The Human-Bacterial Pathogen Protein Interaction Networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis

Bacillus anthracis, Francisella tularensis, and Yersinia pestis are bacterial pathogens that can cause anthrax, lethal acute pneumonic disease, and bubonic plague, respectively, and are listed as NIAID Category A priority pathogens for possible use as biological weapons. However, the interactions between human proteins and proteins in these bacteria remain poorly characterized leading to an incomplete understanding of their pathogenesis and mechanisms of immune evasion.In this study, we used a high-throughput yeast two-hybrid assay to identify physical interactions between human proteins and proteins from each of these three pathogens. From more than 250,000 screens performed, we identified 3,073 human-B. anthracis, 1,383 human-F. tularensis, and 4,059 human-Y. pestis protein-protein interactions including interactions involving 304 B. anthracis, 52 F. tularensis, and 330 Y. pestis proteins that are uncharacterized. Computational analysis revealed that pathogen proteins preferentially interact with human proteins that are hubs and bottlenecks in the human PPI network. In addition, we computed modules of human-pathogen PPIs that are conserved amongst the three networks. Functionally, such conserved modules reveal commonalities between how the different pathogens interact with crucial host pathways involved in inflammation and immunity.These data constitute the first extensive protein interaction networks constructed for bacterial pathogens and their human hosts. This study provides novel insights into host-pathogen interactions

Compassion: a scoping review of the healthcare literature

BACKGROUND: Recent concerns about suboptimal patient care and a lack of compassion have prompted policymakers to question the preparedness of clinicians for the challenging environment in which they practice. Compassionate care is expected by patients and is a professional obligation of clinicians; however, little is known about the state of research on clinical compassion. The purpose of this scoping review was to map the literature on compassion in clinical healthcare. METHODS: Searches of eight electronic databases and the grey literature were conducted to identify empirical studies published over the last 25 years. Eligible studies explored perceptions or interventions of compassionate care in clinical populations, healthcare professionals, and healthcare students. Following the title and abstract review, two reviewers independently screened full-texts articles, and extracted study data. A narrative approach to synthesizing and mapping the literature was used. RESULTS AND DISCUSSION: Of 36,637 records, 648 studies were retrieved and 44 studies were included in the review. Less than one third of studies included patients. Six themes emerged from studies that explored perceptions of compassionate care: nature of compassion, development of compassion, interpersonal factors related to compassion, action and practical compassion, barriers and enablers of compassion, and outcomes of compassion. Intervention studies included two compassionate care trials with patients and eight educational programs that aimed to improve compassionate care in clinicians and students. CONCLUSIONS: This review identifies the limited empirical understanding of compassion in healthcare, highlighting the lack of patient and family voices in compassion research. A deeper understanding of the key behaviors and attitudes that lead to improved patient-reported outcomes through compassionate care is necessary

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Detecting the signature of permafrost thaw in Arctic rivers

Climate change induced permafrost thaw in the Arctic is mobilizing ancient dissolved organic carbon (DOC) in to headwater streams, however DOC exported from the mouth of major arctic rivers appears predominantly modern. Here we highlight that ancient (>20,000 ybp) permafrost-DOC is rapidly utilized by microbes (~50% DOC loss in <7 days), and that permafrost-DOC decay rates (0.12 to 0.19 d-1) exceed those for DOC in a major arctic river (Kolyma: 0.09 d-1). Permafrost-DOC exhibited unique molecular signatures, including high levels of aliphatics that were rapidly utilized by microbes. As microbes processed permafrost-DOC, its distinctive chemical signatures were degraded and converged towards those of DOC in the Kolyma River. The extreme biolability of permafrost-DOC and the rapid loss of its distinct molecular signature may explain the apparent contradiction between observed permafrost-DOC release to headwaters and the lack of a permafrost signal in DOC exported via major arctic rivers to the ocean

Common barriers to the use of patient-generated data across clinical settings

Patient-generated data, such as data from wearable fitness trackers and smartphone apps, are viewed as a valuable information source towards personalised healthcare. However, studies in specific clinical settings have revealed diverse barriers to their effective use. In this paper, we address the following question: are there barriers prevalent across distinct workflows in clinical settings to using patient-generated data? We conducted a two-part investigation: a literature review of studies identifying such barriers; and interviews with clinical specialists across multiple roles, including emergency care, cardiology, mental health, and general practice. We identify common barriers in a six-stage workflow model of aligning patient and clinician objectives, judging data quality, evaluating data utility, rearranging data into a clinical format, interpreting data, and deciding on a plan or action. This workflow establishes common ground for HCI practitioners and researchers to explore solutions to improving the use of patient-generated data in clinical practices

Inparanoid ortholog groups.

<p>Summary of ortholog groups identified by Inparanoid <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012089#pone.0012089-Remm1" target="_blank">[28]</a>. The column marked “# clusters (>2 proteins)” is the number of orthologous clusters that contain more than a single protein from each organism. The column marked “# clusters (pathogen interactors)” is the number of orthologous clusters which contain a pathogen protein from each organism that is known to interact with a human protein in our dataset.</p

CPIM results.

<p>Summary of the number of identified CPIMs for each of the algorithms used in this study.</p