Generating human artery and vein cells from pluripotent stem cells highlights the arterial tropism of Nipah and Hendra viruses.

Stem cell research endeavors to generate specific subtypes of classically defined "cell types." Here, we generate >90% pure human artery or vein endothelial cells from pluripotent stem cells within 3-4 days. We specified artery cells by inhibiting vein-specifying signals and vice versa. These cells modeled viral infection of human vasculature by Nipah and Hendra viruses, which are extraordinarily deadly (∼57%-59% fatality rate) and require biosafety-level-4 containment. Generating pure populations of artery and vein cells highlighted that Nipah and Hendra viruses preferentially infected arteries; arteries expressed higher levels of their viral-entry receptor. Virally infected artery cells fused into syncytia containing up to 23 nuclei, which rapidly died. Despite infecting arteries and occupying ∼6%-17% of their transcriptome, Nipah and Hendra largely eluded innate immune detection, minimally eliciting interferon signaling. We thus efficiently generate artery and vein cells, introduce stem-cell-based toolkits for biosafety-level-4 virology, and explore the arterial tropism and cellular effects of Nipah and Hendra viruses.

Ancient DNA and deep population structure in sub-Saharan African foragers.

Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa1-4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations3,5. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80-20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.

A Computational Strategy for the Rapid Identification and Ranking of Patient-Specific T Cell Receptors Bound to Neoantigens.

T cell receptor (TCR) recognition of a peptide-major histocompatibility complex (pMHC) is crucial for adaptive immune response. The identification of therapeutically relevant TCR-pMHC protein pairs is a bottleneck in the implementation of TCR-based immunotherapies. The ability to computationally design TCRs to target a specific pMHC requires automated integration of next-generation sequencing, protein-protein structure prediction, molecular dynamics, and TCR ranking. A pipeline to evaluate patient-specific, sequence-based TCRs to a target pMHC is presented. Using the three most frequently expressed TCRs from 16 colorectal cancer patients, the protein-protein structure of the TCRs to the target CEA peptide-MHC is predicted using Modeller and ColabFold. TCR-pMHC structures are compared using automated equilibration and successive analysis. ColabFold generated configurations require an ≈2.5× reduction in equilibration time of TCR-pMHC structures compared to Modeller. The structural differences between Modeller and ColabFold are demonstrated by root mean square deviation (≈0.20 nm) between clusters of equilibrated configurations, which impact the number of hydrogen bonds and Lennard-Jones contacts between the TCR and pMHC. TCR ranking criteria that may prioritize TCRs for evaluation of in vitro immunogenicity are identified, and this ranking is validated by comparing to state-of-the-art machine learning-based methods trained to predict the probability of TCR-pMHC binding.

The evolution and changing ecology of the African hominid oral microbiome.

The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine-platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.

Exploring the potential of a school-based online health and wellbeing screening tool: professional stakeholders' perspectives and experiences.

BACKGROUND: Supporting children and young people's (CYP) mental and physical health is a global policy priority but detecting need and facilitating access to health services and support is challenging. This paper explores professional stakeholders' perspectives of the acceptability, utility and effectiveness of a school-based online health and wellbeing screening tool, the Digital Health Contact (DHC). The DHC, delivered by Public Health School Nurses (PHSN), aims to identify, and put in place strategies to support, unmet health needs among CYP. METHODS: We employed a qualitative study design, using semi-structured interviews. Fourteen key stakeholders involved in the design and implementation of the DHC (commissioners, providers, PHSN and healthcare staff, school leaders) were purposively sampled. Data were analysed thematically. RESULTS: Our analysis generated two key themes: the perceived benefits of the DHC; and challenges in delivering the DHC. Stakeholders perceived the universal application of the DHC with linked follow-up intervention as an effective means of identifying and supporting CYP with unmet needs, and an efficient way to target limited service resources. There were barriers around enabling school engagement in the DHC, typically in terms of logistics, school infrastructure, and perspectives of fit with schools. These barriers were seen as being negated through developing effective working relationships between schools and PHSN. Effective relationships could highlight the potential benefits of participation. Overall, the DHC was seen as a valuable and effective use of resources, with a low burden on school staff. CONCLUSIONS: The DHC, as a universal school-based health and wellbeing screening tool with linked follow-up intervention, has great potential in identifying and supporting unmet health needs among CYP. The perspectives and experiences of those involved in delivering the DHC highlight important considerations which may enable effective implementation and delivery of school screening programmes across other areas.

Twins Support the Absence of Parity-Dependent Fertility Control in Pretransition Populations.

A conclusion of the European Fertility Project in 1986 was that pretransition populations mostly displayed natural fertility, where parity-dependent birth control was absent. This conclusion has recently been challenged for England by new empirical results and has also been widely rejected by theorists of long-run economic growth, where pre-industrial fertility control is integral to most models. In this study, we use the accident of twin births to show that for three Western European-derived pre-industrial populations-namely, England (1730-1879), France (1670-1788), and Québec (1621-1835)-we find no evidence for parity-dependent control of marital fertility. If a twin was born in any of these populations, family size increased by 1 compared with families with a singleton birth at the same parity and mother age, with no reduction of subsequent fertility. Numbers of children surviving to age 14 also increased. Twin births also show no differential effect on fertility when they occurred at high parities; this finding is in contrast to populations where fertility is known to have been controlled by at least some families, such as in England, 1900-1949, where a twin birth increased average births per family by significantly less than 1.

Proteomic Profiling of Serum-Derived Exosomes from Ethnically Diverse Prostate Cancer Patients.

Prostate cancer (PCa) remains the most frequently diagnosed male malignancy in Western countries and the second most common cause of male cancer death in the United States. The relatively elevated PCa incidence and mortality among African American men makes this cancer type a challenging health disparity disease. To increase the chance for successful trea tment, earlier detection and prediction of tumor aggress iveness will be important and need to be resolved. This study demonstrates that small membrane-bound vesicles shed from the tumor called exosomes contain ethnically and tumor-specific biomarkers, and could be exploited for their diagnostic and therapeutic potential.

Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15†Minutes of Antibiotic Exposure.

Rapid antimicrobial susceptibility testing (AST) would decrease misuse and overuse of antibiotics. The "holy grail" of AST is a phenotype-based test that can be performed within a doctor visit. Such a test requires the ability to determine a pathogen's susceptibility after only a short antibiotic exposure. Herein, digital PCR (dPCR) was employed to test whether measuring DNA replication of the target pathogen through digital single-molecule counting would shorten the required time of antibiotic exposure. Partitioning bacterial chromosomal DNA into many small volumes during dPCR enabled AST results after short exposure times by 1) precise quantification and 2) a measurement of how antibiotics affect the states of macromolecular assembly of bacterial chromosomes. This digital AST (dAST) determined susceptibility of clinical isolates from urinary tract infections (UTIs) after 15 min of exposure for all four antibiotic classes relevant to UTIs. This work lays the foundation to develop a rapid, point-of-care AST and strengthen global antibiotic stewardship.

Schlieren visualization of fluid dynamics effects in direct analysis in real time mass spectrometry.

RATIONALE: The success of ambient analysis using plasma-based ion sources depends heavily on fluid dynamics and mass transport efficiency in the sample region. To help characterize the influence of these determining factors, visualization of the gas flow profile for a Direct Analysis in Real Time (DART) ion source at the mass spectrometer atmospheric pressure (AP) interface was performed using the Schlieren technique. METHODS: The DART helium flow pattern was imaged in model systems incorporating different interface designs, i.e. skimmer or capillary inlet, and for sampling strategies using several types of traditional DART sample probes including a glass capillary, swab, and drug tablet. Notably, Schlieren experiments were conducted on instruments equipped with the gas-ion separator tube (GIST) adapter and Vapur® pump, and on setups featuring the transmission mode (TM) DART module used in standard practice. RESULTS: DART sources were seen to expel a collimated, highly laminar helium stream across interface distances up to ~8 cm. The helium stream was robust to the influence of gas temperature (50-500 °C) and flow rate (≤3.5 L min(-1) ), but considerable DART gas deflection or full disruption was observed in each sampling scenario. The severity of the flow disturbance depended on probe size and placement, the GIST/Vapur® settings, or counter-current gas movements present at the interface. CONCLUSIONS: The real-time Schlieren visualizations introduced in this work provide new insight on the fluid dynamics within the DART-MS sample gap while also helping to identify those experimental parameters requiring optimization for improved transmission.

Process and Outcomes From a Youth-Led Campaign to Address Healthy Eating in an Urban High School.

This article describes a pilot youth advocacy initiative for obesity prevention informed by social cognitive theory, social network theory, and theories of community mobilization. With assistance from school and health leaders, adolescent-aged youth led a cafeteria food labeling and social marketing campaign. We implemented an anonymous survey 2 weeks prior to and again at the conclusion of the campaign, and used cafeteria records to track servings of fruits and vegetables. The campaign resulted in a significant increase in youths' confidence to identify healthy foods (OR 1.97, 95 % CI 1.01, 3.84, p = .048), and a significant increase in per person per day servings of fruits (0.02, p = .03) and vegetables (0.01, p = .02). The results of our pilot were promising, and the integration of concepts from multiple theories benefited the implementation process. Obesity prevention initiatives should include strategies that encourage youth to create health promotion community networks and lead changes to their social and physical environments.

How did the European Marriage Pattern persist? Social versus familial inheritance: England and Quebec, 1650-1850.

The European Marriage Pattern (EMP), in place in NW Europe for perhaps 500 years, substantially limited fertility. But how could such limitation persist when some individuals who deviated from the EMP norm had more children? If their children inherited their deviant behaviors, their descendants would quickly become the majority of later generations. This puzzle has two possible solutions. The first is that all those that deviated actually had lower net fertility over multiple generations. We show, however, no fertility penalty to future generations from higher initial fertility. Instead the EMP survived because even though the EMP persisted at the social level, children did not inherit their parents' individual fertility choices. In the paper we show evidence consistent with lateral, as opposed to vertical, transmission of EMP fertility behaviors.

Enhancing Gene Synthesis Security: An Updated Framework for Synthetic Nucleic Acid Screening and the Responsible Use of Synthetic Biological Materials.

Introduction: In response to continuous advancements in synthetic biotechnologies and in the availability of synthetic nucleic acids to the biological research community since the publication of the 2010 HHS synthetic double-stranded DNA (dsDNA) screening framework, the U.S. government undertook a comprehensive and stakeholder-driven review and revision process. This culminated in the publication of a new screening framework for synthetic nucleic acids in October 2023, followed by an Executive Order directing departments and agencies of the U.S. government to take certain measures in support of implementing the screening framework. This review provides an overview of the process by which stakeholder comments were considered and by which the 2023 screening framework was drafted. A summary of expected impacts on the life sciences research community is also provided. Methods: Comments were solicited from synthetic biology stakeholders through the publication of two Federal Register Notices, in 2020 and 2022. The 2020 Notice elicited 15 unique responses totaling 220 pages, and the 2022 Notice elicited 26 unique responses totaling 79 pages. These were considered by a deliberative interagency group, resulting in a revised screening framework in 2023. Discussion and Conclusion: The adoption of the 2023 screening framework, and related provisions in the Executive Order that followed, will impact researchers and biosafety officers across the U.S. bioeconomy. For instance, this screening framework is no longer limited in its recommendations to providers of synthetic dsDNA containing sequences unique to regulated pathogens or toxins, but now includes recommendations to all entities involved in the sale, use, and transfer of all forms of synthetic nucleic acids encoding genetic sequences that contribute to pathogenicity or toxicity-whether from regulated agents or not. Biosafety professionals are emerging as a critical resource for establishing and fostering a culture of biosecurity surrounding synthetic nucleic acids containing these high consequence genetic sequences. Significance: The work presented is significant because the scope of the 2010 screening framework has been expanded to include roles and responsibilities for new entities across the life sciences research landscape. This will likely impact biosafety professionals, who may be well positioned in their institutions to coordinate these new responsibilities.

Cyclic strain dominates over microtopography in regulating cytoskeletal and focal adhesion remodeling of human mesenchymal stem cells.

Human bone marrow-derived mesenchymal stem cell (hMSCs) function depends on chemical factors and also on the physical cues of the microenvironmental niche. Here, this physical microenvironment is recapitulated with controlled modes of mechanical strain applied to substrata containing three-dimensional features in order to analyze the effects on cell morphology, focal adhesion distribution, and gene expression. Ten percentage of strain at 1 Hz is delivered for 48 h to hMSCs cultured on flat surfaces, or on substrata with 15 µm-high microtopographic posts spaced 75 µm apart. Adding strain to microtopography produced stable semicircular focal adhesions, and actin spanning from post to post. Strain dominated over microtopography for expression of genes for the cytoskeleton (caldesmon-1 and calponin 3), cell adhesion (integrin-α2, vinculin, and paxillin), and extracellular matrix remodeling (MMP13) (p<0.05). Overall, attention to external mechanical stimuli is necessary for optimizing the stem cell niche for regenerative medicine.

The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa.

We report the first large-scale palaeoproteomics research on eastern and southern African zooarchaeological samples, thereby refining our understanding of early caprine (sheep and goat) pastoralism in Africa. Assessing caprine introductions is a complicated task because of their skeletal similarity to endemic wild bovid species and the sparse and fragmentary state of relevant archaeological remains. Palaeoproteomics has previously proved effective in clarifying species attributions in African zooarchaeological materials, but few comparative protein sequences of wild bovid species have been available. Using newly generated type I collagen sequences for wild species, as well as previously published sequences, we assess species attributions for elements originally identified as caprine or 'unidentifiable bovid' from 17 eastern and southern African sites that span seven millennia. We identified over 70% of the archaeological remains and the direct radiocarbon dating of domesticate specimens allows refinement of the chronology of caprine presence in both African regions. These results thus confirm earlier occurrences in eastern Africa and the systematic association of domesticated caprines with wild bovids at all archaeological sites. The combined biomolecular approach highlights repeatability and accuracy of the methods for conclusive contribution in species attribution of archaeological remains in dry African environments.

Organotypic stromal cells impact endothelial cell transcriptome in 3D microvessel networks.

Endothelial cells line all major blood vessels and serve as integral regulators of many functions including vessel diameter, cellular trafficking, and transport of soluble mediators. Despite similar functions, the phenotype of endothelial cells is highly organ-specific, yet our understanding of the mechanisms leading to organ-level differentiation is incomplete. We generated 3D microvessel networks by combining a common naïve endothelial cell with six different stromal cells derived from the lung, skin, heart, bone marrow, pancreas, and pancreatic cancer. Single cell RNA-Seq analysis of the microvessel networks reveals five distinct endothelial cell populations, for which the relative proportion depends on the stromal cell population. Morphologic features of the organotypic vessel networks inversely correlate with a cluster of endothelial cells associated with protein synthesis. The organotypic stromal cells were each characterized by a unique subpopulation of cells dedicated to extracellular matrix organization and assembly. Finally, compared to cells in 2D monolayer, the endothelial cell transcriptome from the 3D in vitro heart, skin, lung, and pancreas microvessel networks are more similar to the in vivo endothelial cells from the respective organs. We conclude that stromal cells contribute to endothelial cell and microvessel network organ tropism, and create an endothelial cell phenotype that more closely resembles that present in vivo.

Concept Mapping as a Metacognition Tool in a Problem-Solving-Based BME Course During In-Person and Online Instruction.

Metacognitive skills can have enormous benefits for students within engineering courses. Unfortunately, these metacognitive skills tend to fall outside the content area of most courses, and consequently, they can often be neglected in instruction. In this context, previous research on concept mapping as a teaching strategy points to meaningful learning. The purpose of this innovation paper is to report an application of concept mapping (1) to facilitate metacognition steps in students, and (2) to identify the muddiest points students struggle with, during both in-person and online instruction of a problem-solving-based biomedical engineering course. This innovation article also looks at the usefulness of concept mapping through instructor and student perceptions and students' class performance. The entire concept mapping intervention was conducted during weeks 8-10 of the Spring 2019 in-person quarter and during weeks 3-4 and 8-10 of the Spring 2021 online quarter. The exercise involved concept mapping, explanation and discussion with peers, and answering structured reflection prompts. Each concept map activity was contextualized to the metacognitive knowledge domain of the revised Bloom's taxonomy. The average class performance was compared between students who completed concept mapping vs. those who did not, using a t-test and one-way ANOVA at alpha = 0.05 significance level followed by a Tukey HSD test. Students' concept maps and reported answers were analyzed qualitatively following the concept mapping intervention. During the Spring 2019 in-person quarter, 59.30% of students completed concept mapping with reflection, whereas 47.67% completed it in spring 2021 online instruction. A two-tailed, unpaired t-test indicated that concept mapping did not significantly enhance students' class performance (p > 0.05) within each of the in-person and online instructions. Peers' suggestions to students to improve concept maps revealed themes related to course concepts, prerequisite concepts, and the act of concept mapping itself. Concept mapping was effective in revealing the muddiest points of the course. Concept mapping did not significantly enhance students' class performance either in-person or online instruction (effect sizes were 0.29 for the 2019 in-person quarter and 0.33 for the 2021 online quarter). However, instructors and students' perceptions reflected that concept mapping facilitated metacognition in a problem-solving-based biomedical engineering course both during in-person and online instruction. Most students (78%) were optimistic about the usefulness of concept mapping for this course, and 84% were inclined to apply it for a variety of other courses. Supplementary Information: The online version contains supplementary material available at 10.1007/s43683-022-00066-3.

Single-cell measurement of higher-order 3D genome organization with scSPRITE.

Although three-dimensional (3D) genome organization is central to many aspects of nuclear function, it has been difficult to measure at the single-cell level. To address this, we developed 'single-cell split-pool recognition of interactions by tag extension' (scSPRITE). scSPRITE uses split-and-pool barcoding to tag DNA fragments in the same nucleus and their 3D spatial arrangement. Because scSPRITE measures multiway DNA contacts, it generates higher-resolution maps within an individual cell than can be achieved by proximity ligation. We applied scSPRITE to thousands of mouse embryonic stem cells and detected known genome structures, including chromosome territories, active and inactive compartments, and topologically associating domains (TADs) as well as long-range inter-chromosomal structures organized around various nuclear bodies. We observe that these structures exhibit different levels of heterogeneity across the population, with TADs representing dynamic units of genome organization across cells. We expect that scSPRITE will be a critical tool for studying genome structure within heterogeneous populations.

Organ-on-a-chip model of vascularized human bone marrow niches.

Bone marrow niches (endosteal and perivascular) play important roles in both normal bone marrow function and pathological processes such as cancer cell dormancy. Unraveling the mechanisms underlying these events in humans has been severely limited by models that cannot dissect dynamic events at the niche level. Utilizing microfluidic and stem cell technologies, we present a 3D in vitro model of human bone marrow that contains both the perivascular and endosteal niches, complete with dynamic, perfusable vascular networks. We demonstrate that our model can replicate in vivo bone marrow function, including maintenance and differentiation of CD34+ hematopoietic stem/progenitor cells, egress of neutrophils (CD66b+), and niche-specific responses to doxorubicin and granulocyte-colony stimulating factor. Our platform provides opportunities to accelerate current understanding of human bone marrow function and drug response with high spatial and temporal resolution.

A modified "cross-talk" between histone H2B Lys-120 ubiquitination and H3 Lys-79 methylation.

Western blot analysis is currently the major method utilized for quantitatively assessing histone global modifications. However, there is a growing need to develop a highly specific, accurate, and multisite quantitative method. Herein, we report a liquid chromatography-tandem mass spectrometry-multiple reaction monitoring method to simultaneously quantify multisite modifications with unmatched specificity, sensitivity, and throughput. With one set of purification of histones by high pressure liquid chromatography or SDS-PAGE, nearly 20 modification sites including acetylation, propionylation, methylation, and ubiquitination were quantified within 2 h for two samples to be compared. Using this method, the relative levels of H2B ubiquitination and H3 Lys-79 methylation were quantified in the U937 human leukemia cell line, U937 derivative cell lines overexpressing anti-secretory factor 10 (AF10) and mutant AF10 with the deletion of the hDot1 binding domain OM-LZ. We found that H2B ubiquitination is inversely correlated with H3 Lys-79 methylation. Therefore, we propose that a catalytic and inhibitory loop mechanism may better describe the cross-talk relationship between H2B ubiquitination and H3 Lys-79 methylation.