Continent-wide genomic analysis of the African buffalo (Syncerus caffer).

The African buffalo (Syncerus caffer) is a wild bovid with a historical distribution across much of sub-Saharan Africa. Genomic analysis can provide insights into the evolutionary history of the species, and the key selective pressures shaping populations, including assessment of population level differentiation, population fragmentation, and population genetic structure. In this study we generated the highest quality de novo genome assembly (2.65 Gb, scaffold N50 69.17 Mb) of African buffalo to date, and sequenced a further 195 genomes from across the species distribution. Principal component and admixture analyses provided little support for the currently described four subspecies. Estimating Effective Migration Surfaces analysis suggested that geographical barriers have played a significant role in shaping gene flow and the population structure. Estimated effective population sizes indicated a substantial drop occurring in all populations 5-10,000 years ago, coinciding with the increase in human populations. Finally, signatures of selection were enriched for key genes associated with the immune response, suggesting infectious disease exert a substantial selective pressure upon the African buffalo. These findings have important implications for understanding bovid evolution, buffalo conservation and population management.

Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation.

Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.

The genomes of the yaws bacterium, Treponema pallidum subsp. pertenue, of nonhuman primate and human origin are not genomically distinct.

BACKGROUND: Treponema pallidum subsp. pertenue (TPE) is the causative agent of human yaws. Yaws is currently reported in 13 endemic countries in Africa, southern Asia, and the Pacific region. During the mid-20th century, a first yaws eradication effort resulted in a global 95% drop in yaws prevalence. The lack of continued surveillance has led to the resurgence of yaws. The disease was believed to have no animal reservoirs, which supported the development of a currently ongoing second yaws eradication campaign. Concomitantly, genetic evidence started to show that TPE strains naturally infect nonhuman primates (NHPs) in sub-Saharan Africa. In our current study we tested hypothesis that NHP- and human-infecting TPE strains differ in the previously unknown parts of the genomes. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we determined complete (finished) genomes of ten TPE isolates that originated from NHPs and compared them to TPE whole-genome sequences from human yaws patients. We performed an in-depth analysis of TPE genomes to determine if any consistent genomic differences are present between TPE genomes of human and NHP origin. We were able to resolve previously undetermined TPE chromosomal regions (sequencing gaps) that prevented us from making a conclusion regarding the sequence identity of TPE genomes from NHPs and humans. The comparison among finished genome sequences revealed no consistent differences between human and NHP TPE genomes. CONCLUSION/SIGNIFICANCE: Our data show that NHPs are infected with strains that are not only similar to the strains infecting humans but are genomically indistinguishable from them. Although interspecies transmission in NHPs is a rare event and evidence for current spillover events is missing, the existence of the yaws bacterium in NHPs is demonstrated. While the low risk of spillover supports the current yaws treatment campaign, it is of importance to continue yaws surveillance in areas where NHPs are naturally infected with TPE even if yaws is successfully eliminated in humans.

Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons.

Baboons (genus Papio) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high-coverage whole-genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and interspecies gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes.

Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons.

Baboons (genus Papio ) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high coverage whole genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and inter-species gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal novel patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes. One-Sentence Summary: Genomic data for 225 baboons reveal novel sites of inter-species gene flow and local effects due to differences in admixture.

"I Am a Human": A Process Evaluation of a Nurse-Led Community-Based, Palliative Care Program in Liberia, West Africa.

Liberia is a postwar, post-Ebola, and low-income nation in West Africa with minimal to no palliative care access. In 2017, Partners In Health in collaboration with the Liberian Ministry of Health invested in the development of a nurse-led, community-based palliative care team in southeastern Maryland County at JJ Dossen Memorial Hospital. Between 2017 and 2022, the 9-member team (8 nurses, 1 physician assistant) has enrolled 142 patients under their care. This is a qualitative process evaluation eliciting the experiences, perspectives, and attitudes of patients with cancer to inform future palliative care program delivery improvement and development. Using an exploratory design, n = 8 participants were interviewed using a semi-structured guide. The sample had a mean age of 48 years with an average palliative care clinic enrollment period of 22.5 weeks at the time of interview. The interdisciplinary coding team used an applied thematic text analysis approach and identified 5 themes: history and disease progression, follow-up clinic services, psychological distress and its sources, social support, and spiritual and cultural beliefs. Implications emphasize the need for increased community engagement, primary palliative care capacity development of clinical colleagues in the region, and the support of local and national decision-makers to prioritize palliative care service expansion.

Dysregulation of miR-155 Expression in Professional Mixed Martial Arts (MMA) Fighters.

Psychological and physical stress can induce dysregulation of gene expression via changes in DNA methylation and microRNA (miRNA) expression. Such epigenetic modifications are yet to be investigated in professional Mixed Martial Arts (MMA) fighters subject to highly stressful training involving repetitive head impacts. This study examined differences in DNA methylation and miRNA expression in elite MMA fighters compared to active controls. Global methylation differences between groups were assessed via a LINE-1 assay. At the same time, PCR arrays were used to estimate differential expression in samples of 21 fighters and 15 controls for 192 different miRNAs associated with inflammatory diseases. An Independent-Samples t-Test found no significant difference in LINE-1 methylation between groups. However, an Independent-Samples Mann-Whitney U Test revealed a significant upregulation in the expression of miR-155 in MMA fighter plasma. Since miR-155 has been recognized as an important regulator of neuroinflammation, this dysregulation suggests a possible epigenetic mechanism responsible for chronic inflammation associated with professional-level MMA training. Consistent with other published works, this study highlights the potential of miR-155 not only as a biomarker for monitoring long-term health risks linked to head trauma but also as a target to remediate the impact of chronic neuroinflammation.

Scalable Combinatorial Assembly of Synthetic DNA for Tracking Applications.

Synthetic DNA barcodes are double-stranded DNA molecules designed to carry recoverable information, information that can be used to represent and track objects and organisms. DNA barcodes offer robust, sensitive detection using standard amplification and sequencing techniques. While numerous research groups have promoted DNA as an information storage medium, less attention has been devoted to the design of economical, scalable DNA barcode libraries. Here, we present an alternative modular approach to sequence design. Barcode sequences were constructed from smaller, interchangeable blocks, allowing for the combinatorial assembly of numerous distinct tags. We demonstrated the design and construction of first-generation (N = 256) and second-generation (N = 512) modular barcode libraries, from fewer than 50 total single-stranded oligonucleotides for each library. To avoid contamination during experimental validation, a liquid-handling robot was employed for oligonucleotide mixing. Generating barcode sequences in-house reduces dependency upon external entities for unique tag generation, increasing flexibility in barcode generation and deployment. Next generation sequencing (NGS) detection of 256 different samples in parallel highlights the multiplexing afforded by the modular barcode design coupled with high-throughput sequencing. Deletion variant analysis of the first-generation library informed sequence design for enhancing barcode assembly specificity in the second-generation library.

Ligand Presentation Inside Protein Crystal Nanopores: Tunable Interfacial Adhesion Noncovalently Modulates Cell Attachment.

Protein crystals with sufficiently large solvent pores can non-covalently adsorb polymers in the pores. In principle, if these polymers contain cell adhesion ligands, the polymer-laden crystals could present ligands to cells with tunable adhesion strength. Moreover, porous protein crystals can store an internal ligand reservoir, so that the surface can be replenished. In this study, we demonstrate that poly(ethylene glycol) terminated with a cyclic cell adhesion ligand peptide (PEG-RGD) can be loaded into porous protein crystals by diffusion. Through atomic force microscopy (AFM), force-distance correlations of the mechanical interactions between activated AFM tips and protein crystals were precisely measured. The activation of AFM tips allows the tips to interact with PEG-RGD that was pre-loaded in the protein crystal nanopores, mimicking how a cell might attach to and pull on the ligand through integrin receptors. The AFM experiments also simultaneously reveal the detailed morphology of the buffer-immersed nanoporous protein crystal surface. We also show that porous protein crystals (without and with loaded PEG-RGD) serve as suitable substrates for attachment and spreading of adipose-derived stem cells. This strategy can be used to design surfaces that non-covalently present multiple different ligands to cells with tunable adhesive strength for each ligand, and with an internal reservoir to replenish the precisely defined crystalline surface.

Mathematical modelling Treponema infection in free-ranging Olive baboons (Papio anubis) in Tanzania.

Yaws is a chronic infection caused by the bacterium Treponema pallidum susp. pertenue (TPE) that was thought to be an exclusive human pathogen but was recently found and confirmed in nonhuman primates. In this paper, we develop the first compartmental ODE model for TPE infection with treatment of wild olive baboons. We solve for disease-free and endemic equilibria and give conditions on local and global stability of the disease-free equilibrium. We calibrate the model based on the data from Lake Manyara National Park in Tanzania. We use the model to help the park managers devise an effective strategy for treatment. We show that an increasing treatment rate yields a decrease in disease prevalence. This indicates that TPE can be eliminated through intense management in closed population. Specifically, we show that if the whole population is treated at least once every 5-6 years, a disease-free equilibrium can be reached. Furthermore, we demonstrate that to see a substantial decrease of TPE infection to near-elimination levels within 15 years, the whole population needs to be treated every 2-3 years.

A novel modular modeling approach for understanding different electromechanics between left and right heart in rat.

While ion channels and transporters involved in excitation-contraction coupling have been linked and constructed as comprehensive computational models, validation of whether each individual component of a model can be reused has not been previously attempted. Here we address this issue while using a novel modular modeling approach to investigate the underlying mechanism for the differences between left ventricle (LV) and right ventricle (RV). Our model was developed from modules constructed using the module assembly principles of the CellML model markup language. The components of three existing separate models of cardiac function were disassembled as to create smaller modules, validated individually, and then the component parts were combined into a new integrative model of a rat ventricular myocyte. The model was implemented in OpenCOR using the CellML standard in order to ensure reproducibility. Simulated action potential (AP), Ca2+ transient, and tension were in close agreement with our experimental measurements: LV AP showed a prolonged duration and a more prominent plateau compared with RV AP; Ca2+ transient showed prolonged duration and slow decay in LV compared to RV; the peak value and relaxation of tension were larger and slower, respectively, in LV compared to RV. Our novel approach of module-based mathematical modeling has established that the ionic mechanisms underlying the APs and Ca2+ handling play a role in the variation in force production between ventricles. This simulation process also provides a useful way to reuse and elaborate upon existing models in order to develop a new model.

Mito-phylogenetic relationship of the new subspecies of gentle monkey Cercopithecus mitis manyaraensis, Butynski & De Jong, 2020.

In 2020, a new subspecies was described in the Cercopithecus mitis complex, the Manyara monkey C. m. manyaraensis, Butynski & De Jong, 2020. The internal taxonomy of this species complex is still debated, and the phylogenetic relationships among the taxa are unclear. Here we provide the first mitochondrial sequence data for C. m. manyaraensis to determine its position within the mitochondrial phylogeny of C. mitis. This subspecies clusters within the youngest (internal divergences between 1.01 and 0.42 Ma) of three main taxonomic clades of C. mitis. Its sister lineages are C. m. boutourlinii (Ethiopia), C. m. albotorquatus (Kenya and Somalia), C. m. albogularis (Kenya and Tanzania), and C. m. monoides (Tanzania and Mozambique). In general, the phylogenetic tree of C. mitis based on mitochondrial sequence data indicates several paraphyletic relationships within the C. mitis complex. As in other African cercopithecines (e.g. Papio and Chlorocebus), these data are suitable for reconstructing historic biogeographical patterns, but they are only of limited value for delimitating taxa.

Optimizing the Global Nursing Workforce to Ensure Universal Palliative Care Access and Alleviate Serious Health-Related Suffering Worldwide.

CONTEXT: Palliative care access is fundamental to the highest attainable standard of health and a core component of universal health coverage. Forging universal palliative care access is insurmountable without strategically optimizing the nursing workforce and integrating palliative nursing into health systems at all levels. The COVID-19 pandemic has underscored both the critical need for accessible palliative care to alleviate serious health-related suffering and the key role of nurses to achieve this goal. OBJECTIVES: 1) Summarize palliative nursing contributions to the expansion of palliative care access; 2) identify emerging nursing roles in alignment with global palliative care recommendations and policy agendas; 3) promote nursing leadership development to enhance universal access to palliative care services. METHODS: Empirical and policy literature review; best practice models; recommendations to optimize the palliative nursing workforce. RESULTS: Nurses working across settings provide a considerable untapped resource that can be leveraged to advance palliative care access and palliative care program development. Best practice models demonstrate promising approaches and outcomes related to education and training, policy and advocacy, and academic-practice partnerships. CONCLUSION: An estimated 28 million nurses account for 59% of the international healthcare workforce and deliver up to 90% of primary health services. It has been well-documented that nurses are often the first or only healthcare provider available in many parts of the world. Strategic investments in international and interdisciplinary collaboration, as well as policy changes and the safe expansion of high-quality nursing care, can optimize the efforts of the global nursing workforce to mitigate serious health-related suffering.

Mosquito tagging using DNA-barcoded nanoporous protein microcrystals.

Conventional mosquito marking technology for mark-release-recapture (MRR) is quite limited in terms of information capacity and efficacy. To overcome both challenges, we have engineered, lab-tested, and field-evaluated a new class of marker particles, in which synthetic, short DNA oligonucleotides (DNA barcodes) are adsorbed and protected within tough, crosslinked porous protein microcrystals. Mosquitoes self-mark through ingestion of microcrystals in their larval habitat. Barcoded microcrystals persist trans-stadially through mosquito development if ingested by larvae, do not significantly affect adult mosquito survivorship, and individual barcoded mosquitoes are detectable in pools of up to at least 20 mosquitoes. We have also demonstrated crystal persistence following adult mosquito ingestion. Barcode sequences can be recovered by qPCR and next-generation sequencing (NGS) without detectable amplification of native mosquito DNA. These DNA-laden protein microcrystals have the potential to radically increase the amount of information obtained from future MRR studies compared to previous studies employing conventional mosquito marking materials.

Concordance in HPV Detection Between Self-Collected and Health Provider-Collected Cervicovaginal Samples Using careHPV in Tanzanian Women.

PURPOSE: Cervical cancer screening is one of the strategies to prevent the disease among women at risk. Human papillomavirus (HPV) DNA testing is increasingly used as the cervical cancer screening method because of its high sensitivity. Self-collection of cervical specimens has the potential to improve participation. However, there is only limited information on comparison between self-collected and provider-collected samples with regard to detection of high-risk HPV using the careHPV method. The study aimed to compare HPV detection by careHPV in self-collected and provider-collected cervical samples and to assess the acceptability of self-collection techniques. MATERIAL AND METHODS: Women attending cervical cancer screening clinics at Ocean Road Cancer Institute, Kilimanjaro Christian Medical Centre or Mawenzi Hospital in Tanzania were included in the study. They underwent a face-to-face interview, HIV testing, and collected a self-sample using Evalyn Brush. Subsequently, they had a cervical sample taken by a health provider. Both samples were tested for high-risk HPV DNA using careHPV. RESULTS: Overall, 464 women participated in the study. The high-risk HPV prevalence was 19.0% (95% CI, 15.6 to 22.9) in the health provider samples, but lower (13.8%; 95% CI, 10.9 to 17.3) in the self-collected samples. There was a good overall agreement 90.5% (95% CI, 87.5 to 93.0) and concordance (κ = 0.66; 95% CI, 0.56 to 0.75) between the two sets of samples. Sensitivity and specificity were 61.4% (95% CI, 50.4 to 71.6) and 97.3% (95% CI, 95.2 to 98.7), respectively, varying with age. Most women preferred self-collection (79.8%). CONCLUSION: Overall, self-sampling seems to be a reliable alternative to health-provider collection and is acceptable to the majority of women. However, instructions on proper procedures for sample collection to the women are important.

Measuring interactions of DNA with nanoporous protein crystals by atomic force microscopy.

Crosslinked porous protein crystals are a new biomaterial that can be engineered to encapsulate, stabilize, and organize guest molecules, nanoparticles, and biological moieties. In this study, for the first time, the combined interactions of DNA strands with porous protein crystals are quantitatively measured by high-resolution atomic force microscopy (AFM) and chemical force microscopy. The surface structure of protein crystals with unusually large pores was observed in liquid via high-resolution AFM. Force-distance (F-D) curves were also obtained using AFM tips modified to present or capture DNA. The modification of AFM tips allowed the tips to covalently bind DNA that was pre-loaded in the protein crystal nanopores. The modified tips enabled the interactions of DNA molecules with protein crystals to be quantitatively studied while revealing the morphology of the buffer-immersed protein crystal surface in detail, thereby preserving the structure and properties of protein crystals that could be disrupted or destroyed by drying. The hexagonal space group was manifest at the crystal surface, as were the strong interactions between DNA and the porous protein crystals in question. In sum, this study furthered our understanding of how a new protein-based biomaterial can be used to bind guest DNA assemblies.

A Virtual Coaching Workshop for a Nurse-Led Community-Based Palliative Care Team in Liberia, West Africa, to Promote Staff Well-Being During COVID-19.

ABSTRACT: The coronavirus disease 2019 (COVID-19) pandemic has caused unprecedented system and clinician strain worldwide, disproportionately impacting resource poor settings. This project describes the use of a virtual nurse coaching session to improve the well-being of a nurse-led community-based palliative care team in Liberia, West Africa. Staff response was overwhelmingly positive. Discussion is underway to expand this educational coaching intervention to support additional teams confronting COVID-19 in both East and West Africa. Virtual nurse coaching is an innovative way to enhance staff well-being, improve global health partnerships and knowledge exchange, and foster communication across all levels of education and clinical practice.

Molecular detection of Coxiella burnetii infection in small mammals from Moshi Rural and Urban Districts, northern Tanzania.

Coxiella burnetii is an obligate intracellular bacterium that causes Q fever, a zoonotic disease of public health importance. In northern Tanzania, Q fever is a known cause of human febrile illness, but little is known about its distribution in animal hosts. We used a quantitative real-time PCR (qPCR) targeting the insertion element IS1111 to determine the presence and prevalence of C. burnetii infections in small mammals trapped in 12 villages around Moshi Rural and Moshi Urban Districts, northern Tanzania. A total of 382 trapped small mammals of seven species were included in the study; Rattus rattus (n = 317), Mus musculus (n = 44), Mastomys natalensis (n = 8), Acomys wilson (n = 6), Mus minutoides (n = 3), Paraxerus flavovottis (n = 3) and Atelerix albiventris (n = 1). Overall, 12 (3.1%) of 382 (95% CI: 1.6-5.4) small mammal spleens were positive for C. burnetii DNA. Coxiella burnetii DNA was detected in five of seven of the small mammal species trapped; R. rattus (n = 7), M. musculus (n = 1), A. wilson (n = 2), P. flavovottis (n = 1) and A. albiventris (n = 1). Eleven (91.7%) of twelve (95% CI: 61.5-99.8) C. burnetii DNA positive small mammals were trapped within Moshi Urban District. These findings demonstrate that small mammals in Moshi, northern Tanzania are hosts of C. burnetii and may act as a source of C. burnetii infection to humans and other animals. This detection of C. burnetii infections in small mammals should motivate further studies into the contribution of small mammals to the transmission of C. burnetii to humans and animals in this region.

Factors related to completion of referral among women with suspected cervical cancer and dysplasia in Tanzania.

OBJECTIVE: To investigate completion of referral among women with suspected cervical cancer in Tanzania. METHODS: Retrospective cohort study of 196 women referred from two healthcare clinics to Ocean Road Cancer Institute, Dar es Salaam, between March 2016 and June 2018. Women with precancerous lesions or suspected cancer were interviewed about their knowledge and perception of cervical cancer and referred for follow-up. RESULTS: Most participants were unable to name symptoms (55.1%), prevention methods (88.3%), or treatments (59.0%), although 79.1% rated the disease as severe. Women who came for routine early detection were less likely to complete referral than those who did not (odds ratio [OR], 0.18; 95% confidence interval [CI], 0.05-0.70). Women who knew someone who died from cervical cancer were 5.40 times more likely to complete referral than those who did not. Knowing someone with cervical cancer was a predictor of referral completion in three multivariate models: OR, 5.62 (95% CI, 2.20-14.38); 4.34 (1.64-11.47); and 4.61 (1.72-12.36). Having severe symptoms was a predictor of non-completion in two models: 0.30 (0.12-0.75) and 0.35 (0.14-0.87). CONCLUSION: Patient-directed interventions should include education involving survivors of cancer and dysplasia, whereas system-directed interventions should utilize reminders to increase referral completion.

Comprehensive Cervical Cancer Prevention in Tanzania (CONCEPT) study: Cohort profile.

PURPOSE: Cervical cancer is a major cause of death among women in Eastern Africa, and the distribution of human papillomavirus (HPV) according to HIV status is inadequately characterised in this region. In order to guide future cervical cancer preventive strategies that involve HPV testing, the Comprehensive Cervical Cancer Prevention in Tanzania (CONCEPT) study was established in 2015. The CONCEPT cohort aims to investigate the natural history of HPV and determine acquisition and persistence patterns of high-risk (HR) HPV among HIV-positive and HIV-negative women. Further, the influence of lifestyle and sexual/reproductive factors will be investigated. The main objective of this article is to describe how the CONCEPT cohort was established. PARTICIPANTS: Women aged 25-60 years were enrolled from cervical cancer screening clinics in Dar-es-Salaam and Moshi, Tanzania. Data were collected at baseline, at 14 months (first follow-up) and at 28 months (second follow-up). Biological samples included two cervical swabs for careHPV DNA testing, cytology, Hybrid Capture 2, genotyping and blood samples for HIV. Visual inspection with acetic acid was performed, and sociodemographic, lifestyle and sexual/reproductive characteristics were collected through a standardised questionnaire. FINDINGS TO DATE: 4043 women were included in the cohort from August 2015 to May 2017. At baseline, 696 (17.1%) women were HR HPV positive, and among these, 31.6% were HIV positive; 139 women (3.4%) had high-grade squamous intraepithelial lesions. 3074 women (81%) attended the first follow-up. The majority attended after receiving a phone call reminder (35%) or from home via self-samples (41%). At first follow-up, 438 (14.4%) were HR HPV positive and 30.4% of these were HIV positive. FUTURE PLANS: A second follow-up is underway (17 December 2018-October 2020). We plan to integrate our data with a previous cross-sectional HPV study from Tanzania to increase the power of our findings. Researchers interested in collaborating are welcomed, either by extracting data or jointly requesting further investigation from the cohort.