Three-dimensional chromatin in infectious disease-A role for gene regulation and pathogenicity?

The recent Coronavirus Disease 2019 pandemic has once again reminded us the importance of understanding infectious diseases. One important but understudied area in infectious disease research is the role of nuclear architecture or the physical arrangement of the genome in the nucleus in controlling gene regulation and pathogenicity. Recent advances in research methods, such as Genome-wide chromosome conformation capture using high-throughput sequencing (Hi-C), have allowed for easier analysis of nuclear architecture and chromosomal reorganization in both the infectious disease agents themselves as well as in their host cells. This review will discuss broadly on what is known about nuclear architecture in infectious disease, with an emphasis on chromosomal reorganization, and briefly discuss what steps are required next in the field.

Targeting Patients' Cognitive Load for Telehealth Video Visits Through Student-Delivered Helping Sessions at a United States Federally Qualified Health Center: Equity-Focused, Mixed Methods Pilot Intervention Study.

BACKGROUND: The task complexity involved in connecting to telehealth video visits may disproportionately impact health care access in populations already experiencing inequities. Human intermediaries can be a strategy for addressing health care access disparities by acting as technology helpers to reduce the cognitive load demands required to learn and use patient-facing telehealth technologies. OBJECTIVE: We conducted a cognitive load theory-informed pilot intervention involving warm accompaniment telehealth helping sessions with patients at a Federally Qualified Health Center (FQHC). We demonstrate how to design and report recruitment methods, reach, delivery process, and the preliminary impact of a novel equity-focused intervention. METHODS: Early into the COVID-19 pandemic a telehealth helping session was offered to patients at FQHC via phone. Graduate students led the sessions on conducting a telehealth video test run or helping with patient portal log-in. They systematically recorded their recruitment efforts, intervention observations, and daily reflection notes. Following the intervention, we asked the intervention participants to participate in an interview and all patients who had telehealth visits during and 4 weeks before and after the intervention period to complete a survey. Electronic health records were reviewed to assess telehealth visit format changes. Descriptive and inferential statistical analyses of the recruitment records, electronic health record data, and surveys were performed. Through integrative analysis, we developed process-related themes and recommendations for future equity-focused telehealth interventions. RESULTS: Of the 239 eligible patients, 34 (14.2%) completed the intervention and 3 (1.2%) completed subsequent interviews. The intervention participants who completed the survey (n=15) had lower education and less technological experience than the nonintervention survey participants (n=113). We identified 3 helping strategies for cognitive load reduction: providing step-by-step guidance for configuring and learning, building rapport to create confidence while problem-solving, and being on the same page to counter informational distractions. Intervention participants reported increased understanding but found that learning the video visit software was more difficult than nonintervention participants. A comparison of visit experiences did not find differences in difficulty (cognitive load measure) using telehealth-related technologies, changes to visit modality, or reported technical problems during the visit. However, the intervention participants were significantly less satisfied with the video visits. CONCLUSIONS: Although a limited number of people participated in the intervention, it may have reached individuals more likely to need technology assistance. We postulate that significant differences between intervention and nonintervention participants were rooted in baseline differences between the groups' education level, technology experience, and technology use frequency; however, small sample sizes limit conclusions. The barriers encountered during the intervention suggest that patients at FQHC may require both improved access to web-based technologies and human intermediary support to make telehealth video visits feasible. Future large, randomized, equity-focused studies should investigate blended strategies to facilitate video visit access.

Hackathons as a means of accelerating scientific discoveries and knowledge transfer.

Scientific research plays a key role in the advancement of human knowledge and pursuit of solutions to important societal challenges. Typically, research occurs within specific institutions where data are generated and subsequently analyzed. Although collaborative science bringing together multiple institutions is now common, in such collaborations the analytical processing of the data is often performed by individual researchers within the team, with only limited internal oversight and critical analysis of the workflow prior to publication. Here, we show how hackathons can be a means of enhancing collaborative science by enabling peer review before results of analyses are published by cross-validating the design of studies or underlying data sets and by driving reproducibility of scientific analyses. Traditionally, in data analysis processes, data generators and bioinformaticians are divided and do not collaborate on analyzing the data. Hackathons are a good strategy to build bridges over the traditional divide and are potentially a great agile extension to the more structured collaborations between multiple investigators and institutions.

The extended recovery ring-stage survival assay provides a superior association with patient clearance half-life and increases throughput.

BACKGROUND: Tracking and understanding artemisinin resistance is key for preventing global setbacks in malaria eradication efforts. The ring-stage survival assay (RSA) is the current gold standard for in vitro artemisinin resistance phenotyping. However, the RSA has several drawbacks: it is relatively low throughput, has high variance due to microscopy readout, and correlates poorly with the current benchmark for in vivo resistance, patient clearance half-life post-artemisinin treatment. Here a modified RSA is presented, the extended Recovery Ring-stage Survival Assay (eRRSA), using 15 cloned patient isolates from Southeast Asia with a range of patient clearance half-lives, including parasite isolates with and without kelch13 mutations. METHODS: Plasmodium falciparum cultures were synchronized with single layer Percoll during the schizont stage of the intraerythrocytic development cycle. Cultures were left to reinvade to early ring-stage and parasitaemia was quantified using flow cytometry. Cultures were diluted to 2% haematocrit and 0.5% parasitaemia in a 96-well plate to start the assay, allowing for increased throughput and decreased variability between biological replicates. Parasites were treated with 700 nM of dihydroartemisinin or 0.02% dimethyl sulfoxide (DMSO) for 6 h, washed three times in drug-free media, and incubated for 66 or 114 h, when samples were collected and frozen for PCR amplification. A SYBR Green-based quantitative PCR method was used to quantify the fold-change between treated and untreated samples. RESULTS: 15 cloned patient isolates from Southeast Asia with a range of patient clearance half-lives were assayed using the eRRSA. Due to the large number of pyknotic and dying parasites at 66 h post-exposure (72 h sample), parasites were grown for an additional cell cycle (114 h post-exposure, 120 h sample), which drastically improved correlation with patient clearance half-life compared to the 66 h post-exposure sample. A Spearman correlation of - 0.8393 between fold change and patient clearance half-life was identified in these 15 isolates from Southeast Asia, which is the strongest correlation reported to date. CONCLUSIONS: eRRSA drastically increases the efficiency and accuracy of in vitro artemisinin resistance phenotyping compared to the traditional RSA, which paves the way for extensive in vitro phenotyping of hundreds of artemisinin resistant parasites.

Pairwise growth competitions identify relative fitness relationships among artemisinin resistant Plasmodium falciparum field isolates.

BACKGROUND: Competitive outcomes between co-infecting malaria parasite lines can reveal fitness disparities in blood stage growth. Blood stage fitness costs often accompany the evolution of drug resistance, with the expectation that relatively fitter parasites will be more likely to spread in populations. With the recent emergence of artemisinin resistance, it is important to understand the relative competitive fitness of the metabolically active asexual blood stage parasites. Genetically distinct drug resistant parasite clones with independently evolved sets of mutations are likely to vary in asexual proliferation rate, contributing to their chance of transmission to the mosquito vector. METHODS: An optimized in vitro 96-well plate-based protocol was used to quantitatively measure-head-to-head competitive fitness during blood stage development between seven genetically distinct field isolates from a hotspot of emerging artemisinin resistance and the laboratory strain, NF54. These field isolates were isolated from patients in Southeast Asia carrying different alleles of kelch13 and included both artemisinin-sensitive and artemisinin-resistant isolates. Fluorescent labeled microsatellite markers were used to track the relative densities of each parasite throughout the co-growth period of 14-60 days. All-on-all competitions were conducted for the panel of eight parasite lines (28 pairwise competitions) to determine their quantitative competitive fitness relationships. RESULTS: Twenty-eight pairwise competitive growth outcomes allowed for an unambiguous ranking among a set of seven genetically distinct parasite lines isolated from patients in Southeast Asia displaying a range of both kelch13 alleles and clinical clearance times and a laboratory strain, NF54. This comprehensive series of assays established the growth relationships among the eight parasite lines. Interestingly, a clinically artemisinin resistant parasite line that carries the wild-type form of kelch13 outcompeted all other parasites in this study. Furthermore, a kelch13 mutant line (E252Q) was competitively more fit without drug than lines with other resistance-associated kelch13 alleles, including the C580Y allele that has expanded to high frequencies under drug pressure in Southeast Asian resistant populations. CONCLUSIONS: This optimized competitive growth assay can be employed for assessment of relative growth as an index of fitness during the asexual blood stage growth between natural lines carrying different genetic variants associated with artemisinin resistance. Improved understanding of the fitness costs of different parasites proliferating in human blood and the role different resistance mutations play in the context of specific genetic backgrounds will contribute to an understanding of the potential for specific mutations to spread in populations, with the potential to inform targeted strategies for malaria therapy.

A Peer-led Diabetes Education Program in a Homeless Community to Improve Diabetes Knowledge and Empowerment.

Peer-led diabetes education has been shown to be as effective, or more effective, than traditional education in improving glycemic control and diabetes self-care measures. A 4-week peer-led diabetes education program was conducted in a homeless community in Grand Rapids, Michigan to increase diabetes knowledge and empowerment. Knowledge scores increased significantly during sessions covering signs, symptoms, and complications of diabetes and diabetes medications (ps <.05). Empowerment scores after attending the 4-week program were significantly increased when compared to scores prior to the first session (p = .027). Field notes and postimplementation focus group support increased empowerment and knowledge among participants.

Providing Oligonucleotides with Steric Selectivity by Brush-Polymer-Assisted Compaction.

Difficult biopharmaceutical characteristics of oligonucleotides, such as poor enzymatic stability, rapid clearance by reticuloendothelial organs, immunostimulation, and coagulopathies, limit their application as therapeutics. Many of these side effects are initiated via sequence-specific or nonsequence-specific interactions with proteins. Herein, we report a novel form of brush-polymer/DNA conjugate that provides the DNA with nanoscale steric selectivity: Hybridization kinetics with complementary DNA remains nearly unaffected, but interactions with proteins are significantly retarded. The relative lengths of the brush side chain and the DNA strand are found to play a critical role in the degree of selectivity. Being able to evade protein adhesion also improves in vivo biodistribution, thus making these molecular nanostructures promising materials for oligonucleotide-based therapies.

Human technology intermediation to reduce cognitive load: understanding healthcare staff members' practices to facilitate telehealth access in a Federally Qualified Health Center patient population.

OBJECTIVES: The aim of this study was to investigate how healthcare staff intermediaries support Federally Qualified Health Center (FQHC) patients' access to telehealth, how their approaches reflect cognitive load theory (CLT) and determine which approaches FQHC patients find helpful and whether their perceptions suggest cognitive load (CL) reduction. MATERIALS AND METHODS: Semistructured interviews with staff (n = 9) and patients (n = 22) at an FQHC in a Midwestern state. First-cycle coding of interview transcripts was performed inductively to identify helping processes and participants' evaluations of them. Next, these inductive codes were mapped onto deductive codes from CLT. RESULTS: Staff intermediaries used 4 approaches to support access to, and usage of, video visits and patient portals for FQHC patients: (1) shielding patients from cognitive overload; (2) drawing from long-term memory; (3) supporting the development of schemas; and (4) reducing the extraneous load of negative emotions. These approaches could contribute to CL reduction and each was viewed as helpful to at least some patients. For patients, there were beneficial impacts on learning, emotions, and perceptions about the self and technology. Intermediation also resulted in successful visits despite challenges. DISCUSSION: Staff intermediaries made telehealth work for FQHC patients, and emotional support was crucial. Without prior training, staff discovered approaches that aligned with CLT and helped patients access technologies. Future healthcare intermediary interventions may benefit from the application of CLT in their design. Staff providing brief explanations about technical problems and solutions might help patients learn about technologies informally over time. CONCLUSION: CLT can help with developing intermediary approaches for facilitating telehealth access.