Single Population Research Articles

Development and implementation of natural killer cell simultaneous ADCC and direct killing assay

Assays to quantify natural killer (NK) cell killing efficacy have traditionally focused on assessing either direct killing or antibody dependent cell-mediated cytotoxicity (ADCC) independently. Due to the probability that immunotherapeutic interventions affect NK cell-mediated direct killing and NK cell-mediated ADCC differently, we developed an assay with the capacity to measure NK cell-mediated direct killing and ADCC simultaneously with cells from the same human donor. Specifically, this design allows for a single NK cell population to be split into several experimental conditions (e.g., direct killing, ADCC), thus controlling for potential confounders associated with human-to-human variation when assessing immunotherapy impacts. Our Natural Killer cell Simultaneous ADCC and Direct Killing Assay (NK-SADKA) allows researchers to reproducibly quantify both direct killing and ADCC by human NK cells. Furthermore, this optimized experimental design allows for concurrent analysis of the NK cells via flow cytometric immunophenotyping of NK cell populations which will facilitate the identification of relationships between NK cell phenotype and the subsequent killing potential. This assay will be valuable for assessing the broader impact(s) of immunotherapy strategies on both modes of NK cell killing.

The 3237 cm−1 diamond defect: Ultrafast vibrational dynamics, concentration calibration, and relationship to the N3VH0 defect

The dynamics of the 3237 cm−1 local vibrational mode in diamond, associated with an unknown defect, was investigated using ultrafast infrared pump-probe spectroscopy. When pumped at 3237 cm−1, a degenerate probe was used to study the ground state's recovery, while a non-degenerate probe tracked excited state absorption at 3029 cm−1, corresponding to the 1 → 2 vibrational state transition. The similar population lifetimes for the ground state recovery and excited state absorption suggests a single population decay pathway, with a lifetime of T1=2.2±0.1ps. Perturbed free induction decay signals observed in negative time delays gave the dephasing time of the coherent state between the 0 and 1 vibrational states, and further predicted the 3029 cm−1 transition. Images from FTIR microscopy show that the 3237 cm−1 feature and the 3107 cm−1 absorption line from the N3VH0 defect are not correlated, and our pump-probe study shows the 3237 cm−1 feature does not share a common ground state with the N3VH0 defect, both of which suggest that this local vibrational mode does not originate from the N3VH0 defect. A calibration factor was obtained via a Morse potential model constrained by the observed transition energies, which relates the concentration of the defect producing the 3237 cm−1 feature to its absorption coefficient measured by FTIR spectroscopy. Based on FTIR absorption spectroscopy under uniaxial stress, we further assign a trigonal symmetry character to the defect that gives the 3237 cm−1 feature. The results presented are consistent with the theory that the 3237 cm−1 feature originates from the N4VH defect, the quantification of which allows better tracking of the nitrogen content in diamond.

Within- and between-population comparisons suggest independently acting selection maintaining parallel clines in Scots pine (Pinus sylvestris).

Parallel clines in traits related to adaptation in a species can be due to independent selection on a pair of traits, or due to selection in one trait resulting in a parallel cline in a correlated trait. To distinguish between the mechanisms giving rise to parallel adaptive population divergence of multiple traits along an environmental gradient we need to study variation, correlations, and selective forces within individual populations along the gradient. In many tree species, budset timing (BST) forms a latitudinal cline, and parallel clinal variation is also found in other seedling traits, such as first-year height (FYH) and fall frost injury (FFI). In this study, we set up a common garden experiment with open pollinated progeny from natural populations of Scots pine (Pinus sylvestris), with one large sample from single population (500 families) and smaller samples from across a latitudinal gradient. BST, FYH and induced FFI were first measured in a greenhouse. The seedlings were then planted in the field, where survival and height were measured at the age of 9 years as fitness proxies. We compared between- and within-population variation and genetic correlations of these three seedling traits, and estimated selection gradients at the family level in our main population, taking into account the potential effects of seed weight. Between-population genetic correlations between seedling traits were high (0.76-0.95). Within-population genetic correlations in the main population were lower (0.14-0.35), as in other populations (0.10-0.39). Within population, extensive adaptive variation persists in the seedling traits, in line with rather weak selection gradients, yet maintaining the clines. Although our sampling does not cover the whole cline equally, the results suggest that the individual clines in these traits are maintained by largely independently acting selection, which results in fewer constraints in adaptation under changing climate.

CHALLENGES OF COORDINATION AND PUBLIC UNDERSTANDING IN IMPLEMENTING NIK AND NPWP INTEGRATION POLICIES

The use of single or integrated population identity data is starting to be commonly used in many countries, including Indonesia. One of the main population identity data in Indonesia that is starting to be integrated with NIK data is taxation data via the Taxpayer Identification Number (NPWP). Currently, the implementation of the policy for integrating NIK data with NPWP has been implemented and will continue until all taxpayers actually use NIK numbers. as a basis for tax obligations. This journal aims to provide an overview of the problems that occur and need to be mitigated in the implementation of the NIK and NPWP Integration Policy currently underway in Indonesia. The results of the research illustrate that even though the implementation of the NIK and NPWP integration policy has gone quite well, there are still main issues that still need to be faced, where these main issues have the same root thread, namely: (1) Challenges of Coordination and Synergy between K/L Sectors; and (2) Risk of Differences in Understanding at Community Level.

Discovery of an extended GeV counterpart to the TeV source 1LHAASO J1945+2424 in Fermi-LAT data

ABSTRACT With almost 15 yr of data taken by the Large Area Telescope (LAT) onboard the Fermi satellite we discovered an extended source of GeV emission in the region of the very high energy (TeV) source 1LHAASO J1945+2424. This TeV source is more extended than the LAT source. The spectrum of the GeV emission is hard (with a photon spectral index ∼1.5) and connects smoothly with that of the TeV source, indicating a likely common origin. In order to explain the origin of the γ-rays we explore scenarios that are typically used for supernova remnants (SNRs) and pulsar wind nebulae (PWNe). For an SNR with a single particle population, a leptonic particle distribution in the form of a broken power law with a break energy of ∼3.7 TeV explains the spectra well, while in the hadronic scenario a simple power law with a hard spectral index of ∼1.64 is necessary. In the PWN scenario, reasonable parameters are obtained for a source age of 10 kyr and current pulsar spin-down luminosity of ∼1034 erg s−1.

Utilization of Imaging for Severe Injuries at the Beijing 2022 Winter Olympic Games.

Purpose: In order to better understand the imaging of severe trauma in sport, this study describes the imaging modalities utilized to image athletes who experienced severe traumatic injuries at the Beijing Winter Olympic Games 2022, the distribution of these modalities in relation to the sporting facilities, and the types of injuries imaged in each sport. Methods: This is a retrospective analysis with descriptive tables and figures, performed on a single population (athletes of the Beijing Winter Olympic Games 2022). Results: Of the 2871 athletes in the Beijing Winter Olympic Games, there were 40 athletes with severe injuries who underwent medical imaging. MRI was used more often than Radiography or CT. Athletes at venues without MRI on site had to be transferred to adjacent hospitals for care. Alpine and Freestyle skiing athletes experienced the majority of severe traumatic injuries at this Olympic Games, and the majority of injuries were to the lower limb. Conclusions: Access to medical imaging for severely injured athletes is a critical consideration in the organization of any sporting event. MRI in particular is highly utilized in this population.

Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen

BackgroundIn agricultural ecosystems, outbreaks of diseases are frequent and pose a significant threat to food security. A successful pathogen undergoes a complex and well-timed sequence of regulatory changes to avoid detection by the host immune system; hence, well-tuned gene regulation is essential for survival. However, the extent to which the regulatory polymorphisms in a pathogen population provide an adaptive advantage is poorly understood.ResultsWe used Zymoseptoria tritici, one of the most important pathogens of wheat, to generate a genome-wide map of regulatory polymorphism governing gene expression. We investigated genome-wide transcription levels of 146 strains grown under nutrient starvation and performed expression quantitative trait loci (eQTL) mapping. We identified cis-eQTLs for 65.3% of all genes and the majority of all eQTL loci are within 2kb upstream and downstream of the transcription start site (TSS). We also show that polymorphism in different gene elements contributes disproportionally to gene expression variation. Investigating regulatory polymorphism in gene categories, we found an enrichment of regulatory variants for genes predicted to be important for fungal pathogenesis but with comparatively low effect size, suggesting a separate layer of gene regulation involving epigenetics. We also show that previously reported trait-associated SNPs in pathogen populations are frequently cis-regulatory variants of neighboring genes with implications for the trait architecture.ConclusionsOverall, our study provides extensive evidence that single populations segregate large-scale regulatory variation and are likely to fuel rapid adaptation to resistant hosts and environmental change.

Clinical Chemistry and Haematology Values of a Captive Population of Humboldt Penguins (Spheniscus humboldti).

Reference intervals for clinical chemistry and haematology analytes are essential for the interpretation of blood results, but limited data are available for Humboldt penguins (Spheniscus humboldti) in zoological collections as well as in the wild. The aim of the present study was therefore to establish reference intervals for a series of clinical chemistry and haematology analytes in a single zoological population of Humboldt penguins. Furthermore, possible variations of the analytes influenced by the age and sex of the individuals were investigated. Lithium heparinized plasma and whole blood samples from 39 animals were analysed and statistically evaluated. The following clinical chemistry analytes were significantly higher in females: glutamate dehydrogenase (p = 0.0003), alanine transaminase (p = 0.0005), alkaline phosphatase (p = 0.0245), aspartate aminotransferase (p = 0.0043), creatine kinase (p = 0.0016), lactate dehydrogenase (p < 0.0001), inorganic phosphorus (p = 0.0223), and sodium (p = 0.0415). No significant differences between males and females were found for any haematology analyte. Cholesterol (p = 0.0233; -0.39), white blood cell count (p = 0.0208; -0.40), and absolute heterophiles (p = 0.0148; -0.42) had significant negative correlations with the age of the penguins. The results indicate that the factors of sex and age should be considered when interpreting the results of haematological and clinical biochemistry assays, and further studies are needed to determine whether there are more differences in other age groups or seasons.

Baseline Urinalysis of the Fully Marine, Herbivorous Dugong (Dugong dugon)

The dugong (Dugong dugon) is a fully marine mammal that grazes in nearshore seagrass meadows and whose health is vulnerable to human coastal activities. This study establishes urine baseline ranges for apparently healthy dugongs that can be used as health biomarkers. Voluntary urine samples (uncontaminated by seawater) were collected from 71 wild-caught dugongs in Moreton Bay, Australia, that were held out of water during an annual health assessment from 2008 to 2022. Urine was analysed for qualitative characteristics (colour, turbidity, odour), biochemistry through reactive urinalysis test strips, urine specific gravity (USG) by refractometer, electrolytes by flame photometry, sediment by microscopy, and bacterial culture. Urine of dugongs was typically pale yellow, clear to slightly cloudy, and mildly odorous. Urine was usually slightly alkaline (mean pH 8), and USG was low (mean 1.018). Urinalysis from dipstick indicated consistently negative readings for the presence of glucose, urobilinogen, bilirubin, ketones, and nitrites. Urinary protein was detected in 85% of sampled dugongs. Haemolysed red blood cells were recorded in &gt; 85% of urine samples; microscopy indicated light haematuria (intact red blood cells) in 16% of samples. Seven percent of dugongs had detectable levels of leukocytes suggesting the possibility of mild urinary tract infection. Urinary sediment containing epithelial cells, keratinaceous debris, calcium carbonate crystalluria, and rare struvite crystals were typical. Light to moderate levels of bacteria were present in urine samples, with variable mixed growths, including Halomonas aquamarina, Pseudomonas stutzeri, Photobacterium damselae, Psychrobacter spp., and Staphylococcus aureus. Spermatozoa were present in the urine of 32% of the sexually mature males. Physical characteristics and chemistry of dugong urine showed some similarities to those of manatees and other herbivores. These baseline urinalysis data for healthy wild dugongs in a single population are valuable benchmarks against which dugongs of variable health status (including compromised dugongs) and from other localities may be compared.

Sanitary condition and hygienic practice of street food vendors in selected towns of Ethiopia: A cross-sectional study addressing public health concern

BackgroundStreet foods are ready-to-eat foods prepared and/or sold by vendors and hawkers in public places such as streets and plazas. Despite being widely available and affordable, they pose a significant public health risk. ObjectiveThis study aims to assess the hygienic practices of street food vendors, sanitary condition of their stalls and associated factors in selected towns of Ethiopia. MethodCommunity-based Cross-sectional study design was used from December 2022 to January 2023 in Addis Ababa, Dire Dawa, Hawassa, and Jimma towns of Ethiopia. A total of 1168 street food-vending stalls were determined using a single population proportion formula. Proportional allocation to the total population of the towns was used to assign the number of street food vending stalls to each town and sub cities. The interviewer-administered questionnaire and an observational checklist were used to collect data. Bivariate and multivariate analyses were run using statistical Package for Social Sceinces (SPSS) V-23. ResultThe study included 926 street food vendors from Addis Ababa, 84 from Dire Dawa, 99 from Hawassa, and 59 from Jimma. The majority of respondents (86%) were female, with a mean age of 31.26. 60% of respondents were married, and 57% had completed primary school. 18% of street food vendors prepared their food on the street, with no shelter or shade. The overall good hygienic practices of the street food vendors were 16% while the good sanitary status of the vending stalls was 6.8 %. Sex, work experience, receiving training on food safety, having medical checkup, availability of hand washing facilities, and having good knowledge on food safety were predictors of good hygienic practice. ConclusionMost of the street food vendors had poor hygienic practices as well as their vending stalls had poor sanitary conditions. Hence, encouragement and support for street food vendors to have improved water, sanitation, and hygiene facilities in the vicinity, along with strict regulations, will help the vendors provide safe food to consumers, thereby protecting the public's health.

Optimal antiplatelet therapy for patients after antiplatelet therapy-induced gastrointestinal bleeding: when to resume?

Abstract Background Adjusting antiplatelet strategies after antiplatelet-associated gastrointestinal bleeding (GIB) is a complex clinical challenge. there is no uniform answer to the question of when it is safe to restart antiplatelet therapy after GIB. Objective To assess the risk of outcomes at different times of resumption of antiplatelet therapy and explored the optimal time to resume therapy. Methods The study analyzed consecutive patients with antiplatelet-associated GIB from our hospital information system between October 2019 and June 2022. The primary outcomes were recurrent bleeding, major adverse cardiovascular and cerebrovascular events (MACE), and all-cause death. Multivariate-adjusted Cox proportional hazards models were used to evaluate the risks of these outcomes. The receiver operating characteristic curve was used to find the optimal time to resume treatment. Results Of the 617 patients with GIB after antiplatelet therapy successfully followed up, the median follow-up was 246 (interquartile range: 120–466) days, The mean age was 68.38 ± 10.68 years, 70.99% were male, and the age-adjusted Charlson comorbidity index score was 7.16 ± 1.96 points. Most patients (87.36%) interrupted therapy after GIB and 45.22% resumed within 90 days, of which 35.13% resumed within 7 days and 64.87% resumed after 7 days. Resumption therapy had a low risk of recurrent bleeding (uninterrupted as a reference: HR 0.32, 95% CI 0.15–0.67, p = 0.003), MACE (no resumption as a reference: HR 0.66, 95% CI 0.45–0.98, p = 0.037), and all-cause death (no resumption as a reference: HR 0.18, 95% CI 0.08–0.40, p＜0.001). And resuming therapy within 7 days had a lower risk of MACE (HR 0.18, 95% CI 0.08–0.44, p＜0.001) than after 7 days without a significantly higher risk of re-bleeding. The optimal time point for resuming therapy in this study was 9 days. Conclusion Resuming antiplatelet therapy after GIB provides a higher net clinical benefit. Early resumption of antiplatelet therapy (&amp;lt;7 days) significantly reduces the risk of MACE events. Although the risk of re-bleeding is increased, it is not statistically significant and has good clinical benefit. After analyzing the composite endpoint events, 9 days might be the optimal time to resume therapy for the antiplatelet population, especially for the single antiplatelet population. Our study provides new clinical data for the antiplatelet population after GIB to help physicians make better clinical decisions.

Neural landscape diffusion resolves conflicts between needs across time

Animals perform flexible goal-directed behaviours to satisfy their basic physiological needs1–12. However, little is known about how unitary behaviours are chosen under conflicting needs. Here we reveal principles by which the brain resolves such conflicts between needs across time. We developed an experimental paradigm in which a hungry and thirsty mouse is given free choices between equidistant food and water. We found that mice collect need-appropriate rewards by structuring their choices into persistent bouts with stochastic transitions. High-density electrophysiological recordings during this behaviour revealed distributed single neuron and neuronal population correlates of a persistent internal goal state guiding future choices of the mouse. We captured these phenomena with a mathematical model describing a global need state that noisily diffuses across a shifting energy landscape. Model simulations successfully predicted behavioural and neural data, including population neural dynamics before choice transitions and in response to optogenetic thirst stimulation. These results provide a general framework for resolving conflicts between needs across time, rooted in the emergent properties of need-dependent state persistence and noise-driven shifts between behavioural goals.

Genetic diversity of Citrullus colocynthis populations using phytochemical analysis and SCoT marker variations

AbstractCitrullus colocynthis L. Schard (bitter melon) is a drought-resistant medicinal plant growing in Egypt and many other countries in the arid environments of the World. In Egypt, it is abundant in several locations in Egypt's Eastern Desert, extending from the Nile River eastward to the Red Sea, particularly in the Kosseir region on the Red Sea coast. It has a wide range of applications in traditional medicine due to its anti-inflammatory, antibacterial, antioxidant, and anesthetic features. In this study, the genetic diversity was explored using chemical analysis of the secondary metabolites in seed extract in 15 populations from different sites in the Eastern Desert of Egypt to correlate the chemical variation with genetic differences among populations as revealed by DNA fingerprinting using the Start Codon Targeted (SCoT) markers. A total of 81 chemical compounds were identified from the 15 populations. Retention time, peak area percentage, molecular weight, and chemical formula were determined for each compound. Ten SCoT primers produced 137 bands in the 15 populations of these; 85 bands were polymorphic, 50 were monomorphic, and two bands were unique to a single population. Populations located in the southern part of the Eastern Desert have similar levels of phytochemical and genetic diversity and are differentiated from populations in the northern part. On the other hand, populations in the middle part show a small resemblance to other populations in the north and south, indicating an impact of the ecology on the genetic differentiation and the chemical composition of the secondary metabolites in C. colocynthis.

117 Combining Large Broiler Populations into a Single Genomic Evaluation: Dealing with Genetic Divergence

Abstract Combining populations that diverged at some point is a common practice, especially in poultry, where generation intervals are short and genetic evaluations should be available often. This study assessed whether combining large, divergent broiler populations into one genomic evaluation is feasible and the best strategy for doing that in single-step GBLUP. The pedigree for populations 1 and 2 included 397,954 and 411,780 animals, of which 154,911 and 168,429 were genotyped. Phenotypes for body weight (g), carcass yield (%), mortality (0-1), and feet health (0-6) were available for 397,954 animals in population 1 and 411,780 in population 2. A four-trait model was used in the analyses, and the genetic differences between the two populations were modeled in different ways: M1) included an extra fixed effect that accounted for population origin; M2) added origin-specific fixed effects, where the animal origin was concatenated with all fixed effects in the model. The two models were compared against a conventional model without accounting for the animal origin as a fixed effect (M0). Unknown parent groups (UPG) were fit to account for the genetic differences in M0, M1, and M2; therefore, they were set based origin population of the animal and sex. The models were evaluated based on accuracy, bias, and dispersion from the linear regression (LR) method and predictive ability (PA), where GEBV in the reduced data was compared against phenotypes adjusted for fixed effects. Validations were done separately in single and multi-populations to better assess the benefits of combining the two populations. Overall, the accuracy obtained by PA was less than by LR. No apparent accuracy, PA, bias, and dispersion differences were observed among the multi-population models across all traits. This was also true when comparing validation parameters in a multi-population against the ones from a single population. However, we observed that animals from one population were always superior to the other. A multi-trait model was applied, treating the same trait in each population differently. Genetic correlations between the same trait in different populations were moderate to low, suggesting that the two lines should possibly be evaluated separately. Defining whether populations should be combined in a single evaluation may go beyond validation parameters. Identifying if traits are the same across populations is crucial for the feasibility of combined evaluations.

Genetic Mapping of a Novel Gene PmAege7M from Aegilops geniculata Conferring Resistance to Wheat Powdery Mildew.

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most damaging foliage diseases of wheat across the world. Aegilops geniculata Roth is a valuable gene resource for enhancing wheat resistance to powdery mildew. This study identified Ae. geniculata accession PI 487224 as immune and PI 487228 as susceptible to powdery mildew. Genetic analysis of the F1, F2, and F2:3 progeny derived from PI 487224 × PI 487228 showed that powdery mildew resistance in PI 487224 was controlled by two independent dominant genes located on two different nonhomologous chromosomes. By combing bulked segregant RNA-Seq, genetic linkage analysis of a single resistance gene segregation population, and marker analysis of a set of 14 wheat-Ae. geniculata chromosome addition lines, one of the resistance genes, temperately designated PmAege7M, was mapped to a 4.9-cM interval flanked by markers STS7-55926 and SNP7-45792/STS7-65911 on the long arm of chromosome 7 Mg of PI 487224, spanning 604.73 to 622.82 Mb on the 7D long arm based on the Ae. tauschii reference genome (Aet_v4.0). The map and closely linked markers of PmAege7M from Ae. geniculata in this study will facilitate the transfer of PmAege7M into common wheat and fine mapping of the gene.

Client satisfaction and associated factors towards the health service provided to members of a community-based health insurance scheme in Southern Ethiopia.

Globally, 1.3 billion poor people have no access to health services due to their inability to afford payment when they need services. According to a report published by the WHO in 2014, globally 150 million people are pushed into poverty as a result of direct payment for health services. This study aims to assess the satisfaction level of clients and associated factors toward health services provided to members of a community-based health insurance (CBHI) scheme. An institutional-based cross-sectional study design was employed. A total sample size of 393 people was estimated using a single population formula, and three health facilities (HFs) were selected using a simple random sampling method, whereas study participants were selected by using a systematic sampling method. All patients who visited the HFs were included, whereas women who visited the HFs for maternity service were excluded from the study. A reliability test (Cronbach's alpha) was performed to determine the internal consistency for these items to measure the satisfaction level of the clients. Epi Info software version 7 was used to calculate the sample size and to enter data, whereas further data cleaning and analysis were conducted using SPSS software version 20. A total of 367 clients enrolled in the community-based health insurance scheme were interviewed, showing a response rate of 93%. The reliability test (Cronbach's alpha) value for the items used to measure level of client satisfaction was 0.817. The overall level of the clients' mean satisfaction toward health service provision was 63.1% (3.95 + 0.47 SD). This study found that age with AOR = 0.11 [95% CI (0.01-0.79)], residence with AOR = 1.80 [95% CI (1.79-3.66)], number of family with AOR = 2.27 [95% CI (1.46-11.22)], frequency of visits to HFs with AOR = 13.62 [95% CI (2.09-88.58)], and clients' level of knowledge with AOR = 3.33 [95% CI (1.06-10.42) had a statistical significant association with client satisfaction toward health service provision. Our study found that the perceived level of client satisfaction is higher than previous studies. Residence, frequency of visits, level of knowledge, payment during referral time, number of family members, and frequency of visits were identified as predictors of client satisfaction on the health service provision.

Human Adult Long-Term Repopulating Hematopoietic Stem Cells Can be Purified By Surface cMPL Expression

Simple combinations of markers that reliably demarcate human long-term repopulating hematopoietic stem cells (LT-HSCs) would facilitate our understanding of their unique molecular state and the development of stem cell-based therapeutics. The complex CD34+CD38-CD45RA-CD90+CD49f+ phenotype is now routinely accepted to define a subset of cord blood CD34+ cells enriched in LT-HSCs (Notta, Science 2011). The same phenotype with the addition of rhodamine can enrich human LT-HSCs within mobilized peripheral blood (MPB) CD34+ cells, but lower stem cell enrichment is observed (Huntsman, Blood 2015). The hematopoietic cytokine thrombopoietin (TPO) and its receptor cMPL act as primary regulators of HSC function. In recent clinical studies, the synthetic TPO agonist eltrombopag was shown to improve long-term trilineage hematopoiesis in patients with immune aplastic anemia, providing evidence that activation of cMPL receptor stimulates residual multipotent LT-HSCs within the bone marrow (BM). Building on these observations, we hypothesized that cMPL might also be a relevant marker to delineate LT-HSC activity within human adult CD34+ cell populations and provide the basis for a novel LT-HSC purification scheme. To assess the utility of surface cMPL expression for purification of human adult LT-HSCs, we first performed cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) of human MPB CD34+ cells from a healthy volunteer. CITE-seq was conducted with antibodies designed to react with human cMPL receptor and previously described HSC epitopes (CD34, CD38, CD90, CD45RA, and CD49f). We identified 7 distinct clusters in dimension-reduction (UMAP) analysis. By confirming expression levels of HSPC gene signatures and HSC surface markers, such as CD38, we assigned each CD34+ cell cluster to a distinct HSPC subpopulation, including a single LT-HSC population (cluster 2) (Fig A). Notably, CD34+ cell subsets expressing higher levels of surface cMPL expression were highly enriched in transcriptionally defined HSC population (cluster 2) and consistently co-expressing the known human LT-HSC phenotypic markers, including lower levels of surface CD38 and CD45RA expression and higher levels of surface CD90 and CD49f expression (Fig B). To determine whether surface cMPL expression can enrich functional LT-HSCs, we next performed serial xenotransplantation assays. We used fluorescence-activated cell sorting to partition human MPB CD34+ cells into cMPL high (top 10%) and cMPL low (bottom 10%) populations, and transplanted these cells into immunodeficient NBSGW mice. Serial peripheral blood (PB) sampling of primary xenografted mice revealed a striking difference in patterns of hematopoietic reconstitution over time between the two groups. In mice transplanted with cMPL high cells, human cell chimerism increased gradually throughout the 16-week engraftment period, while a progressive decline in engraftment was observed in the cMPL low group. Notably, mean human cell engraftment within the PB, BM and spleen of mice transplanted with cMPL high cells was 209-fold (p &amp;lt; 0.01), 37-fold (p &amp;lt; 0.0001) and 283-fold (p &amp;lt; 0.001) higher than mean human cell chimerism in the cMPL low group at 16 weeks post-transplantation, respectively. These data suggest that cMPL high and cMPL low populations are distinctly enriched in LT-HSCs and hematopoietic progenitors, respectively. Next, to quantitatively compare the frequency of self-renewing LT-HSCs within the cMPL high and cMPL low HSPC subsets, human CD45+ cells obtained from the BM of primary mice were injected into secondary NBSGW mice at limiting dilution and BM engraftment was measured at 16 weeks post-transplantation (total period of engraftment: 32 weeks). After accounting for engraftment parameters (i.e., cell dose and engraftment levels) in both primary and secondary mice, extreme limiting dilution analysis computed self-renewing LT-HSC frequencies of 1 in 1,267 within the cMPL high CD34+ cell population, and 1 in 149,010 in the cMPL low CD34+ cell fraction, representing a 116-fold enrichment of LT-HSCs using cMPL as a single marker purification strategy. Collectively, these data suggest that cMPL expression can effectively delineate LT-HSCs in human adult CD34+ HSPCs and thus serve as an additional relevant marker for the development of human adult HSC targeting therapeutics.

Genetic analysis of two species of Mnomen in the Kalamazoo Watershed reveal panmixia in Z. Aquatica, structure among Z. Palustris, and hybridization in areas of sympatry.

Mnomen or wild rice of the genus Zizania is an important part of Native American culture, especially in Michigan for the Ojibwe nation. An oil spill in 2010 along the Kalamazoo River and the subsequent clean-up lead to renewed interest in management of Mnomen within the Kalamazoo watershed. The affected water bodies were surveyed for Zizania species to map existing populations, determine the existing genetic diversity and species present, and to identify potential hybridization. Using Traditional Ecological Knowledge of rice beds and opportunistic sampling of encountered plants, 28 rice beds were sampled. Two species of Zizania were identified Z. palustris and Z. aquatica. Genetic diversity was measured using 11 microsatellite loci and was moderately high for both species (Z. aquatica HE = 0.669, H0 = 0.672, n=26 and Z. palustris HE = 0.697, H0 = 0.636, n=57). No evidence of population bottle-necking was found. Z. palustris was found to have k=3 populations on the landscape, while Z. aquatica was found to be a single panmictic population. Several individual hybrids were confirmed using genotyping and they were all found in areas where the two species co-occurred. Additionally, Z. aquatica was found to have expanded into areas historically with only Z. palustris downstream of the oil spill, potentially due to dredging and sediment relocation as part of the clean-up effort.

Across-country genetic and genomic analyses of foot score traits in American and Australian Angus cattle

BackgroundHoof structure and health are essential for the welfare and productivity of beef cattle. Therefore, we assessed the genetic and genomic background of foot score traits in American (US) and Australian (AU) Angus cattle and investigated the feasibility of performing genomic evaluations combining data for foot score traits recorded in US and AU Angus cattle. The traits evaluated were foot angle (FA) and claw set (CS). In total, 109,294 and ~ 1.12 million animals had phenotypic and genomic information, respectively. Four sets of analyses were performed: (1) genomic connectedness between US and AU Angus cattle populations and population structure, (2) estimation of genetic parameters, (3) single-step genomic prediction of breeding values, and (4) single-step genome-wide association studies for FA and CS.ResultsThere was no clear genetic differentiation between US and AU Angus populations. Similar heritability estimates (FA: 0.22–0.24 and CS: 0.22–0.27) and moderate-to-high genetic correlations between US and AU foot scores (FA: 0.61 and CS: 0.76) were obtained. A joint-genomic prediction using data from both populations outperformed within-country genomic evaluations. A genomic prediction model considering US and AU datasets as a single population performed similarly to the scenario accounting for genotype-by-environment interactions (i.e., multiple-trait model considering US and AU records as different traits), even though the genetic correlations between countries were lower than 0.80. Common significant genomic regions were observed between US and AU for FA and CS. Significant single nucleotide polymorphisms were identified on the Bos taurus (BTA) chromosomes BTA1, BTA5, BTA11, BTA13, BTA19, BTA20, and BTA23. The candidate genes identified were primarily from growth factor gene families, including FGF12 and GDF5, which were previously associated with bone structure and repair.ConclusionsThis study presents comprehensive population structure and genetic and genomic analyses of foot scores in US and AU Angus cattle populations, which are essential for optimizing the implementation of genomic selection for improved foot scores in Angus cattle breeding programs. We have also identified candidate genes associated with foot scores in the largest Angus cattle populations in the world and made recommendations for genomic evaluations for improved foot score traits in the US and AU.

Acahualinca, Nicaragua, a scientifically significant site of ancient human footprints in the New World

Abstract Ancient human footprints have been known from Managua, Nicaragua, since the 1880s. The main footprint site, long preserved in the Acahualinca Tracks Museum ( Huellas de Acahualinca ), reveals hundreds of human footprints that represent a minimum of 12 clearly defined trackways and a trampled trail or path. Deer, opossum and bird tracks are also present at Acahualinca, and bison and tapir tracks have been documented from the nearby and stratigraphically equivalent El Recreo site. The age of the Acahualinca footprints is controversial, but the best current estimate is about 2–2.2 ka BP. The Acahualinca site is one of the most scientifically important human footprint sites known from the Holocene. It exhibits footprints that are very abundant, well-preserved, accessible for study and part of a large sample that demonstrates variation within a single population. The Acahualinca site has historical, cultural and archaeological importance in preserving at least two intervals of human occupation, that of the footprints and of the ceramics in much younger layers. Its significance to anthropology and palaeontology as a sub-fossil footprint locality is clear and the volcanological history of the area is intimately related to determining the age and the circumstances of footprint registration at Acahualinca. The Acahualinca footprints merit geoheritage status.