients. Here we exploited a recently developed novel monocyte based
solid phase T cell selection system, in which monocytes are immobilized on solid support, for
antigen-specifi c T cell purifi cation. The underlying hypothesis of this new method is that
antigen-specifi c T cells recognize, bind their cognate antigens faster than non-specifi c T cells
and are concentrated on the surface after removing the non-adherent cells by washing. Moreover,
activated antigen-specifi c T cel.
Molecule Transport across Cell Membranes: Electrochemical Quantification at t...InsideScientific
In this webinar, Dr. Sabine Kuss will discuss the importance of transmembrane molecule exchange and how to detect and quantify membrane transport of molecules in cells.
Complex biological processes, such as the transport of molecules across cell membranes, are difficult to understand using purely biological methodologies. Investigating cellular transport processes is challenging, because of the highly complex chemical composition of cells and the diffusion of molecules in and around cells at low concentrations. The development and advancement of electroanalytical methods over the last two decades has enabled the monitoring of living cells and their interaction with the environment, including external stimuli, such as pharma-molecules.
This presentation emphasizes electrochemical and electrophysiological methods of detection and quantification but also makes a comparison to other bioanalytical approaches. Join us to discover a substantial diversity in methods used to monitor the transport of cell metabolites, crucial for cell survival, and pharmaceutical compounds, involved in cell characteristics such as drug resistance.
Key Topics Include:
- Understanding transmembrane molecule transport through bioanalytical methods
- Electrochemical approaches to monitor molecule transport across cell membranes
- What bioanalytical and especially electrochemical approaches can reveal
- Challenges associated with instrument limitations
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Empowering the Data Analytics Ecosystem: A Laser Focus on Value
The data analytics ecosystem thrives when every component functions at its peak, unlocking the true potential of data. Here's a laser focus on key areas for an empowered ecosystem:
1. Democratize Access, Not Data:
Granular Access Controls: Provide users with self-service tools tailored to their specific needs, preventing data overload and misuse.
Data Catalogs: Implement robust data catalogs for easy discovery and understanding of available data sources.
2. Foster Collaboration with Clear Roles:
Data Mesh Architecture: Break down data silos by creating a distributed data ownership model with clear ownership and responsibilities.
Collaborative Workspaces: Utilize interactive platforms where data scientists, analysts, and domain experts can work seamlessly together.
3. Leverage Advanced Analytics Strategically:
AI-powered Automation: Automate repetitive tasks like data cleaning and feature engineering, freeing up data talent for higher-level analysis.
Right-Tool Selection: Strategically choose the most effective advanced analytics techniques (e.g., AI, ML) based on specific business problems.
4. Prioritize Data Quality with Automation:
Automated Data Validation: Implement automated data quality checks to identify and rectify errors at the source, minimizing downstream issues.
Data Lineage Tracking: Track the flow of data throughout the ecosystem, ensuring transparency and facilitating root cause analysis for errors.
5. Cultivate a Data-Driven Mindset:
Metrics-Driven Performance Management: Align KPIs and performance metrics with data-driven insights to ensure actionable decision making.
Data Storytelling Workshops: Equip stakeholders with the skills to translate complex data findings into compelling narratives that drive action.
Benefits of a Precise Ecosystem:
Sharpened Focus: Precise access and clear roles ensure everyone works with the most relevant data, maximizing efficiency.
Actionable Insights: Strategic analytics and automated quality checks lead to more reliable and actionable data insights.
Continuous Improvement: Data-driven performance management fosters a culture of learning and continuous improvement.
Sustainable Growth: Empowered by data, organizations can make informed decisions to drive sustainable growth and innovation.
By focusing on these precise actions, organizations can create an empowered data analytics ecosystem that delivers real value by driving data-driven decisions and maximizing the return on their data investment.
Levelwise PageRank with Loop-Based Dead End Handling Strategy : SHORT REPORT ...Subhajit Sahu
Abstract — Levelwise PageRank is an alternative method of PageRank computation which decomposes the input graph into a directed acyclic block-graph of strongly connected components, and processes them in topological order, one level at a time. This enables calculation for ranks in a distributed fashion without per-iteration communication, unlike the standard method where all vertices are processed in each iteration. It however comes with a precondition of the absence of dead ends in the input graph. Here, the native non-distributed performance of Levelwise PageRank was compared against Monolithic PageRank on a CPU as well as a GPU. To ensure a fair comparison, Monolithic PageRank was also performed on a graph where vertices were split by components. Results indicate that Levelwise PageRank is about as fast as Monolithic PageRank on the CPU, but quite a bit slower on the GPU. Slowdown on the GPU is likely caused by a large submission of small workloads, and expected to be non-issue when the computation is performed on massive graphs.
Techniques to optimize the pagerank algorithm usually fall in two categories. One is to try reducing the work per iteration, and the other is to try reducing the number of iterations. These goals are often at odds with one another. Skipping computation on vertices which have already converged has the potential to save iteration time. Skipping in-identical vertices, with the same in-links, helps reduce duplicate computations and thus could help reduce iteration time. Road networks often have chains which can be short-circuited before pagerank computation to improve performance. Final ranks of chain nodes can be easily calculated. This could reduce both the iteration time, and the number of iterations. If a graph has no dangling nodes, pagerank of each strongly connected component can be computed in topological order. This could help reduce the iteration time, no. of iterations, and also enable multi-iteration concurrency in pagerank computation. The combination of all of the above methods is the STICD algorithm. [sticd] For dynamic graphs, unchanged components whose ranks are unaffected can be skipped altogether.
Adjusting primitives for graph : SHORT REPORT / NOTESSubhajit Sahu
Graph algorithms, like PageRank Compressed Sparse Row (CSR) is an adjacency-list based graph representation that is
Multiply with different modes (map)
1. Performance of sequential execution based vs OpenMP based vector multiply.
2. Comparing various launch configs for CUDA based vector multiply.
Sum with different storage types (reduce)
1. Performance of vector element sum using float vs bfloat16 as the storage type.
Sum with different modes (reduce)
1. Performance of sequential execution based vs OpenMP based vector element sum.
2. Performance of memcpy vs in-place based CUDA based vector element sum.
3. Comparing various launch configs for CUDA based vector element sum (memcpy).
4. Comparing various launch configs for CUDA based vector element sum (in-place).
Sum with in-place strategies of CUDA mode (reduce)
1. Comparing various launch configs for CUDA based vector element sum (in-place).
2. Paramagnetic beads have been extensively studied for their
unique magnetic properties9
and application to a wide array of
bioanalytical processes; these include immunoseparation,10
transportation,11
mixing,12
and the detection13,14
of select
analytes of interest. Recently, we reported the “pinwheel
effect”,8
which describes chaotropic-driven adsorption of DNA
onto paramagnetic silica beads in a quantitative manner.
Captured images of the induced bead−DNA aggregates
followed by image analysis (using a simple algorithm) allows
for direct quantification of DNA in crude biological samples.
The simplicity of the chemistry (guanidine + beads + sample),
the instrumentation (magnetic field + digital camera), and the
method (pipet + magnetize + capture image) make this a cost-
effective, low-tech method for quantifying DNA in microliter
samples with a picogram limit of detection. We showed
preliminary evidence for the potential to count WBCs in whole
blood, and this spawned a more in-depth exploration of the
capabilities of the pinwheel effect for cell counting.
In this report, we show that the same assay can be used to
monitor the growth of cultured cells using only a few
microliters of sample. We also demonstrate that leukocytes
can be directly enumerated in whole blood without labeling or
purification with an accuracy and precision that compares
favorably with Coulter counting. Finally, we make quantifica-
tion cell-specific by coupling pinwheel with immunomagnetic
cell capture, demonstrating that CD4+ T cells can be
enumerated with sufficient sensitivity and accuracy to monitor
HIV/AIDS patients. As such, the pinwheel assay represents a
new, label-free method for cell counting where the simple
protocol and cost-effective instrumentation provides a highly
accessible alternative to more expensive counting techniques.
■ METHODS AND MATERIALS
Reagents. MagneSil paramagnetic particles were purchased
from Promega (Madison, WI). GdnHCl was bought from MP
Biomedicals (Solon, OH). MES was bought from Acros
Organics. Tris base was bought from Fisher Scientific. EDTA
was bought from Sigma-Aldrich. Human SH-SY5Y cells and
mouse RAW 264.7 cells were obtained from ATCC. E. coli
BL21(DE3) and D29 bacteriophage were obtained from New
England Biolabs (Ipswich, MA). Whole blood samples were
donated by consenting donors. CD4 isolation kit was bought
from Life Technologies. All solutions were prepared in
Nanopure water (Barnstead/Thermolyne, Dubuque, IA).
Reagent Preparation. Thirty microliters of stock Magnesil
beads was washed once with deionized, distilled water
(Nanopure) followed by one wash with GdnHCl solution (8
M, 1× TE, adjusted to pH 6.1 with 100 mM MES) and
resuspended in 1 mL of GdnHCl solution to make the
suspension.
Microwell Fabrication, Assay Instrumentation, and
Magnetic Field Application. Details have been described
previously. The system, with a rotating magnetic field (RMF),
of the pinwheel assay for DNA quantification was employed for
cell counting without any modifications.15
Image Processing. A gray level threshold was set in the
images of magnetic beads and aggregates by an isodata
algorithm written in Mathematica software, which identifies
the pixels representing the beads and aggregates. The total
number of these pixels in the photograph without DNA is
defined as 100%, and as more DNA molecules are released
from cells, tighter aggregation evolves, corresponding to a
smaller percentage. The change of the percentage is defined as
degree of aggregation (DA). More DNA molecules result in
tighter bead aggregation and higher DA values.
Establishment of Calibration Curves. Samples were first
incubated with GdnHCl solution in 1:100 volume ratio at room
temperature for 30 min. The samples were then serially diluted
in GdnHCl solution to appropriate concentrations as shown in
the figures. Five microliters of diluted sample, 3 μL of bead
suspension, and 12 μL of GdnHCl were mixed and exposed to
the RMF for 5 min, after which three photographs of the beads
and aggregates were acquired for image analysis. The
calibration curve was generated by correlating the mean DA
value of three images for each diluted sample with the
corresponding final cell concentration in the pinwheel assay.
Microbial Growth Testing. E. coli strain BL21(DE3) was
cultured in 1000 mL of liquid LB medium and incubated at 37
°C. Samples (1 mL) were collected at hour intervals for 5 h.
The culture was split into two equal volumes at t = 3 h, and one
volume was treated with 0.1 mg/mL ampicillin. Cell counting
based on absorbance measurements at 600 nm was obtained
with a UV/Visible spectrophotomer (Beckman Coulter,
DU800) in a 1 mL plastic cuvette at room temperature.
White Blood Cell Counting for Unknown Samples.
Raw blood samples were first incubated with GdnHCl solution
in 1:100 volume ratio at room temperature for 30 min. The
samples were diluted by 2000 fold. Five μL of diluted sample, 3
μL of bead suspension, and 12 μL of GdnHCl were mixed and
exposed to the RMF for 5 min, after which photographs of the
beads and aggregates were acquired for image analysis.
Considering mixing sample and beads results in another 4-
fold dilution, the samples were diluted by 8000 fold from raw
blood to the pinwheel assay. The concentration of white blood
cells in blood was acquired by comparing DA value with the
calibration curve (Figure 4). For the samples with WBC count
lower than 4 × 103
per μL, a final 4000-fold dilution was
performed in the pinwheel assay, and more accurate results
were acquired because of an optimized dynamic range.
Immunomagnetic Separation of CD4+ T Cells from
Blood. CD4+ T cells were isolated by a Dynal T4 Quant kit
following its protocols. Briefly, whole blood was incubated and
rotated with CD14-coated beads for 10 min, followed by
another 10 min incubation and rotation with CD4-coated
beads. Samples were then washed three times with PBS buffer.
Enumeration of CD4+ T Cells with Hemocytometer.
Isolated CD4+ T cells were lysed by the lysis solution provided
in the Dynal T4 Quant kit. The lysed cells were stained with
Sternheimer−Malbin solution and loaded on a hemocytometer,
and the nuclei were counted using a conventional white light
microscope.
Enumeration of CD4+ T Cells with the Pinwheel
Assay. After immunomagnetic separation, the isolated CD4+
T cells were incubated in 100 μL of 8 M GdnHCl solutions for
30 min, and the solution was further diluted 20, 40, 80, and
160-fold with 8 M GdnHCl. These four aliquots were then
loaded into the pinwheel microwell following the same
procedure as white blood cell counting.
■ RESULTS AND DISCUSSION
Paramagnetic Bead Aggregation Enables Cell Enu-
meration. With the pinwheel effect, DNA adsorbs to silica-
coated paramagnetic beads under chaotropic conditions, and
driven by a rotating magnetic field (RMF), the beads are
intertwined by DNA and rapidly aggregate (in seconds to
minutes) (Figure 1A). The degree of aggregation correlates
Analytical Chemistry Article
dx.doi.org/10.1021/ac401402h | Anal. Chem. 2013, 85, 11233−1123911234
3. well with the concentration of DNA, allowing for fast DNA
quantification without the need of fluorescent labels.15
Owing
to the specificity of the chaotrope-driven DNA adsorption on
silica,16
bead aggregation induced by DNA released from the
cell lysate is unaffected by protein, lipid, and other cellular
components present at concentrations orders of magnitude
higher; this is the case for even a few cells (Figure 1B). Given
that each DNA-containing cell in a blood sample releases the
same mass of DNA (6.25 pg), the extent of bead aggregation
defines the number of cells in the sample. Figure 1 panels B2−
B4 show images of beads that have been aggregated by 13, 52,
and 195 pg of DNA, respectively. While the protein released
from 30 cells is ∼15 ng, it is noteworthy that augmenting the
solution with additional protein (BSA; to a final concentration
of 1 μg/μL) does not adversely affect aggregation.17
An inherent advantage of the chemistry that induces the
pinwheel effect (i.e., guanidine) is that it also lyses cells
effectively; thus, no additional reagents are required for direct
cell counting. A cell solution added to 8 M GdnHCl at a 1:100
volume ratio induces bead aggregation immediately following
vortexing, which is key to the pinwheel assay enabling the
enumeration of cells. The rapidity with which cell lysis occurs is
supported by the fact that aggregate formation (visually
detectable aggregates in seconds) does not improve with
longer incubation times (e.g., up to 60 min) (see Supporting
Information Figure S1). This yields a simple protocol for cell
enumeration: (a) lyse cells in 8 M GdnHCl to release DNA,
(b) bring the sample DNA concentration within the dynamic
range of the assay through sample dilution, (c) mix the sample
with silica-coated magnetic beads in a RMF to induce
aggregation, (d) capture digital images and process the images
through an algorithm to generate a % DA and, finally, (e)
compare resultant value to a standard curve to calculate cell
concentration (details are provided in the experimental
section). As DNA begins to entangle with the beads,15
small
bead aggregates evolve from the initial dispersed state, growing
through nucleation with other beads, allowing smaller
aggregates to coalesce into larger ones. The higher the DNA
concentration, the more aggressive the aggregate formation and
subsequent coalescing become. Overall, the beads experience a
transition from the dispersed state in the negative control (i.e.,
without DNA) to a condensed aggregation state with sufficient
DNA. Even with only a few cells, aggregation induced by
released DNA leads to a decrease of the total number of pixels
representing the beads and/or bead aggregates; this we refer to
as dark area.15
A threshold is set by an isodata algorithm15
to
separate the beads and/or aggregates from image background,
shown as the black line in the histogram (Figure 1C). The peak
area below the threshold stands for the dark area, and the
decrease of dark area represents the loss of dispersed beads due
to aggregation. Therefore, we define the decrease of dark area
that is normalized against the negative control as DA.
Correlating DNA concentration and DA generates a calibration
curve for DNA quantification. With each somatic cell
containing 6.25 pg DNA (discussed earlier), a simple
calculation allows for plotting DA against the number of cells
in a particular volume (typically 1 μL). Regardless of the source
of DNA, the higher the DNA concentration, the larger the DA.
This provides a quantitative correlation between the extent of
aggregation and the number of cells in a specific volume of
sample, for example, as in Figure 2.
Pinwheel assay standard curves for the enumeration of: (a)
eukaryotic cells (human WBCs and mouse cells), (b)
prokaryotic cells (E. coli), and (c) bacteriophage (D29) are
given in Figure 2. While not a “cell”, phage are virus-like
macromolecular assemblies of protein and nucleic acid, with an
intact genome of length of 49 × 103
base pairs. The DNA
extracted from this phage is double-stranded, and with a 49 kbp
length, a rough estimate of the length is ∼16 μm.18
As shown in
Figure 2, it is still capable of inducing aggregates, but it does so
with an effectiveness that is roughly an order of magnitude less
than E. coli, whose genome is 4.6 Mb. There is a 3 order of
Figure 1. Schematic of the pinwheel effect induced by lysed cells. (A) GdnHCl lyses the cells and drives the released DNA to adsorb on to silica-
coated paramagnetic beads, which form aggregates in a rotating magnetic field (RMF). Images of the aggregation are digitized, from which the initial
concentration of cells can be measured. (B) Photographs of the same amount of beads with different amounts of DNA that are equivalent to 0, 2, 8,
and 32 cells, respectively. Magnetic beads, which remain dispersed in RMF, form visually detectable aggregates within minutes upon mixture with
lysed human cells. (C) Gray level histogram of the four photographs. Three regions are identified as aggregates, dispersed beads, and background,
respectively, on the basis of the gray level value. The change of the histogram clearly illustrates the loss of dispersed beads and the formation of
aggregates.
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4. magnitude differential in the size of the E. coli DNA versus
mouse or human DNA. As the curve in Figure 2 (a semilog
plot) shifts from left to right, the sensitivity decreases over 3
orders of magnitude; not surprisingly, this roughly correlates
with the decrease in genome size with each cell type. For
human cells, ∼8 cells in 20 μL corresponds to 0.4 cells/μL and
a DNA concentration of 2.5 pg/μL. Despite this miniscule
mass, the induced aggregation is still visually detectable (Figure
1B), with the limit of detection (through image analysis)
approaching 0.1 cell/μL, that is, 2 cells in a total of 20 μL
(Figure 2). The concept that sensitivity is proportional to DNA
length is consistent with our previous observations15
and is
rationalized as longer strands of DNA induce bead aggregation
more effectively than shorter ones. As a result, each cell type
should be calibrated individually in order to acquire accurate
results. To further study the size dependence, the actual DNA
size distribution should be measured by other techniques such
as electrophoresis and correlated more quantitatively with the
sensitivity of the pinwheel assay.
Microbial Growth Testing with the Pinwheel Assay.
Accurate and quick determination of bacteria concentration is
essential in microbiology studies. To test the effectiveness of
measuring microbial growth with the pinwheel assay, E. coli was
cultured in media, and the time evolution of growth was
monitored by two methods: light scattering (spectrophotom-
etry at 600 nm) and the pinwheel assay. From the liquid
culture, 1 mL was sampled every hour, and after 3 h, the cells
were split, where half were dosed with buffer and the other half
with ampicillin (0.1 mg/mL). Monitoring the bacterial growth
conventionally by absorbance at 600 nm (Figure 3A), bacterial
cell doubling is apparent (from a 1 mL sample) by the increase
of cell number up to the 3 h point. However, addition of
ampicillin retards E. coli growth, and not only levels the growth
curve (i.e., no further doubling), but the addition of ampicillin
actually leads to a reduction in the bacterial concentration.19
Similar evaluation was carried out by pipetting 5 μL aliquots
from the growth medium into microwells containing GdnHCl
and paramagnetic beads. As given in Figure 3B, the results
acquired from the pinwheel assay also illustrate a comparable
trend of bacterial growth. For the sake of simplicity, DA is
directly compared to illustrate the change of cell concentration.
Because DA does not increase linearly with cell count (Figure
2), the difference of DA between “with ampicillin” and “without
ampicillin” does not appear to be as substantial as that of the
absorbance measurement. A closer match between the
absorbance measurement and the pinwheel assay can be
obtained by converting the signals in both methods to cell
counts.
Enumeration of White Blood Cells in Whole Blood.
WBCs (leukocytes) are critical components in our defense
against foreign bodies and infectious agents. The white blood
cell count can be a generic indicator of immune system status
and is useful for clinical testing, in particular with molecular
diagnostics. The pinwheel assay has the potential to provide a
simple and rapid method for determining of WBC count.
To generate the calibration curve for WBC counting, blood
samples were drawn from four normal patients on the day of
the analysis, and the WBC counts were determined by Coulter
counter. The samples were lysed with 8 M GdnHCl and serially
diluted for pinwheel analysis. Figure 4 illustrates the correlation
between degree of aggregation and WBC count after dilution.
Curves derived from 4.1, 10.1, and 20.3 (× 103
WBCs/μL
predilution) samples overlap well with each other. The 2.3 ×
103
WBCs/μL sample, however, reproducibly yields a higher
Figure 2. Calibration curve of the pinwheel assay for cell counting. DA
is correlated with cell (or phage) concentration and fitted into an
exponential model. The sensitivity decreases from human and mouse
cells (eukaryote) to phage D29 (although not a cell), which can be
attributed to the decrease of DNA length and genome size. The x-axis
is plotted in log scale in order to illustrate the difference of calibration
curves between human and mouse cells, which have similar genome
sizes. The solid line represents an exponential calibration function
fitted to the data at logarithmic scale; the shaded area and gray lines
show the 95% and 99% confidence bands (the same for all curve
fitting, unless otherwise noted).
Figure 3. Microbial growth testing of E. coli in the presence of
ampicillin. At the 3 h mark, half the cells were dosed with buffer, while
the other half were dosed with ampicillin, as growth monitoring
continued.
Figure 4. Calibration curve of the pinwheel assay for WBC counting
directly in raw blood samples. Four blood samples, with their WBC
counts determined with Coulter counter, were analyzed with the
pinwheel assay, as represented by ▽ = 2.3, Δ = 4.1, □ = 10.1, and • =
20.3 (× 103
per μL) with associated error bar denoting the standard
deviation of three experiments on each sample. The symbol • and the
corresponding error bar denote the mean and standard deviation of
the four samples.
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5. DA at the same [WBC]; this is because it falls outside the
dynamic range of the assay and, thus, results in a larger standard
deviation for the mean values above 40% DA. This may be
caused by components in the blood other than WBCs (e.g.,
proteins such as albumin, or a combination of protein and
divalent cations like Ca2+
), of which the concentration remains
relatively high after dilution due to the low initial WBC
concentration and low dilution factor. Elucidation of the
mechanism is currently ongoing and will be the topic of a
separate report when completed. As a result, only the region
above a DA of 60% is regarded as the effective calibration range
for WBC quantification. Therefore, DA values in that range
(>60%) must be obtained for accurate cell counting.
To evaluate the ability of the pinwheel process to enumerate
the WBCs in unknown samples, dilution is needed so that the
DA falls in the effective calibration range. By comparing the
measured value with the calibration curve, the WBC count can
be estimated following dilution ([WBC]dil), which is then
converted to the initial WBC count ([WBC]init) by multiplying
by the dilution factor. Given that the calibration curve covers
from 0.5 to 5 WBCs/μL, a 4000-fold dilution enables
quantification of blood samples with WBC count between
2000 and 20 000 per μL. Since the WBC count of adults
typically varies between 4000 and 11 000 per μL, a 4000-fold or
8000-fold dilution would be sufficient to cover the normal
range and to identify samples with abnormal WBC count.
To test accuracy of the pinwheel-derived WBC counting,
nine raw blood samples with unknown WBC counts were
acquired, lysed, and diluted appropriately. Three replicates were
performed on each sample, and the mean DA was compared to
the standard curve to determine initial WBC count. These
values were compared to those independently obtained by a
Coulter counter, and the results are given in Figure 5A. The
counts from both compare favorably for the samples with
[WBC]init ranging from 2 × 103
per μL to 14 × 103
per μL; this
covers the normal range for WBC count and suffices for
samples where there is a need to identify counts outside the
normal range (bracketed by the two dashed lines). Figure 5B
provides graphical representation of the excellent correlation
between the pinwheel results and those from Coulter counter
(R2
= 0.97).
Counting CD4+ T Cells with the Pinwheel Assay. While
effective for WBC counting, the pinwheel effect is generic
because the adsorption of DNA on silica is not specific to
genomic sequence; hence, subtyping of cells in a complex
mixture is not possible without invoking the use of a “selective”
step. We chose CD4+ T cells, a WBC subtype, as a model to
demonstrate that selectivity and pinwheel sensitivity could be
coupled in a powerful way. CD4+ T-cell levels are critical in
Figure 5. WBC counts of nine raw blood samples determined by the pinwheel assay are shown in (A) and compared with the results from Coulter
counter. (B) The WBC counts of the nine samples determined with the pinwheel assay correlate well with the results from Coulter counter. The
data points represent the mean results of three experiments on each sample, and the error bars denote the standard deviation. The solid blue line
represents a linear calibration function fitted to the data with R2
= 0.97, and the black dashed line shows y = x.
Figure 6. Immunomagnetic separation of CD4+ T cells from blood and the calibration curve for quantification. (A) Schematic of immunomagnetic
separation of CD4+ T cells from crude blood samples. Monocytes, which also express the CD4 antigen, are depleted prior to CD4+ T cells. (B)
Purified samples are serially diluted after lysis, and the calibration curve is established by correlating degree of aggregation with the CD4 count
determined by microscopy.
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6. assessing the progress of AIDS and also in monitoring anti-HIV
treatment. CD4+ T-cell quantitation is currently accomplished
using flow cytometry, where the obvious drawbacks are high
cost, high maintenance, and poor portability. A rapid,
substantially less expensive and less complex methodology for
CD4+ T-cell counting could be valuable, especially if point-of-
care applications are to be considered. One solution to this
involves a commercial immunomagnetic separation kit. This kit
exploits antiCD4+-coated magnetic beads for isolating CD4+ T
cells from blood, but also captures monocytes (they express
CD4). However, monocytes also express CD14 on their
surface,4
allowing for antiCD14-coated beads to deplete the
sample of monoctyes, prior to the capture of CD4+ T cells
(Figure 6A). In the protocol described by the manufacturer, the
captured CD4+ T cells are partially lysed so that their nuclei
can be released and enumerated with a hemocytometer under a
microscope after staining. While labor-intensive and, in some
ways, subjective, immunocapture with microscope-based
counting certainly provides a cost-effective alternative to flow
cytometry. Studies of normal and HIV-positive individuals have
shown a correlation coefficient of 0.97 for CD4+ cell levels
relative to values from hemacytometer.
To circumvent the microscopic counting of stained cells, we
substituted this step with the pinwheel assay. With the pinwheel
process, the isolated cells are completely lysed, and pinwheel
aggregation is induced by the released DNA, allowing for
quantification of cells. The correlation between DA and cell
concentration is illustrated in Figure 6B, which provides the
calibration curve to determine the CD4+ T-cell count in blood
samples. Since the enumeration of CD4+ T cells involves
preassay isolation of the cells, the effectiveness of this process
relies on the efficient and consistent CD4+ T-cell isolation. The
mean isolation yield that was observed (calculated by dividing
the microscopic cell count with the flow cytometry count of the
original sample) was found to be 91.5 ± 4.3% for four blood
samples when the blood samples were withdrawn within 24 h.
To evaluate the accuracy of the pinwheel assay, two aliquots of
purified cells were acquired from each unknown sample, with
one partially lysed for microscopy quantification and the other
completely lysed for the pinwheel assay. Comparison shows a
good correlation between the two methods with 13 patient
blood samples (see Supporting Information Figure S2), which
suggests that the pinwheel assay can, indeed, enumerate the
isolated cells accurately.
In the clinical setting, CD4+ T-cell count can be indicative of
the immune status of a patient. When the CD4+ T-cell count is
lower, along with other factors, it can represent the progress of
HIV infection; when the count is higher, it can indicate
recovery from immunodeficiency through decreased viral load.
The pinwheel CD4+ levels in 21 blood samples following
immunomagnetic separation were compared with the results
from flow cytometry (Figure 7A,C). The collective data is from
two sample groups from two sources (8 samples analyzed same
day as blood draw; 13 samples analyzed >24 h after blood
draw). A good correlation was observed between the
immunocapture−pinwheel assay and flow cytometry, when
the samples were analyzed within 24 h of the blood draw
(Figure 7A,B). Dramatically poorer correlation between the
pinwheel and flow cytometry methods was observed with
samples analyzed more than 24 h postdraw (Figure 7C). This
observation is consistent with the observation by Diagbouga et
al. that 31%−69% of blood samples exhibit more than a 20%
decrease of CD4 count after a 24 h delay,20
which directly
affects the accuracy of the pinwheel assay.
For HIV-infected patients, initiation of ART is determined by
a CD4+ T-cell count that drops below 350 cells/μL. What we
have demonstrated here is that, with the 21 whole blood
samples evaluated from HIV patients, the pinwheel assay
correctly categorized those determined by flow cytometry to be
above or below the 350 cells/μL cut off. Only one sample (one
Figure 7. Quantification of CD4+ T cells. The pinwheel result correlates well with flow cytometry when the post-drawn time of blood is less than 24
h, as shown in (A) and (B). For the samples with post-drawn time over 24 h, the accuracy of the pinwheel assay is compromised due to the
deterioration of sample quality, as shown in (C) and (D). The solid blue lines in (B) and (D) represent linear calibration functions, and the black
dashed lines show y = x. The gray dashed lines represent the threshold (350 cells per μL) that defines the starting time of ARV for HIV patients (for
(B), R2
= 0.997; for (D), R2
= 0.775). The arrows in (C) and (D) point to the only sample that generated a false result in the pinwheel assay.
Analytical Chemistry Article
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7. from the >24 h storage time group) was categorized as false
positive, and this point is labeled with a gray arrow in Figure
7D. Despite the asynchrony in the storage history of these
samples, this still represents a >95% correlation between the
immunocapture−pinwheel assay and flow cytometry. This is
remarkable and points to the obvious merit of a method that
does not require fluorescent reagents, microscopy, or
cytometric counting.
■ CONCLUSIONS
In conclusion, we have extended the application of the
pinwheel assay from nucleic acid quantification to cell counting,
and demonstrated (1) microbial growth testing, (2) cell
counting in a complex medium (WBC quantification in raw
blood), as well as (3) isolation and enumeration of a specific
subtype of cells from a mixture (CD4+ T cells). While we have
a simple methodology for generic cell counting, specificity was
brought to the method by coupling with immunocapture.
These examples show the versatility of the pinwheel assay (i.e.,
that the assay has the potential to be applied in various fields),
although we do not anticipate that the pinwheel assay will
replace all the conventional methods. As the aggregation of
magnetic particles only requires microliter volume of samples
and a digital camera as the detection modality, the pinwheel
assay could serve as a portable and cost-effective alternative to
conventional technologies for point-of-care applications.
One of the main advantages is that the pinwheel assay does
not require fluorescent labels and complex optics or expensive
instrumentation to enumerate cells. Fluorescence provides
accurate and sensitive quantification of analytes in various
applications, but the labels are often subject to photobleaching,
resulting in unstable optical properties, which increases the cost
for reagent storage and induces the need for repetitive
calibration. By avoiding fluorescent labels, the pinwheel assay
offers enhanced simplicity and cost-effectiveness compared to
conventional techniques, which are always desired when
applying a new technique in resource-limited regions. One of
the major drawbacks of the pinwheel assay is that the cells are
lysed after counting, and thus will not be available to other cell
analyses, which may be problematic if sample availability is
limited.
Day-to-day variability with the pinwheel method was low, a
likely result of the simplicity of the method. User-to-user
variability is more likely to be significant, but this can be
overcome by building a larger database for calibration of the
assay independent of the user. We are currently exploring
designs for integrating all of these processes on a single
microfluidic device to minimize hands-on operation and user-
to-user variabilitythis is essential for progressing toward a cell
counting device with sample-in-answer-out capability. Progress
on device development has been made in terms of enhancing
assay throughput21
and process automation.22
Successful
employment of the pinwheel assay in an integrated microfluidic
system will not only benefit basic biomedical research but also
offer capability to a wide range of clinical applications.
■ ASSOCIATED CONTENT
*S Supporting Information
Additional information as noted in the text. This material is
available free of charge via the Internet at http://pubs.acs.org.
■ AUTHOR INFORMATION
Corresponding Author
*E-mail: jpl5e@virginia.edu.
Present Addresses
■
Microlab Horizon, LLC, 705-D Dale Ave., Charlottesville, VA
22903 (J.L.)
▲
Salisbury University, 1101 Camden Ave., Salisbury, MD
21801 (A.D.)
Notes
The authors declare no competing financial interest.
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