There is a growing appreciation of the extent of transcriptome variation across individual cells of the same cell type. While expression variation may be a byproduct of, for example, dynamic or homeostatic processes, here we consider whether single‐cell molecular variation per se might be crucial for population‐level function. Under this hypothesis, molecular variation indicates a diversity of hidden functional capacities within an ensemble of “identical” cells, and this functional diversity facilitates collective behavior that would be inaccessible to a homogenous (...) population. In reviewing this topic, we explore possible functions that might be carried by a heterogeneous ensemble of cells; however, this question has proven difficult to test, both because methods to manipulate molecular variation are limited and because it is complicated to define, and measure, population‐level function. We consider several possible methods to further pursue the hypothesis that “variation is function” through the use of comparative analysis and novel experimental techniques. (shrink)

Tissues contain complex populations of cells. Like countries, which are comprised of mixed populations of people, tissues are not homogeneous. Gene expression studies that analyze entire populations of cells from tissues as a mixture are blind to this diversity. Thus, critical information is lost when studying samples rich in specialized but diverse cells such as tumors, iPS colonies, or brain tissue. High throughput methods are needed to address, model and understand the constitutive and stochastic differences between individual cells. Here, we (...) describe microfluidics technologies that utilize a combination of molecular biology and miniaturized labs on chips to study gene expression at the single cell level. We discuss how the characterization of the transcriptome of each cell in a sample will open a new field in gene expression analysis, population transcriptomics, that will change the academic and biomedical analysis of complex samples by defining them as quantified populations of single cells. (shrink)

Transcriptional networks regulate cell fate decisions, which occur at the level of individual cells. However, much of what we know about their structure and function comes from studies averaging measurements over large populations of cells, many of which are functionally heterogeneous. Such studies conceal the variability between cells and so prevent us from determining the nature of heterogeneity at the molecular level. In recent years, many protocols and platforms have been developed that allow the high throughput analysis of gene (...) expression in single cells, opening the door to a new era of biology. Here, we discuss the need for single cell gene expression analysis to gain deeper insights into the transcriptional control of cell fate decisions, and consider the insights it has provided so far into transcriptional regulatory networks in development. (shrink)

A recent single cell mRNA sequencing study by Dueck et al. compares neuronal transcriptomes to the transcriptomes of adipocytes and cardiomyocytes. Single cell ‘omic approaches such as those used by the authors are at the leading edge of molecular and biophysical measurement. Many groups are currently employing single cell sequencing approaches to understand cellular heterogeneity in cancer and during normal development. These single cell approaches also are beginning to address long‐standing questions regarding nervous system diversity. Beyond an innate interest in (...) cataloging cell type diversity in the brain, single cell neuronal diversity has important implications for neurotypic neural circuit function and for neurological disease. Herein, we review the authors’ methods and findings, which most notably include evidence of unique expression profiles in some single neurons. (shrink)

Genetic epidemiology is a rapidly advancing field due to the recent availability of large amounts of omics data. In recent years, it has become possible to obtain omics information at the single‐cell level, so genetic epidemiological models need to be updated to integrate with single‐cell expression data. In this perspective paper, we propose a cell population‐based framework for genetic epidemiology in the single‐cell era. In this framework, genetic diversity influences phenotypic diversity through the diversity of cell population (...) profiles, which are defined as high‐dimensional probability distributions of the state spaces of biomolecules of each omics layer. We discuss how biomolecular experimental measurement data can capture the different properties of this distribution. In particular, single‐cell data constitute a sample from this population distribution where only some coordinate values are observable. From a data analysis standpoint, we introduce methodology for feature extraction from cell population profiles. Finally, we discuss how this framework can be applied not only to genetic epidemiology but also to systems biology. (shrink)

Mapping the paths that stem and progenitor cells take en route to differentiate and elucidating the underlying molecular controls are key goals in developmental and stem cell biology. However, with population level analyses it is difficult − if not impossible − to define the transition states and lineage trajectory branch points within complex developmental lineages. Single‐cell RNA‐sequencing analysis can discriminate heterogeneity in a population of cells and even identify rare or transient intermediates. In this review, we propose that (...) using these data, one can infer the lineage trajectories of individual stem cells and identify putative branch points. Clonal lineage tracing of stem cells allows one to define the outcome of differentiation. Integrating these single cell‐based approaches provides a robust strategy for establishing and testing models of how an individual stem cell changes through time to differentiate and self‐renew. (shrink)

Through statistical analysis of datasets describing single cell shape following systematic gene depletion, we have found that the morphological landscapes explored by cells are composed of a small number of attractor states. We propose that the topology of these landscapes is in large part determined by cell‐intrinsic factors, such as biophysical constraints on cytoskeletal organization, and reflects different stable signaling and/or transcriptional states. Cell‐extrinsic factors act to determine how cells explore these landscapes, and the topology of the landscapes themselves. (...) Informational stimuli primarily drive transitions between stable states by engaging signaling networks, while mechanical stimuli tune, or even radically alter, the topology of these landscapes. As environments fluctuate, the topology of morphological landscapes explored by cells dynamically adapts to these fluctuations. Finally we hypothesize how complex cellular and tissue morphologies can be generated from a limited number of simple cell shapes. (shrink)

Multigene delivery and expression systems are emerging as key technologies for many applications in contemporary biology. We have developed new methods for multigene delivery and expression in eukaryotic hosts for a variety of applications, including production of protein complexes for structural biology and drug development, provision of multicomponent protein biologics, and cell‐based assays. We implemented tandem recombineering to facilitate rapid generation of multicomponent gene expression constructs for efficient transformation of mammalian cells, resulting in homogenous cell populations. Analysis of multiple (...) parameters in living cells may require co‐expression of fluorescently tagged sensors simultaneously in a single cell, at defined and ideally controlled ratios. Our method enables such applications by overcoming currently limiting challenges.Here, we review recent multigene delivery and expression strategies and their exploitation in mammalian cells. We discuss applications in drug discovery assays, interaction studies, and biologics production, which may benefit in the future from our novel approach. (shrink)

When we perceive the external world, our brain has to deal with the incompleteness and uncertainty associated with sensory inputs, memory and prior knowledge. In theoretical neuroscience probabilistic approaches have received a growing interest recently, as they account for the ability to reason with incomplete knowledge and to efficiently describe perceptive and behavioral tasks. How can the probability distributions that need to be estimated in these models be represented and processed in the brain, in particular at the single cell level? (...) We consider the basic function carried out by photoreceptor cells which consists in detecting the presence or absence of light. We give a system-level understanding of the process of phototransduction based on a bayesian formalism: we show that the process of phototransduction is equivalent to a temporal probabilistic inference in a Hidden Markov Model (HMM), for estimating the presence or absence of light. Thus, the biochemical mechanisms of phototransduction underlie the estimation of the current state probability distribution of the presence of light. A classical descriptive model describes the interactions between the different molecular messengers, ions, enzymes and channel proteins occurring within the photoreceptor by a set of nonlinear coupled differential equations. In contrast, the probabilistic HMM model is described by a discrete recurrence equation. It appears that the binary HMM has a general solution in the case of constant input. This allows a detailed analysis of the dynamics of the system. The biochemical system and the HMM behave similarly under steady-state conditions. Consequently a formal equivalence can be found between the biochemical system and the HMM. Numerical simulations further extend the results to the dynamic case and to noisy input. All in all, we have derived a probabilistic model equivalent to a classical descriptive model of phototransduction, which has the additional advantage of assigning a function to phototransduction. The example of phototransduction shows how simple biochemical interactions underlie simple probabilistic inferences. (shrink)

Sickle cell disease is a debilitating illness that affects quality of life and life expectancy for patients. In Cameroon, it is now possible to opt for termination of an affected pregnancy where the fetus is found to be affected by SCD. Our earlier studies found that, contrary to the views of Cameroonian physicians, a majority of parents with their children suffering from SCD would choose to abort if the fetuses were found to be affected. What have not yet been investigated (...) are the views of people suffering from/living with SCD. We used a quantitative sociological method, with administered structured questionnaires, to study the attitudes of adult patients suffering from SCD on prenatal genetic diagnosis and possible TAP. The majority of the 89 participants were urban dwellers , women , Christian and single , with a secondary/tertiary education . The majority would consider PND for SCD; almost half would reject TAP while 40.9% would consider it. Respondents who rejected TAP claimed mostly ethical reasons while those who found TAP acceptable cited fear of having an affected child and the poor quality of the affected child's health . Cameroonian patients with SCD are generally supportive of PND and a remarkably high number of patients living with SCD reported that they would consider terminating a pregnancy based on their assessment of the future well-being of the child. Research is required to investigate the burden of SCD on families and their quality of life. (shrink)

We describe a recent approach for distinguishing between stochastic and deterministic sources of variability, focusing on the mammalian cell cycle. Variability between cells is often attributed to stochastic noise, although it may be generated by deterministic components. Interestingly, lineage information can be used to distinguish between variability and determinism. Analysis of correlations within a lineage of the mammalian cell cycle duration revealed its deterministic nature. Here, we discuss the sources of such variability and the possibility that the underlying deterministic (...) process is due to the circadian clock. Finally, we discuss the “kicked cell cycle” model and its implication on the study of the cell cycle in healthy and cancerous tissues. (shrink)

Replication protein A (RPA), the major single‐stranded DNA‐binding protein in eukaryotic cells, is required for processing of single‐stranded DNA (ssDNA) intermediates found in replication, repair, and recombination. Recent studies have shown that RPA binding to ssDNA is highly dynamic and that more than high‐affinity binding is needed for function. Analysis of DNA binding mutants identified forms of RPA with reduced affinity for ssDNA that are fully active, and other mutants with higher affinity that are inactive. Single molecule studies showed (...) that while RPA binds ssDNA with high affinity, the RPA complex can rapidly diffuse along ssDNA and be displaced by other proteins that act on ssDNA. Finally, dynamic DNA binding allows RPA to prevent error‐prone repair of double‐stranded breaks and promote error‐free repair. Together, these findings suggest a new paradigm where RPA acts as a first responder at sites with ssDNA, thereby actively coordinating DNA repair and DNA synthesis. (shrink)

Intensive research and development of electrophoresis methodology and instrumentation during past decades has resulted in unique methods widely implemented in bioanalysis. While two‐dimensional electrophoresis and denaturing polyacrylamide gel electrophoresis in sodium dodecylsulfate are still the most frequently used electrophoretic methods applied to analyses of proteins, new miniaturized capillary and microfluidic versions of electromigrational methods have been developed. High‐throughput electrophoretic instruments with hundreds of capillaries for parallel separations and laser‐induced fluorescence detection of labeled DNA strands have been of key importance for (...) the scientific and commercial success of the Human Genome Project. Another powerful method, capillary isoelectric focusing with pressurized and pH‐driven mobilization, provides efficient separations and on‐line sensitive detection of proteins, bacteria and viruses. Electrophoretic microfluidic devices can integrate single‐cell injection, cell lysis, separation of its components and fluorescence or mass spectrometry detection. These miniaturized devices also proved the capability of single‐molecule detection. (shrink)

Single cell recordings in monkeys provide strong evidence for an important role of the motor system in action understanding. This evidence is backed up by data from studies of the (human) mirror neuron system using neuroimaging or TMS techniques, and behavioral experiments. Although the data acquired from single cell recordings are generally considered to be robust, several debates have shown that the interpretation of these data is far from straightforward. We will show that research based on single-cell recordings allows for (...) unlimited content attribution to mirror neurons. We will argue that a theoretical analysis of the mirroring process, combined with behavioral and brain studies, can provide the necessary limitations. A complexity analysis of the type of processing attributed to the mirror neuron system can help formulate restrictions on what mirroring is and what cognitive functions could, in principle, be explained by a mirror mechanism. We argue that processing at higher levels of abstraction needs assistance of non-mirroring processes to such an extent that subsuming the processes needed to infer goals from actions under the label ?mirroring? is not warranted. (shrink)

Non-medical or Social egg freezing (oocyte cryopreservation) is currently a controversial topic in Islam, with contradictory fatwas being issued in different Muslim countries. While Islamic authorities in Egypt permit the procedure, fatwas issued in Malaysia have banned single Muslim women from freezing their unfertilized eggs (vitrified oocytes) to be used later in marriage. The underlying principles of the Malaysian fatwas are that (i) sperm and egg cells produced before marriage, should not be used during marriage to conceive a child; (ii) (...) extraction of mature egg cells from single women being unacceptable; and (iii) fertility preservation in anticipation of late marriage is a conjecture that has not yet occurred. Ovarian tissue freezing can potentially be a more Shariah-compliant alternative to social egg freezing, because once the frozen ovarian cortical tissue sections have been re-transplanted back into the woman, mature egg cells can readily be produced, collected, and fertilized by the husband’s sperm only during the period of marriage contract (′akd al-nikāḥ). Unlike accidental mix-ups with frozen eggs, muddling of lineage (nasab) would be automatically avoided in ovarian tissue freezing due to immunological rejection. However, upon critical analysis based on Qawā’id Fiqhiyyah (Islamic Legal Maxims), Maqāṣid-al-Shariah (Higher Objectives of Islamic Law), and Maslaḥah-Mafsadah (benefits versus harmful effects on society), elective ovarian tissue freezing by healthy single women for social reasons would likely be a highly contentious and controversial issue within Muslim communities that may conflict with conservative social-religious norms. This thus needs further debate among Islamic jurists in dialogue with medical doctors and biomedical scientists. (shrink)

Analysis of the light‐induced changes of cytosolic Ca2+ ([Ca2+]i) in photoreceptor cells has been taken a step further with two recently published studies(1,2). In one, changes in [Ca2+]i were measured in single detached rod outer segments from Gecko in response to various light intensities. The advances of the other(2) are embodied in its employment of transgenic Drosophila, whose photoreceptors express a visual pigment that is insensitive to the wavelength of light used in the fluorescence imaging of [Ca2+]i. These studies (...) provide a better basis for understanding the regulation of Ca2+‐mediated events in photoreceptor cells. (shrink)

Background: While employers are increasingly considering and implementing COVID-19 vaccination requirements, little is known about the reasons offered by employees seeking religious exemptions.Methods: We conducted a mixed methods analysis of all the requests for religious exemptions submitted during the initial implementation of a COVID-19 vaccination requirement at a single academic medical center in the United States.Results: Five hundred sixty-five (3.4%) employees requested religious exemptions. At least 305 (54.0%) requesters had job titles suggesting that they had direct patient contact. Four (...) hundred ninety-nine (88.3%) of requesters self-identified as Christian, of whom 120 (21.2%) identified as Roman Catholic. Requesters offered 0 to 8 (mean 2.7) categories of reasons for their request. The most frequently stated reasons pertained to the use of fetal cell lines in vaccine development and manufacturing (382, 67.6%), interest in maintaining purity (221, 39.1%), or belief in divine healing (172, 30.4%). Some requesters also volunteered evidence of the sincerity of their beliefs including examples of their religious practices (116, 20.5%), other practices (66, 11.7%), and emotional states (32, 5.7%). One hundred fifty-two applications (26.9%) contained text copied without attribution, primarily from sample religious exemption request letters available on the Internet.Conclusions: Most requesters focused on the use of fetal cell lines in the development or manufacturing of the vaccines as the justification for their request. The development of vaccines that are not reliant on fetal cell lines may increase vaccination rates. Understanding reasons for religious exemption requests may inform vaccine education and vaccination policies. (shrink)

The recent development of single molecule detection techniques has opened new horizons for the study of individual macromolecules under physiological conditions. Conformational subpopulations, internal dynamics and activity of single biomolecules, parameters that have so far been hidden in large ensemble averages, are now being unveiled. Herein, we review a particular attractive solution‐based single molecule technique, fluorescence correlation spectroscopy (FCS). This time‐averaging fluctuation analysis which is usually performed in Confocal setups combines maximum sensitivity with high statistical confidence. FCS has proven (...) to be a very versatile and powerful tool for detection and temporal investigation of biomolecules at ultralow concentrations on surfaces, in solution, and in living cells. The introduction of dual‐color cross‐correlation and two‐photon excitation in FCS experiments is currently increasing the number of promising applications of FCS to biological research. BioEssays 24:758–764, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

A biological explanation for the dependence of genome-wide mutation-rate variation on local base context is now becoming clearer. The proportions of G + C relative to A + T—expressed as GC%—is a species-specific DNA character. The frequencies of these single bases correlate with frequencies of corresponding oligonucleotides that are more-sensitive indicators of species specificity. Thus, when k = 3 there are 64 possible trinucleotide sequences and a GC%-rich species has a high frequency of GC-rich 3-mers. Closely related species have similar (...) k-mer patterns. For distantly related species, even if happening to have the same GC% values, k-mer patterns are widely discordant. Conventionally, a base substitution mutation is viewed as a chemical 1-mer phenomenon. However, the selective difference by which the corresponding mutation is scored usually relates to context. Thus, an A to U codon mutation in sickle cell anemia, rather than attracting an anticodon in a structural loop of glutamate tRNA, pairs with the more complementary anticodon loop of valine tRNA. Likewise, a recent statistical analysis of genome-wide mutation-rate variation supports the view that a failure of discordant DNA loops to pair at meiosis can initiate and/or sustain the speciation process. Such disharmony among base patterns may have unknowingly been hinted at by geneticist William Bateson who invoked a music metaphor when considering speciation mechanisms. (shrink)

We review a recent paper in Genome Research by Guantes et al. showing that nuclear gene expression is influenced by the bioenergetic status of the mitochondria. The amount of energy that mitochondria make available for gene expression varies considerably. It depends on: the energetic demands of the tissue; the mitochondrial DNA (mtDNA) mutant load; the number of mitochondria; stressors present in the cell. Hence, when failing mitochondria place the cell in energy crisis there are major effects on gene expression affecting (...) the risk of degenerative diseases, cancer and ageing. In 2015 the UK parliament approved a change in the regulation of IVF techniques, allowing “Mitochondrial replacement therapy” to become a reproductive choice for women at risk of transmitting mitochondrial disease to their children. This is the first time that this technique will be available. Therefore understanding the interaction between mitochondria and the nucleus has never been more important. (shrink)

We discuss various implications of some radical anti-representationalist views of cognition and what they have to offer with regard to the naturalization of intentionality and the explanation of cognitive phenomena. Our focus is on recent arguments from proponents of enactive views of cognition to the effect that basic cognition is intentional but not representational and that cognition is co-extensive with life. We focus on lower rather than higher forms of cognition, namely the question regarding the intentional and representational nature of (...) cognition found in organisms simpler than human beings, because enactivists do not deny that more sophisticated cognitive phenomena are representational and involve content. After introducing the debate on the naturalization of intentionality, we briefly review different varieties of enactivism and introduce their central claims. In Sect. 4 we turn to radical enactivism in order to focus on the arguments for a thoroughly non-representational, enactive account of perception and basic cognition. In particular, we discuss three major issues: First, what is supposed to replace the representational analysis of perception in a radical-enactive explanation of perception? How does the enactive explanation of perception compare to the best scientific work on the neuroscience of perception? Second, what is—on an enactive account—the function of neural processing in the brain for the generation of perception if not to produce representations? This question is especially pressing since one implication of autopoietic enactivism is that even the simplest organisms, i.e. single-celled organisms, have cognitive capacities. Since they lack brains and nervous systems, enactivists must specify the unique contribution of the brain and nervous system in those animals who have them. In Sect. 5, we evaluate the advantages of an autopoietic–enactive approach to the naturalization of intentionality and end with a suggestion how cognition may relate to intentionality and representation. (shrink)

While the HVTN 505 trial showed no overall efficacy of the tested vaccine to prevent HIV infection over placebo, markers measuring immune response to vaccination were strongly correlated with infection. This finding generated the hypothesis that some marker-defined vaccinated subgroups were partially protected whereas others had their risk increased. This hypothesis can be assessed using the principal stratification framework (Frangakis and Rubin, 2002) for studying treatment effect modification by an intermediate response variable, using methods in the sub-field of principal surrogate (...) (PS) analysis that studies multiple principal strata. Unfortunately, available methods for PS analysis require an augmented study design not available in HVTN 505, and make untestable structural risk assumptions, motivating a need for more robust PS methods. Fortunately, another sub-field of principal stratification, survivor average causal effect (SACE) analysis (Rubin, 2006) – which studies effects in a single principal stratum – provides many methods not requiring an augmented design and making fewer assumptions. We show how, for a binary intermediate response variable, methods developed for SACE analysis can be adapted to PS analysis, providing new and more robust PS methods. Application to HVTN 505 supports that the vaccine partially protected individuals with vaccine-induced T-cells expressing certain combinations of functions. (shrink)

New imaging methodologies in quantitative fluorescence microscopy, such as Förster resonance energy transfer (FRET), have been developed in the last few years and are beginning to be extensively applied to biological problems. FRET is employed for the detection and quantification of protein interactions, and of biochemical activities. Herein, we review the different methods to measure FRET in microscopy, and more importantly, their strengths and weaknesses. In our opinion, fluorescence lifetime imaging microscopy (FLIM) is advantageous for detecting inter‐molecular interactions quantitatively, the (...) intensity ratio approach representing a valid and straightforward option for detecting intra‐molecular FRET. Promising approaches in single molecule techniques and data analysis for quantitative and fast spatio‐temporal protein‐protein interaction studies open new avenues for FRET in biological research. (shrink)

Model organisms are central to contemporary biology and studies of embryogenesis in particular. Biologists utilize only a small number of species to experimentally elucidate the phenomena and mechanisms of development. Critics have questioned whether these experimental models are good representatives of their targets because of the inherent biases involved in their selection (e.g., rapid development and short generation time). A standard response is that the manipulative molecular techniques available for experimental analysis mitigate, if not counterbalance, this concern. But the (...) most powerful investigative techniques and molecular methods are applicable to single-celled organisms (‘microbes’). Why not use unicellular rather than multicellular model organisms, which are the standard for developmental biology? To claim that microbes are not good representatives takes us back to the original criticism leveled against model organisms. Using empirical case studies of microbes modeling ontogeny, we break out of this circle of reasoning by showing: (a) that the criterion of representation is more complex than earlier discussions have emphasized; and, (b) that different aspects of manipulability are comparable in importance to representation when deciding if a model organism is a good model. These aspects of manipulability harbor the prospect of enhancing representation. The result is a better understanding of how developmental biologists conceptualize research using experimental models and suggestions for underappreciated avenues of inquiry using microbes. More generally, it demonstrates how the practical aspects of experimental biology must be scrutinized in order to understand the associated scientific reasoning. (shrink)

Recent years have witnessed an explosion of the single-cell biochemical toolbox including chromosome conformation capture -based methods that provide novel insights into chromatin spatial organization in individual cells. The observations made with these techniques revealed that topologically associating domains emerge from cell population averages and do not exist as static structures in individual cells. Stochastic nature of the genome folding is likely to be biologically relevant and may reflect the ability of chromatin fibers to adopt a number of alternative configurations, (...) some of which could be transiently stabilized and serve regulatory purposes. Single-cell Hi-C approaches provide an opportunity to analyze chromatin folding in rare cell types such as stem cells, tumor progenitors, oocytes, and totipotent cells, contributing to a deeper understanding of basic mechanisms in development and disease. Here, we review key findings of single-cell Hi-C and discuss possible biological reasons and consequences of the inferred dynamic chromatin spatial organization. Single-cell Hi-C expands the molecular biology toolbox for studies of chromatin structure in individual cells. This technique allows one to analyze cell-to-cell variability in TAD and loop structure, and to capture chromosome conformation in rare cell types such as oocytes, totipotent cells, and tumor progenitors. (shrink)

Recent years have witnessed an explosion of the single-cell biochemical toolbox including chromosome conformation capture -based methods that provide novel insights into chromatin spatial organization in individual cells. The observations made with these techniques revealed that topologically associating domains emerge from cell population averages and do not exist as static structures in individual cells. Stochastic nature of the genome folding is likely to be biologically relevant and may reflect the ability of chromatin fibers to adopt a number of alternative configurations, (...) some of which could be transiently stabilized and serve regulatory purposes. Single-cell Hi-C approaches provide an opportunity to analyze chromatin folding in rare cell types such as stem cells, tumor progenitors, oocytes, and totipotent cells, contributing to a deeper understanding of basic mechanisms in development and disease. Here, we review key findings of single-cell Hi-C and discuss possible biological reasons and consequences of the inferred dynamic chromatin spatial organization. Single-cell Hi-C expands the molecular biology toolbox for studies of chromatin structure in individual cells. This technique allows one to analyze cell-to-cell variability in TAD and loop structure, and to capture chromosome conformation in rare cell types such as oocytes, totipotent cells, and tumor progenitors. (shrink)

According to enactivism all living systems, from single cell organisms to human beings, are ontologically endowed with some form of teleological and sense-making agency. Furthermore, enactivists maintain that: there is no fixed pregiven world and as a consequence all organisms “bring forth” their own unique “worlds” through processes of sense-making. The first half of the paper takes these two ontological claims as its central focus and aims to clarify and make explicit the arguments and motivations underlying them. Our analysis (...) here highlights three distinct but connected problems for enactivism: these arguments do not and cannot guarantee that there is no pregiven world, instead, they end up generating a contradiction whereby a pregiven world seems to in fact be tacitly presupposed by virtue of a reliance on a tacit epistemic perspectivalism which is also inherently representationalist and as a consequence makes it difficult to satisfactorily account for the ontological plurality of worlds. Taking these considerations on board, the second half of the paper then aims to develop a more robust ontologically grounded enactivism. Drawing from biosemiotic enactivism, science and technology studies and anthropology, the paper aims to present an account which both rejects a pregiven world and coherently accounts for how organisms bring forth ontologically multiple worlds. (shrink)

According to enactivism all living systems, from single cell organisms to human beings, are ontologically endowed with some form of teleological and sense-making agency. Furthermore, enactivists maintain that: there is no fixed pregiven world and as a consequence all organisms “bring forth” their own unique “worlds” through processes of sense-making. The first half of the paper takes these two ontological claims as its central focus and aims to clarify and make explicit the arguments and motivations underlying them. Our analysis (...) here highlights three distinct but connected problems for enactivism: these arguments do not and cannot guarantee that there is no pregiven world, instead, they end up generating a contradiction whereby a pregiven world seems to in fact be tacitly presupposed by virtue of a reliance on a tacit epistemic perspectivalism which is also inherently representationalist and as a consequence makes it difficult to satisfactorily account for the ontological plurality of worlds. Taking these considerations on board, the second half of the paper then aims to develop a more robust ontologically grounded enactivism. Drawing from biosemiotic enactivism, science and technology studies and anthropology, the paper aims to present an account which both rejects a pregiven world and coherently accounts for how organisms bring forth ontologically multiple worlds. (shrink)

Clustered regularly interspaced short palindromic repeats genome editing has already reinvented the direction of genetic and stem cell research. For more complex diseases it allows scientists to simultaneously create multiple genetic changes to a single cell. Technologies for correcting multiple mutations in an in vivo system are already in development. On the surface, the advent and use of gene editing technologies is a powerful tool to reduce human suffering by eradicating complex disease that has a genetic etiology. Gene drives are (...) CRISPR mediated alterations to genes that allow them to be passed on to subsequent populations at rates that approach one hundred per cent transmission. Therefore, from an anticipatory biomedical ethics perspective, it is possible to conceive gene drive being used with CRISPR to permanently ameliorate aberrant genes from wild-type populations containing mutations. However, there are also a number of possible side effects that could develop as the result of combining gene editing and gene drive technologies in an effort to eradicate complex diseases. In this paper, we critically analyse the hypothesis that the combination of CRISPR and gene drive will have a deleterious effect on human populations from an ethical perspective by developing an anticipatory ethical analysis of the implications for the use of CRISPR together with gene drive in humans. (shrink)

Almost all biomedical research to date has relied upon mean measurements from cell populations, however it is well established that what it is observed at this macroscopic level can be the result of many interactions of several different single cells. Thus, the observable macroscopic ‘average’ cannot outright be used as representative of the ‘average cell’. Rather, it is the resulting emerging behaviour of the actions and interactions of many different cells. Single‐cell RNA sequencing (scRNA‐Seq) enables the comparison of the (...) transcriptomes of individual cells. This provides high‐resolution maps of the dynamic cellular programmes allowing us to answer fundamental biological questions on their function and evolution. It also allows to address medical questions such as the role of rare cell populations contributing to disease progression and therapeutic resistance. Furthermore, it provides an understanding of context‐specific dependencies, namely the behaviour and function that a cell has in a specific context, which can be crucial to understand some complex diseases, such as diabetes, cardiovascular disease and cancer. Here, we provide an overview of scRNA‐Seq, including a comparative review of emerging technologies and computational pipelines. We discuss the current and emerging applications and focus on tumour heterogeneity a clear example of how scRNA‐Seq can provide new understanding of a complex disease. Additionally, we review the limitations and highlight the need of powerful computational pipelines and reproducible protocols for the broader acceptance of this technique in basic and clinical research. (shrink)

Life is perpetuated through a single-cell bottleneck between generations in many organisms. Here, I highlight that this cell holds information in two distinct stores: in the linear DNA sequence that is replicated during cell divisions, and in the three-dimensional arrangement of molecules that can change during development but is recreated at the start of each generation. These two interdependent stores of information – one replicating with each cell division and the other cycling with a period of one generation – coevolve (...) while perpetuating an organism. Unlike the genome sequence, the arrangement of molecules, including DNA, RNAs, proteins, sugars, lipids, etc., is not well understood. Because this arrangement and the genome sequence are transmitted together from one generation to the next, analysis of both is necessary to understand evolution and origins of inherited diseases. Recent developments suggest that tools are in place to examine how all the information to build an organism is encoded within a single cell, and how this cell code is reproduced in every generation. Life relies on the information for making organisms that is encoded in single cells and transmitted between generations. These cell codes include interdependent stores of information that replicate and that cycle. Understanding evolution and the origins of inherited diseases requires analysis of cell codes. (shrink)

The post‐embryonic architecture of higher plants is derived from the activity of two meristems that are formed in the embryo: the shoot meristem and the root meristem. The epidermis of the shoot is derived from the outermost layer of cells covering the shoot meristem through repeated anticlinal divisions. By contrast, the epidermis of the root is derived from an internal ring of cells, located at the centre of the root meristem, by a precise series of both periclinal and anticlinal divisions. (...) Each epidermis has an independent origin. In Arabidopsis the mature shoot epidermis is composed of a small number of cell types: hair cells (trichomes), stomatal guard cells and other epidermal cells. In shoots, hairs take the form of branched trichomes that are surrounded at their base by a ring of accessory cells in a sheet of epidermal cells. The root epidermis is composed of two cell types: trichoblasts that form root hair cells and atrichoblasts that form non‐hair cells. Mutations affecting both the patterning and the morphogenesis of cells in both shoot and root epidermis have recently been described. Most of these mutations affect development in a single epidermis, but at least one, ttg, is involved in development in both epidermal systems. (shrink)

In their theoretical and experimental reflections on the capacities and behaviours of living systems, neuroscientists often formulate generalizations about the behaviour of neural circuits. These generalizations are highly idealized, as they omit reference to the myriads of conditions that could perturb the behaviour of the modelled system in real-world settings. This article analyses an experimental investigation of the behaviour of place cells in the rat hippocampus, in which highly idealized generalizations were tested by comparing predictions flowing from them with real-world (...) experimental results. The aim of the article is to identify under what conditions even single prediction failures regarding the behaviour of single cells sufficed to reject highly idealized generalizations, and under what conditions prima facie counter-examples were deemed to be irrelevant to the testing of highly idealized generalizations. The results of this analysis may contribute to understanding how idealized models are tested experimentally in neuroscience and used to make reliable predictions concerning living systems in real-world settings. (shrink)

Efforts to improve the means to diagnose and treat human genetic diseases have a long history in biomedical research and medicine. Now, preimplantation genetic diagnosis provides a new way to prevent the transmission of certain types of human genetic diseases to the next generation. It is an alternative to elective termination of pregnancies.PGD is used to test for genetic diseases that are due to defective single genes or abnormal chromosomes within days of fertilization and prior to the establishment of pregnancy. (...) The procedure essentially begins with the biopsy of one or more cells of a cleavage stage or blastocyst stage preimplantation human embryo that has been produced by in vitro fertilization. In certain cases, PGD can be done on polar bodies—discarded by-products of egg formation containing excess chromosomes—of unfertilized eggs. Then, the cell, or a polar body, is placed into a tube for single gene analysis ), or for chromosome analysis by spreading the nucleus of the cell on a microscope slide ). (shrink)

Cloning is a biological technique of producing any required number of individuals with identical properties as the parent organism from a single cell of the latter. Cloning of protozoa, plants and lower animals meets with no moral objections, but the as yet hypothetical but increasingly more realistic prospect of cloning human beings appears to be highly objectionable. The analysis of the arguments used in the discussion of cloning indicates that mass-scale or repeated replication of human individuals is unacceptable. Such (...) a practice would probably trigger an avalanche of psychological problems connected with the diluted identity of the cloned offspring, a possible social stigmatization of the clones and the negative effects of a narrowing of the genetic pool of the human species which would limit its ability of biological adaptation to the varying conditions of the environment. (shrink)

The vast majority (> 95%) of single-gene mutations in yeast affect not only the expression of the mutant gene, but also the expression of many other genes. These data suggest the presence of a previously uncharacterized ‘gene expression network’—a set of interactions between genes which dictate gene expression in the native cell environment. Here, we quantitatively analyze the gene expression network revealed by microarray expression data from 273 different yeast gene deletion mutants.(1) We find that gene expression interactions form a (...) robust, error-tolerant ‘scale-free’ network, similar to metabolic pathways(2) and artificial networks such as power grids and the internet.(3-5) Because the connectivity between genes in the gene expression network is unevenly distributed, a scale-free organization helps make organisms resistant to the deleterious effects of mutation, and is thus highly adaptive. The existence of a gene expression network poses practical considerations for the study of gene function, since most mutant phenotypes are the result of changes in the expression of many genes. Using principles of scale-free network topology, we propose that fragmenting the gene expression network via ‘genome-engineering’ may be a viable and practical approach to isolating gene function. BioEssays 24:267–274, 2002. © 2002 Wiley Periodicals, Inc.; DOI 10.1002/bies.10054. (shrink)

Efforts to improve the means to diagnose and treat human genetic diseases have a long history in biomedical research and medicine. Now, preimplantation genetic diagnosis provides a new way to prevent the transmission of certain types of human genetic diseases to the next generation. It is an alternative to elective termination of pregnancies.PGD is used to test for genetic diseases that are due to defective single genes or abnormal chromosomes within days of fertilization and prior to the establishment of pregnancy. (...) The procedure essentially begins with the biopsy of one or more cells of a cleavage stage or blastocyst stage preimplantation human embryo that has been produced by in vitro fertilization. In certain cases, PGD can be done on polar bodies—discarded by-products of egg formation containing excess chromosomes—of unfertilized eggs. Then, the cell, or a polar body, is placed into a tube for single gene analysis ), or for chromosome analysis by spreading the nucleus of the cell on a microscope slide ). (shrink)

Factors affecting transcriptional elongation have been characterized extensively in in vitro, single cell (yeast) and cell culture systems; however, data from the context of multicellular organisms has been relatively scarce. While studies in homogeneous cell populations have been highly informative about the underlying molecular mechanisms and prevalence of polymerase pausing, they do not reveal the biological impact of perturbing this regulation in an animal. The core components regulating pausing are expressed in all animal cells and are recruited to the majority (...) of genes, however, disrupting their function often results in discrete phenotypic effects. Mutations in genes encoding key regulators of transcriptional pausing have been recovered from several genetic screens for specific phenotypes or interactions with specific factors in mice, zebrafish and flies. Analysis of these mutations has revealed that control of transcriptional pausing is critical for a diverse range of biological pathways essential for animal development and survival. (shrink)

Various techniques have attempted to localize imagery. However, early findings using single cell recordings of human receptive fields during imagery tasks have had little impact. Reports by Marg and his coworkers (1968) found no evidence for imagery in human Area 17, 18, and 19. Single cells from humans suggest later imagery-related activity in hippocampus, amygdala, entorhinal cortex, and parahippocampal gyrus.

Embryonic development in Drosophila melanogaster begins with a rapid series of mitotic nuclear divisions, unaccompanied by cytokinesis, to produce a multi‐nucleated single cell embryo, the syncytial blastoderm. The syncytium then undergoes a process of cell formation, in which the individual nuclei become enclosed in individual cells. This process of cellularization involves integrating mechanisms of cell polarity, cell–cell adhesion and a specialized form of cytokinesis. The detailed molecular mechanism, however, is highly complex and, despite extensive analysis, remains poorly understood. Nevertheless, (...) new insights are emerging from recent studies on aspects of membrane polarization and insertion, which show that membrane components from intracellular organelles are involved. In addition, actin and actin‐associated proteins have been heavily implicated while new evidence shows that microtubule cytoskeletal elements are mechanistically involved in all aspects of cellularization. This review will draw on both the traditional models and the new data to provide a current perspective on the nature of cellular blastoderm formation in Drosophila melanogaster. BioEssays 24:1012–1022, 2002. © 2002 Wiley‐Periodicals, Inc. (shrink)

Cell division is an universal process the aim of which is the equitable distribution of subcellular organelles from single cells to their daughters. The extraordinary accuracy with which the genetic material is partitioned requires a complex machinery involving many gene products. Genetic approaches can be used to identify the relevant components and processes, and mutational analysis of loci essential for cell division has been carried out in several eukaryotes, in particular fungi and mammalian cells in culture. Recently, this type (...) of analysis has been extended to Drosophila, an ideal eukaryote for genetic studies. We will review here the genetic dissection of mitosis in Drosophila melanogaster, discussing recent findings of interest and the methodological problems that have been encountered. (shrink)

Single‐cell microinjection has been successfully used to deliver exogenous proteins, cDNA constructs, peptides, drugs and particles into transfection‐challenged cells. With precisely controlled delivery dosage and timing, microinjection has been used in many studies of primary cultured cells, transgenic animal production, in vitro fertilization and RNA inference. This review discusses the advantages and limits of microinjection as a mechanical delivery method and its applications to attached and suspended cells. BioEssays 30:606–610, 2008. © 2008 Wiley Periodicals, Inc.

Period homeostasis is the defining characteristic of a biological clock. Strict period homeostasis is found for the ultradian clocks of eukaryotic microbes. In addition to being temperature-compensated, the period of these rhythms is unaffected by differences in nutrient composition or changes in other environmental variables. The best-studied examples of ultradian clocks are those of the ciliates Paramecium tetraurelia and Tetrahymena sp. and of the fission yeast, Schizosaccharomyces pombe. In these single cell eukaryotes, up to seven different parameters display ultradian rhythmicity (...) with the same, species- and strain-specific period. In fission yeast, the molecular genetic analysis of ultradian clock mechanisms has begun with the systematic analysis of mutants in identified candidate genes. More than 40 “clock mutants” have already been identified, most of them affected in components of major regulatory and signalling pathways. These results indicate a high degree of complexity for a eukaryotic clock mechanism. BioEssays 22:16–22, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

A reductionistic, bottom‐up, cellular‐based concept of the origins of sentience and consciousness has been put forward. Because all life is based on cells, any evolutionary theory of the emergence of sentience and consciousness must be grounded in mechanisms that take place in prokaryotes, the simplest unicellular species. It has been posited that subjective awareness is a fundamental property of cellular life. It emerges as an inherent feature of, and contemporaneously with, the very first life‐forms. All other varieties of mentation are (...) the result of evolutionary mechanisms based on this singular event. Therefore, all forms of sentience and consciousness evolve from this original instantiation in prokaryotes. It has also been identified that three cellular structures and mechanisms that likely play critical roles here are excitable membranes, oscillating cytoskeletal polymers, and structurally flexible proteins. Finally, basic biophysical principles are proposed to guide those processes that underly the emergence of supracellular sentience from cellular sentience in multicellular organisms. (shrink)

Persistent activity can be the product of mechanisms other than attractor reverberations. The single-unit data presented by Amit cannot discriminate between the different mechanisms. In fact, single-unit data do not appear to be adequate for testing neural network models.

This article examines how scientists move from physical measurementsto actual observation of single-cell recordings in the brain. We highlight how easy it is to change the fundamental nature of ourobservations using accepted methodological techniques for manipulatingraw data. Collecting single-cell data is thoroughly pragmatic. Weconclude that there is no deep or interesting difference betweenaccounting for observations by measurements and accounting forobservations by theories.

Bacterial populations are heterogeneous, which in many cases can provide a selective advantage during changes in environmental conditions. In some instances, heterogeneity exists at the genetic level, in which significant allelic variation occurs within a population seeded by a single cell. In other cases, heterogeneity exists due to phenotypic differences within a clonal, genetically identical population. A variety of mechanisms can drive this latter strategy. Stochastic fluctuations can drive differential gene expression, but heterogeneity in gene expression can also be driven (...) by environmental changes sensed by individual cells residing in distinct locales. Utilizing multiple single cell approaches, workers have started to uncover the extent of heterogeneity within bacterial populations. This review will first describe several examples of phenotypic and genetic heterogeneity, and then discuss many single cell approaches that have recently been applied to define heterogeneity within bacterial populations. (shrink)