Single-cell investigative genetics: Single-cell data produces genotype distributions concentrated at the true genotype across all mixture complexities.

In the absence of a suspect the forensic aim is investigative, and the focus is one of discerning what genotypes best explain the evidence. In traditional systems, the list of candidate genotypes may become vast if the sample contains DNA from many donors or the information from a minor contributor is swamped by that of major contributors, leading to lower evidential value for a true donor's contribution and, as a result, possibly overlooked or inefficient investigative leads. Recent developments in single-cell analysis offer a way forward, by producing data capable of discriminating genotypes.

Optimal age-specific vaccination control for COVID-19: An Irish case study.

The outbreak of a novel coronavirus causing severe acute respiratory syndrome in December 2019 has escalated into a worldwide pandemic. In this work, we propose a compartmental model to describe the dynamics of transmission of infection and use it to obtain the optimal vaccination control. The model accounts for the various stages of the vaccination, and the optimisation is focused on minimising the infections to protect the population and relieve the healthcare system.

Simultaneous Assessment of Kinship, Division Number, and Phenotype via Flow Cytometry for Hematopoietic Stem and Progenitor Cells.

Few techniques can assess phenotype and fate for the same cell simultaneously. Most of the current protocols used to characterize phenotype, although able to generate large datasets, necessitate the destruction of the cell of interest, making it impossible to assess its functional fate. Heterogeneous biological differentiating systems like hematopoiesis are therefore difficult to describe.

Evidentiary evaluation of single cells renders highly informative forensic comparisons across multifarious admixtures.

The consistency between DNA evidence and person(s) of interest (PoI) is summarized by a likelihood ratio (LR): the probability of the data given the PoI contributed divided by the probability given they did not. It is often the case that there are several PoI who may have individually or jointly contributed to the stain. If there is more than one PoI, or the number of contributors (NoC) cannot easily be determined, then several sets of hypotheses are needed, requiring significant resources to complete the interpretation.

Cyton2: A Model of Immune Cell Population Dynamics That Includes Familial Instructional Inheritance.

Lymphocytes are the central actors in adaptive immune responses. When challenged with antigen, a small number of B and T cells have a cognate receptor capable of recognising and responding to the insult. These cells proliferate, building an exponentially growing, differentiating clone army to fight off the threat, before ceasing to divide and dying over a period of weeks, leaving in their wake memory cells that are primed to rapidly respond to any repeated infection.

Maintaining naivety of T cells.

Mathematical models encoding biological hypotheses reveal new insight into the dynamics of naive immune cells in mice from birth to old age.

Replicative history marks transcriptional and functional disparity in the CD8 T cell memory pool.

Clonal expansion is a core aspect of T cell immunity. However, little is known with respect to the relationship between replicative history and the formation of distinct CD8 memory T cell subgroups. To address this issue, we developed a genetic-tracing approach, termed the DivisionRecorder, that reports the extent of past proliferation of cell pools in vivo.

High-quality data from a forensically relevant single-cell pipeline enabled by low PBS and proteinase K concentrations.

Interpreting forensic DNA signal is arduous since the total intensity is a cacophony of signal from noise, artifact, and allele from an unknown number of contributors (NOC). An alternate to traditional bulk-processing pipelines is a single-cell one, where the sample is collected, and each cell is sequestered resulting in n single-source, single-cell EPGs (scEPG) that must be interpreted using applicable strategies. As with all forensic DNA interpretation strategies, high quality electropherograms are required; thus, to enhance the credibility of single-cell forensics, it is necessary to produce an efficient direct-to-PCR treatment that is compatible with prevailing downstream laboratory processes.

The a posteriori probability of the number of contributors when conditioned on an assumed contributor.

Forensic DNA signal is notoriously challenging to assess, requiring computational tools to support its interpretation. Over-expressions of stutter, allele drop-out, allele drop-in, degradation, differential degradation, and the like, make forensic DNA profiles too complicated to evaluate by manual methods. In response, computational tools that make point estimates on the Number of Contributors (NOC) to a sample have been developed, as have Bayesian methods that evaluate an A Posteriori Probability (APP) distribution on the NOC.

HSPCs display within-family homogeneity in differentiation and proliferation despite population heterogeneity.

High-throughput single-cell methods have uncovered substantial heterogeneity in the pool of hematopoietic stem and progenitor cells (HSPCs), but how much instruction is inherited by offspring from their heterogeneous ancestors remains unanswered. Using a method that enables simultaneous determination of common ancestor, division number, and differentiation status of a large collection of single cells, our data revealed that murine cells that derived from a common ancestor had significant similarities in their division progression and differentiation outcomes. Although each family diversifies, the overall collection of cell types observed is composed of homogeneous families.

Towards developing forensically relevant single-cell pipelines by incorporating direct-to-PCR extraction: compatibility, signal quality, and allele detection.

Current analysis of forensic DNA stains relies on the probabilistic interpretation of bulk-processed samples that represent mixed profiles consisting of an unknown number of potentially partial representations of each contributor. Single-cell methods, in contrast, offer a solution to the forensic DNA mixture problem by incorporating a step that separates cells before extraction. A forensically relevant single-cell pipeline relies on efficient direct-to-PCR extractions that are compatible with standard downstream forensic reagents.

Manipulating niche composition limits damage to haematopoietic stem cells during Plasmodium infection.

Severe infections are a major stress on haematopoiesis, where the consequences for haematopoietic stem cells (HSCs) have only recently started to emerge. HSC function critically depends on the integrity of complex bone marrow (BM) niches; however, what role the BM microenvironment plays in mediating the effects of infection on HSCs remains an open question. Here, using a murine model of malaria and combining single-cell RNA sequencing, mathematical modelling, transplantation assays and intravital microscopy, we show that haematopoiesis is reprogrammed upon infection, whereby the HSC compartment turns over substantially faster than at steady-state and HSC function is drastically affected.

A large-scale validation of NOCIt's a posteriori probability of the number of contributors and its integration into forensic interpretation pipelines.

Forensic DNA signal is notoriously challenging to interpret and requires the implementation of computational tools that support its interpretation. While data from high-copy, low-contributor samples result in electropherogram signal that is readily interpreted by probabilistic methods, electropherogram signal from forensic stains is often garnered from low-copy, high-contributor-number samples and is frequently obfuscated by allele sharing, allele drop-out, stutter and noise. Since forensic DNA profiles are too complicated to quantitatively assess by manual methods, continuous, probabilistic frameworks that draw inferences on the Number of Contributors (NOC) and compute the Likelihood Ratio (LR) given the prosecution's and defense's hypotheses have been developed.

Sample path properties of the average generation of a Bellman-Harris process.

Motivated by a recently proposed design for a DNA coded randomised algorithm that enables inference of the average generation of a collection of cells descendent from a common progenitor, here we establish strong convergence properties for the average generation of a super-critical Bellman-Harris process. We further extend those results to a two-type Bellman-Harris process where one type can give rise to the other, but not vice versa. These results further affirm the estimation method's potential utility by establishing its long run accuracy on individual sample-paths, and significantly expanding its remit to encompass cellular development that gives rise to differentiated offspring with distinct population dynamics.

Four model variants within a continuous forensic DNA mixture interpretation framework: Effects on evidential inference and reporting.

Continuous mixture interpretation methods that employ probabilistic genotyping to compute the Likelihood Ratio (LR) utilize more information than threshold-based systems. The continuous interpretation schemes described in the literature, however, do not all use the same underlying probabilistic model and standards outlining which probabilistic models may or may not be implemented into casework do not exist; thus, it is the individual forensic laboratory or expert that decides which model and corresponding software program to implement. For countries, such as the United States, with an adversarial legal system, one can envision a scenario where two probabilistic models are used to present the weight of evidence, and two LRs are presented by two experts.

Stochastically Timed Competition Between Division and Differentiation Fates Regulates the Transition From B Lymphoblast to Plasma Cell.

In response to external stimuli, naïve B cells proliferate and take on a range of fates important for immunity. How their fate is determined is a topic of much recent research, with candidates including asymmetric cell division, lineage priming, stochastic assignment, and microenvironment instruction. Here we manipulate the generation of plasmablasts from B lymphocytes by varying CD40 stimulation strength to determine its influence on potential sources of fate control.

Multiplexed Division Tracking Dyes for Proliferation-Based Clonal Lineage Tracing.

The generation of cellular heterogeneity is an essential feature of immune responses. Understanding the heritability and asymmetry of phenotypic changes throughout this process requires determination of clonal-level contributions to fate selection. Evaluating intraclonal and interclonal heterogeneity and the influence of distinct fate determinants in large numbers of cell lineages, however, is usually laborious, requiring familial tracing and fate mapping.

Inhibition of Endosteal Vascular Niche Remodeling Rescues Hematopoietic Stem Cell Loss in AML.

Bone marrow vascular niches sustain hematopoietic stem cells (HSCs) and are drastically remodeled in leukemia to support pathological functions. Acute myeloid leukemia (AML) cells produce angiogenic factors, which likely contribute to this remodeling, but anti-angiogenic therapies do not improve AML patient outcomes. Using intravital microscopy, we found that AML progression leads to differential remodeling of vasculature in central and endosteal bone marrow regions.

A large-scale dataset of single and mixed-source short tandem repeat profiles to inform human identification strategies: PROVEDIt.

DNA-based human identity testing is conducted by comparison of PCR-amplified polymorphic Short Tandem Repeat (STR) motifs from a known source with the STR profiles obtained from uncertain sources. Samples such as those found at crime scenes often result in signal that is a composite of incomplete STR profiles from an unknown number of unknown contributors, making interpretation an arduous task. To facilitate advancement in STR interpretation challenges we provide over 25,000 multiplex STR profiles produced from one to five known individuals at target levels ranging from one to 160 copies of DNA.

Production of high-fidelity electropherograms results in improved and consistent DNA interpretation: Standardizing the forensic validation process.

Samples containing low-copy numbers of DNA are routinely encountered in casework. The signal acquired from these sample types can be difficult to interpret as they do not always contain all of the genotypic information from each contributor, where the loss of genetic information is associated with sampling and detection effects. The present work focuses on developing a validation scheme to aid in mitigating the effects of the latter.

Exploring STR signal in the single- and multicopy number regimes: Deductions from an in silico model of the entire DNA laboratory process.

Short tandem repeat (STR) profiling from DNA samples has long been the bedrock of human identification. The laboratory process is composed of multiple procedures that include quantification, sample dilution, PCR, electrophoresis, and fragment analysis. The end product is a short tandem repeat electropherogram comprised of signal from allele, artifacts, and instrument noise.

Retracing the in vivo haematopoietic tree using single-cell methods.

The dynamic process by which self-renewing stem cells and their offspring proliferate and differentiate to create the erythroid, myeloid and lymphoid lineages of the blood system has long since been an important topic of study. A range of recent single cell and family tracing methodologies such as massively parallel single-cell RNA-sequencing, mass cytometry, integration site barcoding, cellular barcoding and transposon barcoding are enabling unprecedented analysis, dissection and re-evaluation of the haematopoietic tree. In addition to the substantial experimental advances, these new techniques have required significant theoretical development in order to make biological deductions from their data.