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2.
Arts Health ; 16(1): 48-63, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37157231

ABSTRACT

BACKGROUND: Older adults living in subsidized housing may be at increased risk of social isolation. Applied theater, a participatory art program, can facilitate social connections among older adults. METHODS: A professionally-facilitated 12-week acting and improvisation course was held in two federally subsidized buildings in an urban setting. The mixed-method design included thematic analysis of interviews, participant observation, field notes, and statistical analysis of change over time in social isolation, community belonging, and social exclusion. RESULTS: Participants were motivated to meet other building residents, and the course included aspects that encouraged social bonding. CONCLUSIONS: Although recruitment of socially-isolated older adults presented challenges, this study presents lessons on what motivates residents of low-income senior housing to enroll in an acting program and how to design a theater course in this setting that promotes group bonding.


Subject(s)
Housing , Social Isolation , Humans , United States , Aged , Poverty , Homes for the Aged
3.
Article in English | MEDLINE | ID: mdl-38157979

ABSTRACT

OBJECTIVE: To test whether childhood mental health symptoms, substance use, and early adversity accelerate the rate of DNA methylation (DNAm) aging from adolescence to adulthood. METHOD: DNAm was assayed from blood samples in 381 participants in both adolescence (mean [SD] age = 13.9 [1.6] years) and adulthood (mean [SD] age = 25.9 [2.7] years). Structured diagnostic interviews were completed with participants and their parents at multiple childhood observations (1,950 total) to assess symptoms of common mental health disorders (attention-deficit/hyperactivity disorder, oppositional defiant disorder, conduct disorder, anxiety, and depression) and common types of substance use (alcohol, cannabis, nicotine) and early adversities. RESULTS: Neither childhood mental health symptoms nor substance use variables were associated with DNAm aging cross-sectionally. In contrast, the following mental health symptoms and substance variables were associated with accelerated DNAm aging from adolescence to adulthood: depressive symptoms (b = 0.314, SE = 0.127, p = .014), internalizing symptoms (b = 0.108, SE = 0.049, p = .029), weekly cannabis use (b =1.665, SE = 0.591, p = .005), and years of weekly cannabis use (b = 0.718, SE = 0.283, p = .012). In models testing all individual variables simultaneously, the combined effect of the variables was equivalent to a potential difference of 3.17 to 3.76 years in DNAm aging. A final model tested a variable assessing cumulative exposure to mental health symptoms, substance use, and early adversities. This cumulative variable was strongly associated with accelerated aging (b = 0.126, SE = 0.044, p = .005). CONCLUSION: Mental health symptoms and substance use accelerated DNAm aging into adulthood in a manner consistent with a shared risk mechanism.

4.
Child Maltreat ; : 10775595231218174, 2023 Nov 21.
Article in English | MEDLINE | ID: mdl-37989270

ABSTRACT

Economic support programs for low-income families may play an important role in preventing child abuse and neglect. In the United States, childcare subsidies are provided to low-income families who meet certain requirements to offset the high cost of childcare. States have flexibility in setting many policies related to the provision of childcare subsidies, which results in a great deal of variation in how the programs operate between states. One policy dimension on which states vary is the number of employment hours required to receive childcare subsidies. A small body of work has begun to investigate the ways in which these state policy variations might relate to child maltreatment. Using 11 years of administrative data from the United States, the current study sought to estimate the relationship between two sources of variation in childcare subsidy policies: employment requirements and copayment size; and child neglect, physical abuse, and emotional abuse substantiations. The study found a nuanced relationship between required employment and neglect substantiations. Specifically, requiring some level of work was not associated with neglect substantiations, but requiring 30 hours of employment was associated with higher rates. The study did not find a relationship between copayment size and maltreatment substantiations.

5.
bioRxiv ; 2023 Oct 10.
Article in English | MEDLINE | ID: mdl-37873181

ABSTRACT

Communication among different neocortical areas is largely thought to be mediated by long-range synaptic interactions between cortical neurons, with the thalamus providing only an initial relay of information from the sensory periphery. Higher-order thalamic nuclei receive strong synaptic inputs from the cortex and send robust projections back to other cortical areas, providing a distinct and potentially critical route for cortico-cortical communication. However, the relative contributions of corticocortical and thalamocortical inputs to higher-order cortical function remain unclear. Using imaging of cortical neurons and projection axon terminals in combination with optogenetic manipulations, we find that the higher-order visual thalamus of mice conveys a specialized stream of information to higher-order visual cortex. Whereas corticocortical projections from lower cortical areas convey robust visual information, higher-order thalamocortical projections convey strong behavioral state information. Together, these findings suggest a key role for higher-order thalamus in providing contextual signals that flexibly modulate sensory processing in higher-order cortex.

6.
BMJ Open ; 13(10): e058439, 2023 10 30.
Article in English | MEDLINE | ID: mdl-37903610

ABSTRACT

OBJECTIVES: To test associations between 11 caregiver aggressive and non-aggressive discipline behaviours and outcomes (aggression, distraction and prosocial peer relations) of children under 5 years in low-income and middle-income countries (LMICs). PARTICIPANTS: Data came from the fourth (2009-2013) and fifth (2012-2017) rounds of the UNICEF Multiple Indicator Cluster Surveys. Analyses were restricted to households with children under 5 years, leaving a sample of 229 465 respondents across 60 LMICs. Data were analysed using Bayesian multilevel logistic regression. RESULTS: Verbal reasoning (80%) and shouting (66%) were the most common parental discipline behaviours towards young children. Psychological and physical aggression were associated with higher child aggression and distraction. Compared with not using verbal reasoning, verbal reasoning was associated with lower odds of aggression (OR)=0.92, 95% credible interval (CI)=0.86 to 0.99) and higher odds of prosocial peer relations (OR=1.30, 95% CI=1.20 to 1.42). Taking away privileges was associated with higher odds of distraction (OR=1.09, 95% CI=1.03 to 1.15) and lower odds of prosocial peer relations (OR=0.92, 95% CI=0.87 to 0.98). Giving the child something else to do was associated with higher odds of distraction (OR=1.06, 95% CI=1.01 to 1.12). The results indicated country-level variation in the associations between parenting behaviours and child socioemotional outcomes. CONCLUSIONS: Psychological and physical aggression were disadvantageous for children's socioemotional development across countries. Only verbal reasoning was associated with positive child socioemotional development. No form of psychological aggression or physical aggression benefited child socioemotional development in any country. Greater emphasis should be dedicated to reducing parental use of psychological and physical aggression across cultural contexts.


Subject(s)
Aggression , Parents , Humans , Child , Child, Preschool , Bayes Theorem , Aggression/psychology , Parents/psychology , Parenting/psychology , Child Development
7.
bioRxiv ; 2023 Aug 09.
Article in English | MEDLINE | ID: mdl-37609173

ABSTRACT

A fundamental question in biology is how a limited number of genes combinatorially govern cellular responses to environmental changes. While the prevailing hypothesis is that relationships between genes, processes, and ontologies could be plastic to achieve this adaptability, quantitatively comparing human gene functional connections between specific environmental conditions at scale is very challenging. Therefore, it remains unclear whether and how human genetic interaction networks are rewired in response to changing environmental conditions. Here, we developed a framework for mapping context-specific genetic interactions, enabling us to measure the plasticity of human genetic architecture upon environmental challenge for ~250,000 interactions, using cell cycle interruption, genotoxic perturbation, and nutrient deprivation as archetypes. We discover large-scale rewiring of human gene relationships across conditions, highlighted by dramatic shifts in the functional connections of epigenetic regulators (TIP60), cell cycle regulators (PP2A), and glycolysis metabolism. Our study demonstrates that upon environmental perturbation, intra-complex genetic rewiring is rare while inter-complex rewiring is common, suggesting a modular and flexible evolutionary genetic strategy that allows a limited number of human genes to enable adaptation to a large number of environmental conditions.

8.
J Pain Symptom Manage ; 66(4): 351-360.e1, 2023 10.
Article in English | MEDLINE | ID: mdl-37433418

ABSTRACT

CONTEXT: Emotion regulation by the physician can influence the effectiveness of serious illness conversations. The feasibility of multimodal assessment of emotion regulation during these conversations is unknown. OBJECTIVES: To develop and assess an experimental framework for evaluating physician emotion regulation during serious illness conversations. METHODS: We developed and then assessed a multimodal assessment framework for physician emotion regulation using a cross-sectional, pilot study on physicians trained in the Serious Illness Conversation Guide (SICG) in a simulated, telehealth encounter. Development of the assessment framework included a literature review and subject matter expert consultations. Our predefined feasibility endpoints included: an enrollment rate of ≥60% of approached physicians, >90% completion rate of survey items, and <20% missing data from wearable heart rate sensors. To describe physician emotion regulation, we performed a thematic analysis of the conversation, its documentation, and physician interviews. RESULTS: Out of 12 physicians approached, 11 (92%) SICG-trained physicians enrolled in the study: five medical oncology and six palliative care physicians. All 11 completed the survey (100% completion rate). Two sensors (chest band, wrist sensor) had <20% missing data during study tasks. The forearm sensor had >20% missing data. The thematic analysis found that physicians': 1) overarching goal was to move beyond prognosis to reasonable hope; 2) tactically focused on establishing a trusting, supportive relationship; and 3) possessed incomplete awareness of their emotion regulation strategies. CONCLUSION: Our novel, multimodal assessment of physician emotion regulation was feasible in a simulated SICG encounter. Physicians exhibited an incomplete understanding of their emotion regulation strategies.


Subject(s)
Emotional Regulation , Physicians , Humans , Physician-Patient Relations , Cross-Sectional Studies , Pilot Projects , Physicians/psychology , Communication
9.
Am J Physiol Regul Integr Comp Physiol ; 325(1): R1-R12, 2023 07 01.
Article in English | MEDLINE | ID: mdl-37125769

ABSTRACT

Intrinsic stressors associated with life-history stages may alter the responsiveness of the hypothalamic-pituitary-adrenal axis and responses to extrinsic stressors. We administered adrenocorticotropic hormone (ACTH) to 24 free-ranging adult female northern elephant seals (NESs) at two life-history stages: early and late in their molting period and measured a suite of endocrine, immune, and metabolite responses. Our objective was to evaluate the impact of extended, high-energy fasting on adrenal responsiveness. Animals were blood sampled every 30 min for 120 min post-ACTH injection, then blood was sampled 24 h later. In response to ACTH injection, cortisol levels increased 8- to 10-fold and remained highly elevated compared with baseline at 24 h. Aldosterone levels increased 6- to 9-fold before returning to baseline at 24 h. The magnitude of cortisol and aldosterone release were strongly associated, and both were greater after extended fasting. We observed an inverse relationship between fat mass and the magnitude of cortisol and aldosterone responses, suggesting that body reserves influenced adrenal responsiveness. Sustained elevation in cortisol was associated with alterations in thyroid hormones; both tT3 and tT4 concentrations were suppressed at 24 h, while rT3 increased. Immune cytokine IL-1ß was also suppressed after 24 h of cortisol elevation, and numerous acute and sustained impacts on substrate metabolism were evident. Our data suggest that female NESs are more sensitive to stress after the molt fast and that acute stress events can have important impacts on metabolism and immune function. These findings highlight the importance of considering life-history context when assessing the impacts of anthropogenic stressors on wildlife.


Subject(s)
Adrenocorticotropic Hormone , Seals, Earless , Animals , Female , Hydrocortisone , Thyroid Gland/metabolism , Hypothalamo-Hypophyseal System/metabolism , Aldosterone/metabolism , Molting , Pituitary-Adrenal System/metabolism , Seals, Earless/metabolism , Immunity
10.
BMC Palliat Care ; 22(1): 59, 2023 May 16.
Article in English | MEDLINE | ID: mdl-37189073

ABSTRACT

INTRODUCTION: Early access to specialty palliative care is associated with better quality of life, less intensive end-of-life treatment and improved outcomes for patients with advanced cancer. However, significant variation exists in implementation and integration of palliative care. This study compares the organizational, sociocultural, and clinical factors that support or hinder palliative care integration across three U.S. cancer centers using an in-depth mixed methods case study design and proposes a middle range theory to further characterize specialty palliative care integration. METHODS: Mixed methods data collection included document review, semi-structured interviews, direct clinical observation, and context data related to site characteristics and patient demographics. A mixed inductive and deductive approach and triangulation was used to analyze and compare sites' palliative care delivery models, organizational structures, social norms, and clinician beliefs and practices. RESULTS: Sites included an urban center in the Midwest and two in the Southeast. Data included 62 clinician and 27 leader interviews, observations of 410 inpatient and outpatient encounters and seven non-encounter-based meetings, and multiple documents. Two sites had high levels of "favorable" organizational influences for specialty palliative care integration, including screening, policies, and other structures facilitating integration of specialty palliative care into advanced cancer care. The third site lacked formal organizational policies and structures for specialty palliative care, had a small specialty palliative care team, espoused an organizational identity linked to treatment innovation, and demonstrated strong social norms for oncologist primacy in decision making. This combination led to low levels of specialty palliative care integration and greater reliance on individual clinicians to initiate palliative care. CONCLUSION: Integration of specialty palliative care services in advanced cancer care was associated with a complex interaction of organization-level factors, social norms, and individual clinician orientation. The resulting middle range theory suggests that formal structures and policies for specialty palliative care combined with supportive social norms are associated with greater palliative care integration in advanced cancer care, and less influence of individual clinician preferences or tendencies to continue treatment. These results suggest multi-faceted efforts at different levels, including social norms, may be needed to improve specialty palliative care integration for advanced cancer patients.


Subject(s)
Hospice and Palliative Care Nursing , Neoplasms , Humans , Palliative Care/methods , Quality of Life , Neoplasms/therapy , Delivery of Health Care
11.
Children (Basel) ; 10(4)2023 Apr 11.
Article in English | MEDLINE | ID: mdl-37189957

ABSTRACT

The current study applied a family systems approach to examine dyadic parental risk factors linked with mother-father co-involved physical abuse, neglect, sexual abuse, and emotional abuse. Parental substance use, mental health problems, disability and medical conditions, inadequate housing, economic insecurity, intimate partner violence, and prior maltreatment history were investigated as key risk factors at the dyadic parental level. Logistic regression analysis was conducted using national child welfare administrative data from the National Child Abuse and Neglect Data System. The results showed differential associations between risk factors and four child maltreatment types: physical abuse, neglect, emotional abuse, and sexual abuse. Intimate partner violence was associated with higher odds of mother-father co-involved neglect and emotional abuse. Parental substance use, inadequate housing, and prior maltreatment history were all associated with higher odds of mother-father co-involved neglect, but lower odds of physical abuse. Parental disability and medical conditions were associated with higher odds of mother-father co-involved sexual abuse, whereas parental substance use was associated with lower odds of sexual abuse. Implications include more nuanced ways of addressing multiple risk factors within the family to prevent future occurrences of child maltreatment involving both mothers and fathers.

12.
Curr Cardiol Rep ; 25(5): 307-314, 2023 05.
Article in English | MEDLINE | ID: mdl-37052760

ABSTRACT

PURPOSE OF REVIEW: In this review, we explore the chromatin-related consequences of laminopathy-linked mutations through the lens of mechanotransduction. RECENT FINDINGS: Multiple studies have highlighted the role of the nuclear lamina in maintaining the integrity of the nucleus. The lamina also has a critical role in 3D genome organization. Mutations in lamina proteins associated with various laminopathies result in the loss of organization of DNA at the nuclear periphery. However, it remains unclear if or how these two aspects of lamin function are connected. Recent data suggests that unlinking the cytoskeleton from the nuclear lamina may be beneficial to slow progress of deleterious phenotypes observed in laminopathies. In this review, we highlight emerging data that suggest interlinked chromatin- and mechanical biology-related pathways are interconnected in the pathogenesis of laminopathies.


Subject(s)
Cell Nucleus , Mechanotransduction, Cellular , Humans , Cell Nucleus/genetics , Cell Nucleus/metabolism , Cell Nucleus/pathology , Nuclear Lamina/genetics , Nuclear Lamina/metabolism , Chromatin/genetics , Chromatin/metabolism , Biophysics
13.
J Mass Spectrom Adv Clin Lab ; 28: 47-55, 2023 Apr.
Article in English | MEDLINE | ID: mdl-36872952

ABSTRACT

Mass spectrometry focusing on small endogenous molecules has become an integral part of biomarker discovery in the pursuit of an in-depth understanding of the pathophysiology of various diseases, ultimately enabling the application of personalized medicine. While LC-MS methods allow researchers to gather vast amounts of data from hundreds or thousands of samples, the successful execution of a study as part of clinical research also requires knowledge transfer with clinicians, involvement of data scientists, and interactions with various stakeholders. The initial planning phase of a clinical research project involves specifying the scope and design, and engaging relevant experts from different fields. Enrolling subjects and designing trials rely largely on the overall objective of the study and epidemiological considerations, while proper pre-analytical sample handling has immediate implications on the quality of analytical data. Subsequent LC-MS measurements may be conducted in a targeted, semi-targeted, or non-targeted manner, resulting in datasets of varying size and accuracy. Data processing further enhances the quality of data and is a prerequisite for in-silico analysis. Nowadays, the evaluation of such complex datasets relies on a mix of classical statistics and machine learning applications, in combination with other tools, such as pathway analysis and gene set enrichment. Finally, results must be validated before biomarkers can be used as prognostic or diagnostic decision-making tools. Throughout the study, quality control measures should be employed to enhance the reliability of data and increase confidence in the results. The aim of this graphical review is to provide an overview of the steps to be taken when conducting an LC-MS-based clinical research project to search for small molecule biomarkers.

14.
Cell ; 186(7): 1478-1492.e15, 2023 03 30.
Article in English | MEDLINE | ID: mdl-36870331

ABSTRACT

Lungs undergo mechanical strain during breathing, but how these biophysical forces affect cell fate and tissue homeostasis are unclear. We show that biophysical forces through normal respiratory motion actively maintain alveolar type 1 (AT1) cell identity and restrict these cells from reprogramming into AT2 cells in the adult lung. AT1 cell fate is maintained at homeostasis by Cdc42- and Ptk2-mediated actin remodeling and cytoskeletal strain, and inactivation of these pathways causes a rapid reprogramming into the AT2 cell fate. This plasticity induces chromatin reorganization and changes in nuclear lamina-chromatin interactions, which can discriminate AT1 and AT2 cell identity. Unloading the biophysical forces of breathing movements leads to AT1-AT2 cell reprogramming, revealing that normal respiration is essential to maintain alveolar epithelial cell fate. These data demonstrate the integral function of mechanotransduction in maintaining lung cell fate and identifies the AT1 cell as an important mechanosensor in the alveolar niche.


Subject(s)
Alveolar Epithelial Cells , Mechanotransduction, Cellular , Alveolar Epithelial Cells/metabolism , Cells, Cultured , Lung , Cell Differentiation/physiology , Respiration
15.
Org Lett ; 25(13): 2196-2200, 2023 Apr 07.
Article in English | MEDLINE | ID: mdl-36972327

ABSTRACT

Reactions of a glucuronic acid (GlcA) ß-thioglycoside with cyclohexadione show initial formation of the two anticipated all-trans decalin-type O2,O3 and O3,O4 cyclohexane-1,2-diacetals (CDAs) along with an epimer of the main O2,O3 acetal. This trans-cis isomer is then interconverted leading to higher amounts of the two all-trans products. Isomerization studies indicate slow interconversion between the all-trans CDA acetals, with only one undergoing significant interconversion with the minor 2,3-diastereomer. Crystal structures of all three isomers are included. These findings are relevant to other uses of CDA protections where occurrence of apparently disfavored isomers may be occurring, along with interconversions between CDA isomers.

16.
J Bacteriol ; 205(4): e0001523, 2023 04 25.
Article in English | MEDLINE | ID: mdl-36920216

ABSTRACT

A novel approach to treat the highly virulent and infectious enteric pathogen Shigella flexneri, with the potential for reduced resistance development, is to target virulence pathways. One promising such target is the AraC-family transcription factor VirF, which activates downstream virulence factors. VirF harbors a conserved C-terminal DNA-binding domain (DBD) and an N-terminal dimerization domain (NTD). Previously, we studied the wild type (WT) and seven alanine DBD mutants of VirF binding to the virB promoter (N. J. Ragazzone, G. T. Dow, and A. Garcia, J Bacteriol 204:e00143-22, 2022, https://doi.org/10.1128/jb.00143-22). Here, we report studies of VirF binding to the icsA and rnaG promoters. Gel shift assays (electrophoretic mobility shift assays [EMSAs]) of WT VirF binding to these promoters revealed multiple bands at higher apparent molecular weights, indicating the likelihood of VirF dimerization when bound to DNA. For three of the mutants, we observed consistent effects on binding to the three promoters. For the four other mutants, we observed differential effects on promoter binding. Results of a cell-based, LexA monohybrid ß-galactosidase reporter assay [D. A. Daines, M. Granger-Schnarr, M. Dimitrova, and R. P. Silver, Methods Enzymol 358:153-161, 2002, https://doi.org/10.1016/s0076-6879(02)58087-3] indicated that WT VirF dimerizes in vivo and that alanine mutations to Y132, L137, and L147 significantly reduced dimerization. However, these mutations negatively impacted protein stability. We did purify enough of the Y132A mutant to determine that it binds in vitro to the virB and rnaG promoters, albeit with weaker affinities. Full-length VirF model structures, generated with I-TASSER, predict that these three amino acids are in a "dimerization" helix in the NTD, consistent with our results. IMPORTANCE Antimicrobial-resistant (AMR) infections continue to rise dramatically, and the lack of new approved antibiotics is not ameliorating this crisis. A promising route to reduce AMR is by targeting virulence. The Shigella flexneri virulence pathway is a valuable source for potential therapeutic targets useful to treat this infection. VirF, an AraC-family virulence transcription factor, is responsible for activating necessary downstream virulence genes that allow the bacteria to invade and spread within the human colon. Previous studies have identified how VirF interacts with the virB promoter and have even developed a lead DNA-binding inhibitor, but not much is known about VirF dimerization or binding to the icsA and rnaG promoters. Fully characterizing VirF can be a valuable resource for inhibitor discovery/design.


Subject(s)
DNA-Binding Proteins , Shigella flexneri , Humans , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Shigella flexneri/genetics , Transcription, Genetic , Bacterial Proteins/metabolism , Interferon Regulatory Factors/genetics , Interferon Regulatory Factors/metabolism , Interferon Regulatory Factors/pharmacology , Virulence Factors/genetics , Virulence Factors/metabolism , AraC Transcription Factor/genetics , DNA/metabolism , Gene Expression Regulation, Bacterial
17.
J Ambul Care Manage ; 46(2): 127-138, 2023.
Article in English | MEDLINE | ID: mdl-36820633

ABSTRACT

The coproduction learning health system (CLHS) model extends the definition of a learning health system to explicitly bring together patients and care partners, health care teams, administrators, and scientists to share the work of optimizing health outcomes, improving care value, and generating new knowledge. The CLHS model highlights a partnership for coproduction that is supported by data that can be used to support individual patient care, quality improvement, and research. We provide a case study that describes the application of this model to transform care within an oncology program at an academic medical center.


Subject(s)
Learning Health System , Humans , Caregivers , Academic Medical Centers , Patient Care Team
18.
Cities ; 134: 104163, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36593904

ABSTRACT

Most government emergency/pandemic response plans feature top-down decision making and communication strategies and a focus on 'hard' (physical) infrastructure. There is nothing about the importance of the ideas and communications originating from communities, the social infrastructure that supports their impact locally and their contribution to the central administration. In this study, we found that the 'soft' (social) infrastructure within communities and between communities and formal institutions is key to an inclusive and more equitable response to large-scale crises like the COVID-19 pandemic. Grassroots leaders in six Toronto neighbourhoods were interviewed between the first and second waves of the COVID-19 pandemic in Toronto about what helped or hindered community action. Three themes emerged: (1) Grassroots leaders and community organizations were able to act as key connection points in a two-way flow of information and resources with residents and service providers; (2) Grassroots leaders and groups were challenged to engage in this work in a sustained capacity without adequate resourcing; and (3) there was a disconnect between community-centred grassroots approaches and the City's emergency response. We conclude that there needs to be pre-disaster investment in community level planning and preparation that fosters two-way connections between all municipal emergency/disaster and pandemic preparedness plans and community-centred organizations and grassroots leaders working in marginalized communities.

19.
Genome Biol ; 24(1): 16, 2023 Jan 23.
Article in English | MEDLINE | ID: mdl-36691074

ABSTRACT

BACKGROUND: Association of chromatin with lamin proteins at the nuclear periphery has emerged as a potential mechanism to coordinate cell type-specific gene expression and maintain cellular identity via gene silencing. Unlike many histone modifications and chromatin-associated proteins, lamina-associated domains (LADs) are mapped genome-wide in relatively few genetically normal human cell types, which limits our understanding of the role peripheral chromatin plays in development and disease. RESULTS: To address this gap, we map LAMIN B1 occupancy across twelve human cell types encompassing pluripotent stem cells, intermediate progenitors, and differentiated cells from all three germ layers. Integrative analyses of this atlas with gene expression and repressive histone modification maps reveal that lamina-associated chromatin in all twelve cell types is organized into at least two subtypes defined by differences in LAMIN B1 occupancy, gene expression, chromatin accessibility, transposable elements, replication timing, and radial positioning. Imaging of fluorescently labeled DNA in single cells validates these subtypes and shows radial positioning of LADs with higher LAMIN B1 occupancy and heterochromatic histone modifications primarily embedded within the lamina. In contrast, the second subtype of lamina-associated chromatin is relatively gene dense, accessible, dynamic across development, and positioned adjacent to the lamina. Most genes gain or lose LAMIN B1 occupancy consistent with cell types along developmental trajectories; however, we also identify examples where the enhancer, but not the gene body and promoter, changes LAD state. CONCLUSIONS: Altogether, this atlas represents the largest resource to date for peripheral chromatin organization studies and reveals an intermediate chromatin subtype.


Subject(s)
Chromatin , Nuclear Lamina , Humans , Chromatin/metabolism , Nuclear Lamina/genetics , Cell Nucleus/genetics , Chromatin Assembly and Disassembly , Cell Differentiation
20.
Biophys J ; 122(2): 301-309, 2023 01 17.
Article in English | MEDLINE | ID: mdl-36523160

ABSTRACT

The sarco(endo)plasmic reticulum calcium ATPase (SERCA) is an ion transporter that creates and maintains intracellular calcium stores. SERCA is inhibited or stimulated by several membrane micropeptides including another-regulin, dwarf open reading frame, endoregulin, phospholamban (PLB), and sarcolipin. We previously showed that these micropeptides assemble into homo-oligomeric complexes with varying affinity. Here, we tested whether different micropeptides can interact with each other, hypothesizing that coassembly into hetero-oligomers may affect micropeptide bioavailability to regulate SERCA. We quantified the relative binding affinity of each combination of candidates using automated fluorescence resonance energy transfer microscopy. All pairs were capable of interacting with good affinity, similar to the affinity of micropeptide self-binding (homo-oligomerization). Testing each pair at a 1:5 ratio and a reciprocal 5:1 ratio, we noted that the affinity of hetero-oligomerization of some micropeptides depended on whether they were the minority or majority species. In particular, sarcolipin was able to join oligomers when it was the minority species but did not readily accommodate other micropeptides in the reciprocal experiment when it was expressed in fivefold excess. The opposite was observed for endoregulin. PLB was a universal partner for all other micropeptides tested, forming avid hetero-oligomers whether it was the minority or majority species. Increasing expression of SERCA decreased PLB-dwarf open reading frame hetero-oligomerization, suggesting that SERCA-micropeptide interactions compete with micropeptide-micropeptide interactions. Thus, micropeptides populate a regulatory network of diverse protein assemblies. The data suggest that the complexity of this interactome increases exponentially with the number of micropeptides that are coexpressed in a particular tissue.


Subject(s)
Calcium , Sarcoplasmic Reticulum Calcium-Transporting ATPases , Calcium/metabolism , Sarcoplasmic Reticulum Calcium-Transporting ATPases/metabolism , Ion Transport , Calcium-Binding Proteins/chemistry , Micropeptides
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