The nucleosome reference frame and standard geometries for octasomes.

There are over 533 nucleosome structures in the Research Collaboratory for Structural Bioinformatics (RCSB). Collectively, numerous variants and species are present, as are sub-nucleosomal and super-nucleosomal assemblies within the nucleosome family. The organization of the histones and DNA is highly conserved in all standard octasomes containing 145, 146, or 147 base pairs. This observation is used to establish a nucleosome reference frame that enables us to describe and compare the gross structure and organization of all nucleosomes. We observe that cumulative sums of Rise, Twist, and DNA arc length are linear functions of the base pair index with R 2 values exceeding 0.999 for almost all octasome structures. These relationships enable us to readily compare the location and orientation of DNA director frames extracted from the crystal structures to ideal superhelix values. Such comparisons reveal that the DNA superhelix extracted from X-ray structures exhibits a sinusoidal variation with an amplitude of approximately 5Å  about a constant superhelix radius of ∼ 42 Å, in agreement with early descriptions of nucleosome organization as tripartite. There is also a distinct straightening of the nucleosomal DNA over the outermost turn of DNA's double helix. The straightening of the DNA superhelix marks the transition to linker DNA and is easily recognized as a rapid increase in superhelix radius and is concomitant with a change in pitch. This provides a rigorous means of separating nucleosomal DNA from linker DNA. For all X-ray structures, we find that near the dyad, there exists a set of DNA director frames for which the spatial location and orientation are highly conserved. Away from the dyad, the DNA superhelix exhibits "singletrack" and "multipath" regions. In the singletrack region, all structures exhibit a single highly conserved pathway along which all base pairs must track, but at varying rates. In the multipath regions, the base pairs are allowed to map out a limited number of different pathways along the surface of the histone octamer. To demonstrate the utility of the proposed reference geometries, standard and distorted octasome structures, super-nucleosomal structures, nucleosomes with linker DNA, and nucleosomes in closed circular DNA are analyzed. Supplementary Information: The online version contains supplementary material available at 10.1007/s12551-024-01206-5.

Post-acute and long-term care: a practical and novel curriculum for medical students.

Most physicians will not practice in post-acute or long-term care (PALTC), yet many will care for older adults who transition across these settings. However, medical student education on PALTC is extremely limited. This is a pilot study of a curriculum on PALTC. The curriculum was developed by a geriatrician and social worker. Students participated in a case-based, didactic lecture with interactive components to learn about various care settings, then engaged in a small group exercise to evaluate a challenging transition of care scenario. 168 students participated in the lecture and 145 provided feedback (86.9%). On average, students scored a 1.8/5 (35%) on the pre-course knowledge assessment and 4.3/5 (86%) at the conclusion of the course. Qualitative feedback was analyzed thematically. Students reported positive sentiments regarding the clarity, relevance, engagement, and practicality of the session. Furthermore, students anticipated that the course would improve their own practice patterns and care of older adults. Students felt more empowered to work with interprofessional colleagues because of this course. Opportunities for improvement included a desire for more interactivity and additional reference resources. The course was well-received; students indicated that it would positively influence their practice patterns. This course structure is both highly practical and replicable.

Faculty and Resident Perspectives of the Complexity of Wellness Program Implementation: A Qualitative Exploration.

Introduction: Developing and implementing a wellness curriculum in a family medicine residency program is a complex process. We developed and implemented a new wellness curriculum in line with the national wellness conversation with a focus on the allocation of dedicated resources, the use of evidence-informed interventions, and the goal to be responsive to the feedback of both residents and residency leadership. Our research aim was to better understand the complexity of wellness curriculum implementation with a focus on identification of challenges to implementation. Methods: We developed a wellness program with structured curricular elements initially focused on evidence-informed skill development that iterated after year 1 to include more process-oriented elements. For the years 2016-2019 we collected and analyzed qualitative, open-ended survey questions, anonymous resident curriculum feedback, and faculty observation forms to assess resident and faculty perspectives on the new curriculum. Results: One hundred eighty-three survey invitations were sent with 122 total responses (66.7% response rate). Forty-eight of 56 residents responded to at least one survey. We analyzed responses along with the additional qualitative data that revealed several themes impacting the work of residency wellness curriculum implementation. These included how to manage curricular time, where the locus of control for the curricular content resides, and how residents and faculty differ in their definitions of wellness. Conclusions: We believe programs will be well positioned if they further investigate the complex structures at play that influence residency wellness, including both systemic factors and individual and community level interventions, and design curriculum that is well-defined, includes essential elements, and is informed by resident participation.

A collaborative approach to improving representation in viral genomic surveillance.

The lack of routine viral genomic surveillance delayed the initial detection of SARS-CoV-2, allowing the virus to spread unfettered at the outset of the U.S. epidemic. Over subsequent months, poor surveillance enabled variants to emerge unnoticed. Against this backdrop, long-standing social and racial inequities have contributed to a greater burden of cases and deaths among minority groups. To begin to address these problems, we developed a new variant surveillance model geared toward building 'next generation' genome sequencing capacity at universities in or near rural areas and engaging the participation of their local communities. The resulting genomic surveillance network has generated more than 1,000 SARS-CoV-2 genomes to date, including the first confirmed case in northeast Louisiana of Omicron, and the first and sixth confirmed cases in Georgia of the emergent BA.2.75 and BQ.1.1 variants, respectively. In agreement with other studies, significantly higher viral gene copy numbers were observed in Delta variant samples compared to those from Omicron BA.1 variant infections, and lower copy numbers were seen in asymptomatic infections relative to symptomatic ones. Collectively, the results and outcomes from our collaborative work demonstrate that establishing genomic surveillance capacity at smaller academic institutions in rural areas and fostering relationships between academic teams and local health clinics represent a robust pathway to improve pandemic readiness.

The Impact of Virtual Interviews on the Resident Candidate: A Before-and-After Comparison.

BACKGROUND AND OBJECTIVES: A significant impact of the COVID-19 pandemic on family medicine residency recruitment has been a requested transition to virtual interviewing by the Association of American Medical Colleges and the academic family medicine community. This has led to creative and adaptive approaches to virtual interviewing with little previous knowledge, experience, or processes. This work describes the impact of transitioning to virtual recruitment on applicants' reported experiences and factors influencing decision-making with family medicine at a large research university. METHODS: We made a comparison of 2 years of in-person interview day surveys with 2 years of virtual interview surveys following transition to virtual recruitment. We tested differences between in-person and virtual interviews for significance using χ2 tests. RESULTS: There were significant differences in factors influencing a candidate's decision to apply. Candidates who participated in virtual interviews were more interested in urban training settings, a community setting, and obstetrical training compared with the in-person interview cohort. Nearly 50% of virtual candidates reported preferring virtual interviews in the future. There were no significant differences in how candidates rated their experience of the interview process and they indicated adequate contact with resident personnel despite a transition to virtual interviews. CONCLUSIONS: The transition to virtual recruitment has been well received by candidates, as indicated by the high positive ratings of the cohorts. The transition has not resulted in a negative impact on the recruitment experience or the ability to meet with resident leadership.

A collaborative approach to improve representation in viral genomic surveillance.

The lack of routine viral genomic surveillance delayed the initial detection of SARS-CoV-2, allowing the virus to spread unfettered at the outset of the U.S. epidemic. Over subsequent months, poor surveillance enabled variants to emerge unnoticed. Against this backdrop, long-standing social and racial inequities have contributed to a greater burden of cases and deaths among minority groups. To begin to address these problems, we developed a new variant surveillance model geared toward building microbial genome sequencing capacity at universities in or near rural areas and engaging the participation of their local communities. The resulting genomic surveillance network has generated more than 1,000 SARS-CoV-2 genomes to date, including the first confirmed case in northeast Louisiana of Omicron, and the first and sixth confirmed cases in Georgia of the emergent BA.2.75 and BQ.1.1 variants, respectively. In agreement with other studies, significantly higher viral gene copy numbers were observed in Delta variant samples compared to those from Omicron BA.1 variant infections, and lower copy numbers were seen in asymptomatic infections relative to symptomatic ones. Collectively, the results and outcomes from our collaborative work demonstrate that establishing genomic surveillance capacity at smaller academic institutions in rural areas and fostering relationships between academic teams and local health clinics represent a robust pathway to improve pandemic readiness. Author summary: Genomic surveillance involves decoding a pathogen’s genetic code to track its spread and evolution. During the pandemic, genomic surveillance programs around the world provided valuable data to scientists, doctors, and public health officials. Knowing the complete SARS-CoV-2 genome has helped detect the emergence of new variants, including ones that are more transmissible or cause more severe disease, and has supported the development of diagnostics, vaccines, and therapeutics. The impact of genomic surveillance on public health depends on representative sampling that accurately reflects the diversity and distribution of populations, as well as rapid turnaround time from sampling to data sharing. After a slow start, SARS-CoV-2 genomic surveillance in the United States grew exponentially. Despite this, many rural regions and ethnic minorities remain poorly represented, leaving significant gaps in the data that informs public health responses. To address this problem, we formed a network of universities and clinics in Louisiana, Georgia, and Mississippi with the goal of increasing SARS-CoV-2 sequencing volume, representation, and equity. Our results demonstrate the advantages of rapidly sequencing pathogens in the same communities where the cases occur and present a model that leverages existing academic and clinical infrastructure for a powerful decentralized genomic surveillance system.

Obstructive sleep apnoea and perioperative medicine: a growing concern.

Obstructive sleep apnoea represents a sizable public health and economic burden. Owing to rising obesity rates, the prevalence of obstructive sleep apnoea is increasing, and it is a condition that is significantly underdiagnosed. Exacerbated by the COVID-19 pandemic, the backlog of elective surgeries is also sizable and growing. A combination of these factors means that many patients due to have surgery will have obstructive sleep apnoea, either diagnosed or otherwise. Patients with obstructive sleep apnoea have a significantly increased risk of operative complications, but the evidence base for optimum perioperative management of these patients is limited. This article reviews sleep apnoea, its prevalence and its impact on operative management and perioperative outcomes for patients. The evidence base for screening and treating undiagnosed obstructive sleep apnoea is also comprehensively assessed. Finally, a pathway to manage patients with possible undiagnosed obstructive sleep apnoea is proposed, and areas for further research identified.

Large volume paracentesis of 39.5 liters chylous ascites in the setting of high-grade follicular lymphoma.

The American Association for the Study of Liver Diseases recognizes large volume paracentesis as draining greater than 5 liters of ascites and states there is no limit in the amount of ascites drained with appropriate replacement of albumin. For many practitioners performing safe large volume paracentesis between 5 and 10 liters or even 20 liters is not an uncommon practice. However, drainage of higher volumes outside common practice may raise concerns of patient intolerance and complication. The largest volume paracentesis reported in the literature to date is 41 liters. However, few other reports approach this volume. This case report demonstrates patient tolerance of a 39.5-liter paracentesis performed with close monitoring and hypertonic albumin replacement in a patient with chylous ascites due to high-grade follicular lymphoma.

When worlds collide: Socio-political conflict in patient care.

The country as a whole has been on high alert since early 2020. That year began with the SARS-CoV-2 pandemic, then moved through the largest single day drop of the Dow Jones industrial average, the murders of Breonna Taylor and George Floyd and subsequent Black Lives Matter protests, murder hornets, the election of Joe Biden, alleged voter fraud, and then culminated on January 6, 2021, with the assault on the United States Capital Building. Societal issues including racism, discrimination, and distrust of leaders have been themes in the news and social media. It should come as no surprise that we may be called upon to provide treatment to patients with whom we have significantly different belief systems, which could result in conflict. The emotional rawness that pervades much of society lays emotions bare for many. Our ethical responsibilities as healthcare providers compel us to think about these complex relationships intentionally, and with compassion. In an interactive workshop conducted at the 42nd Forum for Behavioral Science in Family Medicine, participants were led through scenarios in which conflict could enter the exam room, discussion of the potential consequences, and consideration of ways to respond ethically in those situations. The discussions were couched in the codes of ethics of the American Psychological Association, the National Association of Social Workers, and the American Medical Association. The interactive session was designed to encourage participants to (1) consider potentialities of patient-provider conflict, (2) consider ethical, compassionate responses, and (3) be mindful of social media.

Assessment of the Effect of Soil Sample Preparation, Water Content and Excitation Time on Proximal X-ray Fluorescence Sensing.

X-ray fluorescence (XRF) spectroscopy offers a fast and efficient method for analysing soil elemental composition, both in the laboratory and the field. However, the technique is sensitive to spectral interference as well as physical and chemical matrix effects, which can reduce the precision of the measurements. We systematically assessed the XRF technique under different sample preparations, water contents, and excitation times. Four different soil samples were used as blocks in a three-way factorial experiment, with three sample preparations (natural aggregates, ground to ≤2 mm and ≤1 mm), three gravimetric water contents (air-dry, 10% and 20%), and three excitation times (15, 30 and 60 s). The XRF spectra were recorded and gave 540 spectra in all. Elemental peaks for Si, K, Ca, Ti, Fe and Cu were identified for analysis. We used analysis of variance (anova) with post hoc tests to identify significant differences between our factors and used the intensity and area of the elemental peaks as the response. Our results indicate that all of these factors significantly affect the XRF spectrum, but longer excitation times appear to be more defined. In most cases, no significant difference was found between air-dry and 10% water content. Moisture has no apparent effect on coarse samples unless ground to 1 mm. We suggested that the XRF measurements that take 60 s from dry samples or only slightly moist ones might be an optimum option under field conditions.

Bacterial lipopolysaccharides can initiate regeneration of the Xenopus tadpole tail.

Tadpoles of the frog Xenopus laevis can regenerate tails except for a short "refractory" period in which they heal rather than regenerate. Rapid and sustained production of ROS by NADPH oxidase (Nox) is critical for regeneration. Here, we show that tail amputation results in rapid, transient activation of the ROS-activated transcription factor NF-κB and expression of its direct target cox2 in the wound epithelium. Activation of NF-κB is also sufficient to rescue refractory tail regeneration. We propose that bacteria on the tadpole's skin could influence tail regenerative outcomes, possibly via LPS-TLR4-NF-κB signaling. When raised in antibiotics, fewer tadpoles in the refractory stage attempted regeneration, whereas addition of LPS rescued regeneration. Short-term activation of NF-κB using small molecules enhanced regeneration of tadpole hindlimbs, but not froglet forelimbs. We propose a model in which host microbiome contributes to creating optimal conditions for regeneration, via regulation of NF-κB by the innate immune system.

Space-time modelling of groundwater level and salinity.

Soil salinization resulting from shallow saline groundwater is a major global environmental issue causing land degradation, especially in semi-arid regions such as Australia. The adverse impact of shallow saline groundwater on soil salinization varies in space and time due to the variation in groundwater levels and salt concentration. Understanding the spatio-temporal variation is therefore vital to develop an effective salinity management strategy. In New South Wales, Australia, a hydrogeological landscape unit approach is generally applied, based on spatial information and expert operators, classifying the landscape in relation to landscape and climate. In this paper, a data science approach (random forest model) is introduced, based on historical groundwater quality and quantity data providing predictions in a 4-dimensional space. As a case study, we demonstrate the spatio-temporal factors impacting standing water levels (SWL) and associated salinity and predict the spatial and temporal variability in the Muttama catchment (1059 km2), in NSW, south eastern Australia. The random forest model explains 77% of the variance in the groundwater salinity (electrical conductivity) and 65% of the SWL. Spatial factors were the most significant variables determining the space-time variation in groundwater salinity and the occurrence of groundwater at the surface. Drilled piezometer depth and elevation are dominant factors controlling SWL, while salinity is mainly determined by underlying geology. The methodology in this study predicts salinity and SWL in the landscape at fine scales, through time, improving options for salinity management.

Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?

The structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational changes that lead to local and global changes in the helix geometry are mediated by a complex choreography of base and backbone rearrangements affecting the ability of the B-DNA to recognize ligands and consequently on its functionality. In this sense, the knowledge obtained from the sequence-dependent structural properties of B-DNA has always been thought crucial to rationalize how ligands and, most notably, proteins recognize B-DNA and modulate its activity, i.e. the structural basis of gene regulation. Honouring the anniversary of the first high-resolution X-ray structure of a B-DNA molecule, in this contribution, we present the most important discoveries of the last 40 years on the sequence-dependent structural and dynamical properties of B-DNA, from the early beginnings to the current frontiers in the field.

Genome Dashboards: Framework and Examples.

Genomics is a sequence-based informatics science and a three-dimensional-structure-based material science. However, in practice, most genomics researchers utilize sequence-based informatics approaches or three-dimensional-structure-based material science techniques, not both. This division is, at least in part, the result of historical developments rather than a fundamental necessity. The underlying computational tools, experimental techniques, and theoretical models were developed independently. The primary result presented here is a framework for the unification of informatics- and physics-based data associated with DNA, nucleosomes, and chromatin. The framework is based on the mathematical representation of geometrically exact rods and the generalization of DNA basepair step parameters. Data unification enables researchers to integrate computational, experimental, and theoretical approaches for the study of chromatin biology. The framework can be implemented using model-view-controller design principles, existing genome browsers, and existing molecular visualization tools. We developed a minimal, web-based genome dashboard, G-Dash-min, and applied it to two simple examples to demonstrate the usefulness of data unification and proof of concept. Genome dashboards developed using the framework and design principles presented here are extensible and customizable and are therefore more broadly applicable than the examples presented. We expect a number of purpose-specific genome dashboards to emerge as a novel means of investigating structure-function relationships for genomes that range from basepairs to entire chromosomes and for generating, validating, and testing mechanistic hypotheses.

Genome editing approaches to augment livestock breeding programs.

The prospect of genome editing offers a number of promising opportunities for livestock breeders. Firstly, these tools can be used in functional genomics to elucidate gene function, and identify causal variants underlying monogenic traits. Secondly, they can be used to precisely introduce useful genetic variation into structured livestock breeding programs. Such variation may include repair of genetic defects, the inactivation of undesired genes, and the moving of useful alleles and haplotypes between breeds in the absence of linkage drag. Editing could also be used to accelerate the rate of genetic progress by enabling the replacement of the germ cell lineage of commercial breeding animals with cells derived from genetically elite lines. In the future, editing may also provide a useful complement to evolving approaches to decrease the length of the generation interval through in vitro generation of gametes. For editing to be adopted, it will need to seamlessly integrate with livestock breeding schemes. This will likely involve introducing edits into multiple elite animals to avoid genetic bottlenecks. It will also require editing of different breeds and lines to maintain genetic diversity, and enable structured cross-breeding. This requirement is at odds with the process-based trigger and event-based regulatory approach that has been proposed for the products of genome editing by several countries. In the absence of regulatory harmony, researchers in some countries will have the ability to use genome editing in food animals, while others will not, resulting in disparate access to these tools, and ultimately the potential for global trade disruptions.

Computational Design and Analysis of a Magic Snake.

The Magic Snake (Rubik's Snake) is a toy that was invented decades ago. It draws much less attention than Rubik's Cube, which was invented by the same professor, Erno Rubik. The number of configurations of a Magic Snake, determined by the number of discrete rotations about the elementary wedges in a typical snake, is far less than the possible configurations of a typical cube. However, a cube has only a single three-dimensional (3D) structure while the number of sterically allowed 3D conformations of the snake is unknown. Here, we demonstrate how to represent a Magic Snake as a one-dimensional (1D) sequence that can be converted into a 3D structure. We then provide two strategies for designing Magic Snakes to have specified 3D structures. The first enables the folding of a Magic Snake onto any 3D space curve. The second introduces the idea of "embedding" to expand an existing Magic Snake into a longer, more complex, self-similar Magic Snake. Collectively, these ideas allow us to rapidly list and then compute all possible 3D conformations of a Magic Snake. They also form the basis for multidimensional, multi-scale representations of chain-like structures and other slender bodies including certain types of robots, polymers, proteins, and DNA.

TMB Library of Nucleosome Simulations.

Nucleosomes are the fundamental building blocks of chromatin, the biomaterial that houses the genome in all higher organisms. A nucleosome consists of 145-147 base pairs of DNA wrapped 1.7 times around eight histones. Given a four-letter code (A, C, G, T), there are approximately 4147 or 1088 oligonucleotides that can form a nucleosome. Comparative, rather than comprehensive, studies are required. Here we introduce the TMB Library of nucleosome simulations and present a meta-analysis of over 20 µs of all atom molecular dynamics simulations representing 518 different realizations of the nucleosome. The TMB Library serves as a reference for future comparative, on-demand simulations of nucleosomes and a demonstration of iBIOMES Lite as a tool for managing a laboratory's simulation library. For every simulation, dewatered trajectories, RMSD, and DNA helical parameter data are provided through iBIOMES Lite in a Web browser and a file browser format. A novel view of nucleosomal DNA emerges from our meta-analysis of the TMB Library. DNA conformation is restricted to a specific left-handed superhelix, but the range of conformations observed for individual bases and base pairs is not more restricted nor more highly deformed than DNA free in solution. With the exception of Roll, mean DNA helical parameter values obtained from simulations of nucleosomes are largely within the range of thermal motion of DNA free in solution. The library provides evidence of DNA kinking in the nucleosome and clearly demonstrates the effects of DNA sequence on the gross structure and dynamics of nucleosomes. These effects and mispositioning of the 601 super strong nucleosome positioning sequence can be detected in short simulations (10 ns). Collectively, the results provide a basis for comparative simulation studies of nucleosomes and extend our understanding of the binding of proteins and drugs to nucleosomal DNA. The TMB Library can be found at http://dna.engr.latech.edu/~tmbshare/ .