Social-environmental phenotypes of rapid cystic fibrosis lung disease progression in adolescents and young adults living in the United States.

Background: Cystic fibrosis (CF) is a genetic disease but is greatly impacted by non-genetic (social/environmental and stochastic) influences. Some people with CF experience rapid decline, a precipitous drop in lung function relative to patient- and/or center-level norms. Those who experience rapid decline in early adulthood, compared to adolescence, typically exhibit less severe clinical disease but greater loss of lung function. The extent to which timing and degree of rapid decline are informed by social and environmental determinants of health (geomarkers) is unknown. Methods: A longitudinal cohort study was performed (24,228 patients, aged 6-21 years) using the U.S. CF Foundation Patient Registry. Geomarkers at the ZIP Code Tabulation Area level measured air pollution/respiratory hazards, greenspace, crime, and socioeconomic deprivation. A composite score quantifying social-environmental adversity was created and used in covariate-adjusted functional principal component analysis, which was applied to cluster longitudinal lung function trajectories. Results: Social-environmental phenotyping yielded three primary phenotypes that corresponded to early, middle, and late timing of peak decline in lung function over age. Geographic differences were related to distinct cultural and socioeconomic regions. Extent of peak decline, estimated as forced expiratory volume in 1 s of % predicted/year, ranged from 2.8 to 4.1 % predicted/year depending on social-environmental adversity. Middle decliners with increased social-environmental adversity experienced rapid decline 14.2 months earlier than their counterparts with lower social-environmental adversity, while timing was similar within other phenotypes. Early and middle decliners experienced mortality peaks during early adolescence and adulthood, respectively. Conclusion: While early decliners had the most severe CF lung disease, middle and late decliners lost more lung function. Higher social-environmental adversity associated with increased risk of rapid decline and mortality during young adulthood among middle decliners. This sub-phenotype may benefit from enhanced lung-function monitoring and personalized secondary environmental health interventions to mitigate chemical and non-chemical stressors.

Anatomical Diversity of the Adult Corticospinal Tract Revealed by Single-Cell Transcriptional Profiling.

The corticospinal tract (CST) forms a central part of the voluntary motor apparatus in all mammals. Thus, injury, disease, and subsequent degeneration within this pathway result in chronic irreversible functional deficits. Current strategies to repair the damaged CST are suboptimal in part because of underexplored molecular heterogeneity within the adult tract. Here, we combine spinal retrograde CST tracing with single-cell RNA sequencing (scRNAseq) in adult male and female mice to index corticospinal neuron (CSN) subtypes that differentially innervate the forelimb and hindlimb. We exploit publicly available datasets to confer anatomic specialization among CSNs and show that CSNs segregate not only along the forelimb and hindlimb axis but also by supraspinal axon collateralization. These anatomically defined transcriptional data allow us to use machine learning tools to build classifiers that discriminate between CSNs and cortical layer 2/3 and nonspinally terminating layer 5 neurons in M1 and separately identify limb-specific CSNs. Using these tools, CSN subtypes can be differentially identified to study postnatal patterning of the CST in vivo, leveraged to screen for novel limb-specific axon growth survival and growth activators in vitro, and ultimately exploited to repair the damaged CST after injury and disease.SIGNIFICANCE STATEMENT Therapeutic interventions designed to repair the damaged CST after spinal cord injury have remained functionally suboptimal in part because of an incomplete understanding of the molecular heterogeneity among subclasses of CSNs. Here, we combine spinal retrograde labeling with scRNAseq and annotate a CSN index by the termination pattern of their primary axon in the cervical or lumbar spinal cord and supraspinal collateral terminal fields. Using machine learning we have confirmed the veracity of our CSN gene lists to train classifiers to identify CSNs among all classes of neurons in primary motor cortex to study the development, patterning, homeostasis, and response to injury and disease, and ultimately target streamlined repair strategies to this critical motor pathway.

Neural valuation of rewards and punishments in posttraumatic stress disorder: a computational approach.

Posttraumatic stress disorder (PTSD) is associated with changes in fear learning and decision-making, suggesting involvement of the brain's valuation system. Here we investigate the neural mechanisms of subjective valuation of rewards and punishments in combat veterans. In a functional MRI study, male combat veterans with a wide range of posttrauma symptoms (N = 48, Clinician Administered PTSD Scale, CAPS-IV) made a series of choices between sure and uncertain monetary gains and losses. Activity in the ventromedial prefrontal cortex (vmPFC) during valuation of uncertain options was associated with PTSD symptoms, an effect which was consistent for gains and losses, and specifically driven by numbing symptoms. In an exploratory analysis, computational modeling of choice behavior was used to estimate the subjective value of each option. The neural encoding of subjective value varied as a function of symptoms. Most notably, veterans with PTSD exhibited enhanced representations of the saliency of gains and losses in the neural valuation system, especially in ventral striatum. These results suggest a link between the valuation system and the development and maintenance of PTSD, and demonstrate the significance of studying reward and punishment processing within subject.

Geometry of neural computation unifies working memory and planning.

Real-world tasks require coordination of working memory, decision-making, and planning, yet these cognitive functions have disproportionately been studied as independent modular processes in the brain. Here, we propose that contingency representations, defined as mappings for how future behaviors depend on upcoming events, can unify working memory and planning computations. We designed a task capable of disambiguating distinct types of representations. In task-optimized recurrent neural networks, we investigated possible circuit mechanisms for contingency representations and found that these representations can explain neurophysiological observations from the prefrontal cortex during working memory tasks. Our experiments revealed that human behavior is consistent with contingency representations and not with traditional sensory models of working memory. Finally, we generated falsifiable predictions for neural data to identify contingency representations in neural data and to dissociate different models of working memory. Our findings characterize a neural representational strategy that can unify working memory, planning, and context-dependent decision-making.

Results of the national biomonitoring program show persistent iodine deficiency in Israel.

BACKGROUND: Adequate iodine intake is essential for human health, for normal thyroid function, and for attainment of full intellectual potential in children. In light of Israel's lack of a mandatory salt fortification policy, heavy reliance on desalination and low iodine intake from dairy products and seafood, there is concern in Israel that the population is iodine deficient. Indeed, the first Israeli National Iodine Survey in 2016 found a median urinary iodine concentration (UIC) of 83 µg/L among school age children, falling below the WHO's adequacy range of 100-299 µg/L for children. METHODS: In the framework of the National Human Biomonitoring Program in Israel, spot urine samples and questionnaire data were collected from 166 healthy children aged 4-12 years in 2020-2021. Urinary iodine concentrations were measured at the Ministry of Health National Biomonitoring Laboratory, using mass spectrometry. An international comparison of median urinary iodine concentrations (UIC) was performed taking into consideration the levels of desalinated water per capita, and fortification policies. RESULTS: The overall median (interquartile range [IQR]) UIC was 80.1 µg/L (44.7-130.8 µg/L) indicating that the population's iodine status has not improved in the five years that have passed since inadequacy was first identified. When comparing 13 countries with population size above 150,000, whose desalinated water per capita was at least 1 m3, Israel and Lebanon were the only countries with median UIC below the WHO adequacy range. CONCLUSIONS: There is an urgent need for mandatory salt fortification in Israel. Based on our international comparison, we conclude that the potential impact of desalination on iodine intake can be compensated for using the implementation of salt fortification policy. This study highlights the critical need for public health surveillance of nutritional and environmental exposures using human biomonitoring, with emphasis on vulnerable populations such as pregnant women and children.

Biomechanical correlates of zygomaxillary-surface shape in papionin primates and the effects of hard-object feeding on mangabey facial form.

Extant African papioninans are distinguished from macaques by the presence of excavated facial fossae; however, facial excavation differs among taxa. Mangabeys (Cercocebus, Rungwecebus, and Lophocebus) exhibit fossae that invade the zygomatic forming pronounced suborbital fossae (SOFs). Larger-bodied Papio, Mandrillus, and Theropithecus have lateral rostral fossae with minimal/absent suborbital fossae. Because prior studies have shown that mangabeys exhibit adaptations to anterior dental loading (e.g., palatal retraction), it is plausible that mangabey SOFs represent structural accommodation to masticatory-system shape rather than facial allometry, as commonly hypothesized. We analyzed covariation between zygomaxillary-surface shape, masticatory-system shape, and facial size in 141 adult crania of Macaca fascicularis, Papio kindae, Cercocebus, and Lophocebus. These taxa represent the range of papionin SOF expression while minimizing size variation (narrow allometry). Masticatory-system landmarks (39) registered palate shape, bite points, masticatory muscle attachments, and the temporomandibular joint. Semilandmarks (450) captured zygomaxillary-surface shape. Following Procrustes superimposition with semilandmark sliding and principal components analyses, multivariate regression was used to explore allometry, and two-block partial least-squares analyses (within-configuration and separate-blocks) were used to examine covariation patterns. Scores on principal components 1-2 and the first partial least-square (PLS1) separate mangabeys from Macaca and Papio. Both zygomaxillary-surface shape and masticatory-system shape are correlated with size within taxa and facial morphotypes; however, regression distributions indicate morphotype shape differences are non-allometric. PLS1 accounts for ∼95% of shape covariance (p < 0.0001) and shows strong linear correlations (r-PLS = âˆ¼0.95, p < 0.0001) between blocks. Negative PLS1 scores in mangabeys reflect deep excavation of the suborbital malar surface, palatal retraction, and anterior displacement of jaw adductor muscles and the temporomandibular joint. Neither PC1 nor PLS1 scores ordinate specimens by facial size. Taken together, these results fail to support the allometric hypothesis but suggest that mangabey zygomaxillary morphology is closely linked with adaptations to hard-object feeding.

An improved method for measuring molar wear.

OBJECTIVES: Standard methods of recording occlusal dental wear are problematic in that they either do not allow for individual variation of wear or are not designed to allow for comparisons of wear patterns. In this article, we (a) present a novel method for recording and analyzing molar wear, and (b) evaluate this method in light of existing methods. MATERIALS AND METHODS: Eighty-two lower mandibular first molars from two regions (medieval Denmark, prehistoric Ohio Valley) were used to assess the method for replicability (intra and inter observer error) and accuracy (comparison to established methods of recording wear). Wear scores were recorded using the MolWear Android App (Beta) by both authors, and established methods of Smith and Scott by the first author. Intraobserver and interobserver error and comparison of the three methods were compared using Spearman's correlation coefficients. RESULTS: The MolWear method presented high intraobserver (r = 0.985, p < 0.01) and interobserver (r = 0.978, p < 0.01) repeatability. Compared to other methods, the method was strongly correlated with Smith (r = 0.962, p < 0.01) and Smith (r = 0.891, p < 0.01). DISCUSSION: The new MolWear method provides an improved way of measuring occlusal molar wear. This method bridges the gaps between established methods, performing comparatively while capturing more information about the distribution of wear in addition to the extent of wear. This method should be used for research comparing interpopulation or intrapopulation quantity of dental wear. While designed for a bioarchaeological population, this method could extend to any Y5 molar including nonhuman primates and hominins.

PsychRNN: An Accessible and Flexible Python Package for Training Recurrent Neural Network Models on Cognitive Tasks.

Task-trained artificial recurrent neural networks (RNNs) provide a computational modeling framework of increasing interest and application in computational, systems, and cognitive neuroscience. RNNs can be trained, using deep-learning methods, to perform cognitive tasks used in animal and human experiments and can be studied to investigate potential neural representations and circuit mechanisms underlying cognitive computations and behavior. Widespread application of these approaches within neuroscience has been limited by technical barriers in use of deep-learning software packages to train network models. Here, we introduce PsychRNN, an accessible, flexible, and extensible Python package for training RNNs on cognitive tasks. Our package is designed for accessibility, for researchers to define tasks and train RNN models using only Python and NumPy, without requiring knowledge of deep-learning software. The training backend is based on TensorFlow and is readily extensible for researchers with TensorFlow knowledge to develop projects with additional customization. PsychRNN implements a number of specialized features to support applications in systems and cognitive neuroscience. Users can impose neurobiologically relevant constraints on synaptic connectivity patterns. Furthermore, specification of cognitive tasks has a modular structure, which facilitates parametric variation of task demands to examine their impact on model solutions. PsychRNN also enables task shaping during training, or curriculum learning, in which tasks are adjusted in closed-loop based on performance. Shaping is ubiquitous in training of animals in cognitive tasks, and PsychRNN allows investigation of how shaping trajectories impact learning and model solutions. Overall, the PsychRNN framework facilitates application of trained RNNs in neuroscience research.

Confluence of Timing and Reward Biases in Perceptual Decision-Making Dynamics.

Although the decisions of our daily lives often occur in the context of temporal and reward structures, the impact of such regularities on decision-making strategy is poorly understood. Here, to explore how temporal and reward context modulate strategy, we trained 2 male rhesus monkeys to perform a novel perceptual decision-making task with asymmetric rewards and time-varying evidence reliability. To model the choice and response time patterns, we developed a computational framework for fitting generalized drift-diffusion models, which flexibly accommodate diverse evidence accumulation strategies. We found that a dynamic urgency signal and leaky integration, in combination with two independent forms of reward biases, best capture behavior. We also tested how temporal structure influences urgency by systematically manipulating the temporal structure of sensory evidence, and found that the time course of urgency was affected by temporal context. Overall, our approach identified key components of cognitive mechanisms for incorporating temporal and reward structure into decisions.SIGNIFICANCE STATEMENT In everyday life, decisions are influenced by many factors, including reward structures and stimulus timing. While reward and timing have been characterized in isolation, ecologically valid decision-making involves a multiplicity of factors acting simultaneously. This raises questions about whether the same decision-making strategy is used when these two factors are concurrently manipulated. To address these questions, we trained rhesus monkeys to perform a novel decision-making task with both reward asymmetry and temporal uncertainty. In order to understand their strategy and hint at its neural mechanisms, we used the new generalized drift diffusion modeling framework to model both reward and timing mechanisms. We found two of each reward and timing mechanisms are necessary to explain our data.

Distributed neural representation of saliency controlled value and category during anticipation of rewards and punishments.

An extensive literature from cognitive neuroscience examines the neural representation of value, but interpretations of these existing results are often complicated by the potential confound of saliency. At the same time, recent attempts to dissociate neural signals of value and saliency have not addressed their relationship with category information. Using a multi-category valuation task that incorporates rewards and punishments of different nature, we identify distributed neural representation of value, saliency, and category during outcome anticipation. Moreover, we reveal category encoding in multi-voxel blood-oxygen-level-dependent activity patterns of the vmPFC and the striatum that coexist with value signals. These results help clarify ambiguities regarding value and saliency encoding in the human brain and their category independence, lending strong support to the neural "common currency" hypothesis. Our results also point to potential novel mechanisms of integrating multiple aspects of decision-related information.

Image-Based Phenotypic Screening with Human Primary T Cells Using One-Dimensional Imaging Cytometry with Self-Tuning Statistical-Gating Algorithms.

The parallel microfluidic cytometer (PMC) is an imaging flow cytometer that operates on statistical analysis of low-pixel-count, one-dimensional (1D) line scans. It is highly efficient in data collection and operates on suspension cells. In this article, we present a supervised automated pipeline for the PMC that minimizes operator intervention by incorporating multivariate logistic regression for data scoring. We test the self-tuning statistical algorithms in a human primary T-cell activation assay in flow using nuclear factor of activated T cells (NFAT) translocation as a readout and readily achieve an average Z' of 0.55 and strictly standardized mean difference of 13 with standard phorbol myristate acetate/ionomycin induction. To implement the tests, we routinely load 4 µL samples and can readout 3000 to 9000 independent conditions from 15 mL of primary human blood (buffy coat fraction). We conclude that the new technology will support primary-cell protein-localization assays and "on-the-fly" data scoring at a sample throughput of more than 100,000 wells per day and that it is, in principle, consistent with a primary pharmaceutical screen.

POSTTRAUMATIC STRESS SYMPTOMS AND AVERSION TO AMBIGUOUS LOSSES IN COMBAT VETERANS.

BACKGROUND: Psychiatric symptoms typically cut across traditional diagnostic categories. In order to devise individually tailored treatments, there is a need to identify the basic mechanisms that underlie these symptoms. Behavioral economics provides a framework for studying these mechanisms at the behavioral level. Here, we utilized this framework to examine a widely ignored aspect of trauma-related symptomatology-individual uncertainty attitudes-in combat veterans with and without posttraumatic stress disorder (PTSD). METHODS: Fifty-seven combat veterans, including 30 with PTSD and 27 without PTSD, completed a risk and ambiguity decision-making task that characterizes individual uncertainty attitudes, distinguishing between attitudes toward uncertain outcomes with known ("risk") and unknown ("ambiguity") probabilities, and between attitudes toward uncertain gains and uncertain losses. Participants' choices were used to estimate risk and ambiguity attitudes in the gain and loss domains. RESULTS: Veterans with PTSD were more averse to ambiguity, but not risk, compared to veterans without PTSD, when making choices between possible losses, but not gains. The degree of aversion was associated with anxious arousal (e.g., hypervigilance) symptoms, as well as with the degree of combat exposure. Moreover, ambiguity attitudes fully mediated the association between combat exposure and anxious arousal symptoms. CONCLUSIONS: These results provide a foundation for prospective studies of the causal association between ambiguity attitudes and trauma-related symptoms, as well as etiologic studies of the neural underpinnings of these behavioral outcomes. More generally, these results demonstrate the potential of neuroeconomic and behavioral economic techniques for devising objective and incentive-compatible diagnostic tools, and investigating the etiology of psychiatric disorders.

Quantitation of Mitochondrial DNA Deletions Via Restriction Digestion/Long-Range Single-Molecule PCR.

Quantification of deletions in mtDNA is a long-standing problem in mutational analysis. We describe here an approach that combines the power of single-molecule PCR of the entire mitochondrial genome with the enrichment of the deletions by restriction digestion. This approach is indispensable if information about wide range of deletion types in a sample is critical, such as in studies concerning distribution of deletion breakpoints (as opposed to approaches where fraction of a single deletion or a limited set of deletions is used as a proxy for total deletion load). Because deletions in a sample are quantified almost exhaustively, the other important application of this approach involves studies where only small amounts of tissue, such as biopsies, are available.

Scope of practice of optometrists working in the UK Hospital Eye Service: a national survey.

PURPOSE: The role of the optometrist in the Hospital Eye Service (HES) has undergone significant development in recent years to include extended areas of clinical practice more traditionally undertaken by ophthalmologists, commensurate with a growing demand for increased capacity in ophthalmic services. In this report, we present the findings from a national survey of the scope of practice of optometrists working in the UK HES. METHODS: A survey was designed to incorporate questions on the provision of core services before seeking detailed information on the scope of practice within extended roles to include: ophthalmic sub-specialist areas where optometrists currently practice; the undertaking of specific procedures within these services; the relative autonomy of practice within these extended roles; and the training and accreditation requirements for working within extended roles. SurveyMonkey was used to disseminate the survey to the head of optometry in 79 HES units throughout the UK. RESULTS: Responses were received from 70 of the 79 (89%) survey invitations. A substantial majority of respondents (N = 67/70, 96%) indicated that optometrists undertook extended roles. Glaucoma is the leading extended role service provided by optometrists (92% of respondents providing extended role services), with roles in macula (71%), medical retina/diabetes (67%), cataract (55%) and corneal services (55%) also being relatively common. A wide variety of clinical procedures or interventions are undertaken as part of these services, which for a small number of optometrists now also includes the undertaking of specific laser procedures. There is evidence for a significant degree of autonomy within these extended roles. The primary mode of training is an 'apprentice' model, incorporating sessions worked under supervision in ophthalmology clinics. Methods of accreditation for optometric participation in extended role services are varied. CONCLUSIONS: While optometrists working within the UK HES continue to undertake the traditional clinical roles of refraction, clinically necessary contact lenses, and low vision rehabilitation, it is clear that these professionals now undertake a wide range of extended clinical roles, with a transformed scope of practice now incorporating diverse roles traditionally undertaken by medical practitioners.

Image-based cell-resolved screening assays in flow.

A parallel microfluidic cytometer (PMC) is based on a one-dimensional (1D) scanning detector, a parallel array of flow channels, and new multiparameter analysis algorithms that operate on low-pixel-count 1D images. In this article, we explore a series of image-based live- and fixed-cell screening assays, including two NF-kB nuclear translocations and T-cell capping. We then develop a new multiparametric linear weighted classifier that achieves a Z' factor sufficient for scaled pharmaceutical discovery with Jurkat cells in suspension. We conclude that the PMC should have the throughput and statistical power to permit a new capability for image-based high-sample-number pharmaceutical screening with suspension samples.

Intracellular protein and nucleic acid measured in eight cell types using deep-ultraviolet mass mapping.

We present measurements by deep-ultraviolet mass mapping of nucleic acid (NA) and protein for five commonly cultured and three primary cell types. The dry mass distribution at submicron resolution was determined on a single-cell basis for 250-500 cells from each of these types. Since the method carries a direct reference to a spectrophotometric standard (molar extinction coefficient), we are able to calibrate the absolute weight distributions both on a cell-to-cell basis within each type and across types. We also provide a calibration in absolute mass units for fluorescence-based measurements (flow cytometry and fluorescence microscopy). As might be expected the cultured cell lines show a high concentration of nucleic acids in the nuclear compartment, much larger than the genomic 2C number even in the G1 stage. The whole-cell nucleic-acid/protein ratio was found to be a characteristic of cell lines that persists independent of cell cycle and, as a result, this ratio has some value for phenotyping. Primary chicken red blood cells (cRBC), often used as a cytometry standard, were determined to have a nuclear-isolated nucleic acid content much closer to the genomic number than the cultured cell lines (cRBC: 3.00 pg total NA, 2.30 pg DNA, and 0.70 pg RNA). The individual blastomeres (n = 54) from mouse embryos at eight-cell stage were measured and found to vary by more than a factor or two in total protein and nucleic acid content (0.8-2.3 ng total protein, 70-150 pg total NA). The ratio of nucleic acid to protein was more nearly constant for each blastomere from a particular embryo and this ratio was found to be an identifying characteristic that varies from embryo to embryo obtained from a single flushing of a mouse.

Using molecular mechanics to predict bulk material properties of fibronectin fibers.

The structural proteins of the extracellular matrix (ECM) form fibers with finely tuned mechanical properties matched to the time scales of cell traction forces. Several proteins such as fibronectin (Fn) and fibrin undergo molecular conformational changes that extend the proteins and are believed to be a major contributor to the extensibility of bulk fibers. The dynamics of these conformational changes have been thoroughly explored since the advent of single molecule force spectroscopy and molecular dynamics simulations but remarkably, these data have not been rigorously applied to the understanding of the time dependent mechanics of bulk ECM fibers. Using measurements of protein density within fibers, we have examined the influence of dynamic molecular conformational changes and the intermolecular arrangement of Fn within fibers on the bulk mechanical properties of Fn fibers. Fibers were simulated as molecular strands with architectures that promote either equal or disparate molecular loading under conditions of constant extension rate. Measurements of protein concentration within micron scale fibers using deep ultraviolet transmission microscopy allowed the simulations to be scaled appropriately for comparison to in vitro measurements of fiber mechanics as well as providing estimates of fiber porosity and water content, suggesting Fn fibers are approximately 75% solute. Comparing the properties predicted by single molecule measurements to in vitro measurements of Fn fibers showed that domain unfolding is sufficient to predict the high extensibility and nonlinear stiffness of Fn fibers with surprising accuracy, with disparately loaded fibers providing the best fit to experiment. This work shows the promise of this microstructural modeling approach for understanding Fn fiber properties, which is generally applicable to other ECM fibers, and could be further expanded to tissue scale by incorporating these simulated fibers into three dimensional network models.

Deep ultraviolet mapping of intracellular protein and nucleic acid in femtograms per pixel.

By using imaging spectrophotometry with paired images in the 200- to 280-nm wavelength range, we have directly mapped intracellular nucleic acid and protein distributions across a population of Chinese hamster ovary (CHO-K1) cells. A broadband 100× objective with a numerical aperture of 1.2 NA (glycerin immersion) and a novel laser-induced-plasma point source generated high-contrast images with short (∼100 ms) exposures and a lateral resolution nearing 200 nm that easily resolves internal organelles. In a population of 420 CHO-K1 cells and 477 nuclei, we found a G1 whole-cell nucleic acid peak at 26.6 pg, a nuclear-isolated total nucleic acid peak at 11.4 pg, and, as inferred by RNase treatment, a G1 total DNA mass of 7.4 pg. At the G1 peak, we found a whole-cell protein mass of 95.6 pg, and a nuclear-isolated protein mass of 39.3 pg. An algorithm for protein quantification that senses peptide-bond (220-nm) absorbance was found to have a higher signal-to-noise ratio and to provide more reliable nucleic acid and protein determinations when compared to more classical 280/260-nm algorithms when used for intracellular mass mapping. Using simultaneous imaging with common nuclear stains (Hoechst 33342, Syto-14, and Sytox Orange), we have compared staining patterns to deep-UV images of condensed chromatin and have confirmed bias of these common nuclear stains related to nuclear packaging. The approach allows absolute mass measurements with no special sample preparation or staining. It can be used in conjunction with normal fluorescence microscopy and with relatively modest modification of the microscope.

Parallel imaging microfluidic cytometer.

By adding an additional degree of freedom from multichannel flow, the parallel microfluidic cytometer (PMC) combines some of the best features of fluorescence-activated flow cytometry (FCM) and microscope-based high-content screening (HCS). The PMC (i) lends itself to fast processing of large numbers of samples, (ii) adds a 1D imaging capability for intracellular localization assays (HCS), (iii) has a high rare-cell sensitivity, and (iv) has an unusual capability for time-synchronized sampling. An inability to practically handle large sample numbers has restricted applications of conventional flow cytometers and microscopes in combinatorial cell assays, network biology, and drug discovery. The PMC promises to relieve a bottleneck in these previously constrained applications. The PMC may also be a powerful tool for finding rare primary cells in the clinic. The multichannel architecture of current PMC prototypes allows 384 unique samples for a cell-based screen to be read out in ∼6-10 min, about 30 times the speed of most current FCM systems. In 1D intracellular imaging, the PMC can obtain protein localization using HCS marker strategies at many times for the sample throughput of charge-coupled device (CCD)-based microscopes or CCD-based single-channel flow cytometers. The PMC also permits the signal integration time to be varied over a larger range than is practical in conventional flow cytometers. The signal-to-noise advantages are useful, for example, in counting rare positive cells in the most difficult early stages of genome-wide screening. We review the status of parallel microfluidic cytometry and discuss some of the directions the new technology may take.