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Lee UJ, Mortola EN, Kim EJ, Long MY
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Evolution and maintenance of phenotypic plasticity

BIOSYSTEMS 2022 DEC; 222(?):? Article 104791
We introduce a novel framework for exploring the evolutionary consequences of phenotypic plasticity (adaptive and non-adaptive) integrating both genic and epigenetic effects on phenotype via stochastic differential equations and in-silico selection. In accordance with the most significant results derived from prior models, we demonstrate how plasticity is differentially favored when subjected to small vs large environmental shifts, how plasticity is transiently favorable while accommodating a new environment, and how plasticity decreases during epochs where the environment remains stable (canalization). In contrast to these models, however, by allowing the same phenotypic value to be produced via two different paths, i.e. deterministic, genic, vs stochastic, epigenetic mechanisms, we demonstrate when genic contributions alone cannot produce an optimal phenotype, plastic, epigenetic contributions will instead fully accommodate new environments, allowing for both adaptive and non-adaptive plasticity to evolve. Furthermore, we show that while rates of phenotypic accommodation are relatively constant under a wide range of selective conditions, selection will favor the most efficient route to adaptation: deterministic, genic response, or stochastic, plastic response. As a result, plasticity may evolve or canalization may occur within a given epoch depending on the relative mutation rate of genic and epigenetic contributions to phenotype, highlighting the importance of genetic conflict on the evolution of plasticity.
Canesso MCC, Moreira TG, Faria AMC
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Compartmentalization of gut immune responses: Mucosal niches and lymph node peculiarities

IMMUNOLOGY LETTERS 2022 DEC; 251-252(?):86-90
The intestine is not a homogeneous organ, but rather organized spaces with specific niches and microenvironments filled with different cell types that are involved in physiological and inflammatory processes. The intestinal mucosa shows a high degree of architectural complexity and intratissue specialization that occurs according to luminal composition. These intratissue specialized environments are critical for the developmental and functional adaptation of immune cells in the gut and in the gut-draining lymph nodes. In this review we discuss the compartmentalization of gut immune responses and how the lymph nodes that drain different regions of the intestine are immunologically, anatomically, and physiologically distinct. We also propose that studies on gut immunity should consider the distinctive features of intestinal segments and the differences in their draining lymph nodes to fully understand the complexity of the gut immunological scenario.
Woods C, Contoreggi NH, Johnson MA, Milner TA, Wang G, Glass MJ
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Estrogen receptor beta activity contributes to both tumor necrosis factor alpha expression in the hypothalamic paraventricular nucleus and the resistance to hypertension following angiotensin II in female mice

NEUROCHEMISTRY INTERNATIONAL 2022 DEC; 161(?):? Article 105420
Sex differences in the sensitivity to hypertension and inflammatory processes are well characterized but insufficiently understood. In male mice, tumor necrosis factor alpha (TNF alpha) in the hypothalamic paraventricular nucleus (PVN) contributes to hypertension following slow-pressor angiotensin II (AngII) infusion. However, the role of PVN TNF alpha in the response to AngII in female mice is unknown. Using a combination of in situ hybridization, high-resolution electron microscopic immunohistochemistry, spatial-temporal gene silencing, and dihydroethidium microfluorography we investigated the influence of AngII on both blood pressure and PVN TNF alpha signaling in female mice. We found that chronic (14-day) infusion of AngII in female mice did not impact blood pressure, TNF alpha levels, the expression of the TNF alpha type 1 receptor (TNFR1), or the subcellular distribution of TNFR1 in the PVN. However, it was shown that blockade of estrogen receptor beta (ER beta), a major hypothalamic estrogen receptor, was accompanied by both elevated PVN TNF alpha and hypertension following AngII. Further, AngII hypertension following ER beta blockade was attenuated by inhibiting PVN TNF alpha signaling by local TNFR1 silencing. It was also shown that ER beta blockade in isolated PVN-spinal cord projection neurons (i.e. sympathoexcitatory) heightened TNF alpha-induced production of NADPH oxidase (NOX2)-mediated reactive oxygen species, molecules that may play a key role in mediating the effect of TNF alpha in hypertension. These results indicate that ER beta contributes to the reduced sensitivity of female mice to hypothalamic inflammatory cytokine signaling and hypertension in response to AngII.
Dhaouadi S, Bouchami O, Soufi L, Dhaouadi F, Chaari S, Bouglita W, Cherif A, de Lencastre H, Elandoulsi RB, Miragaia M
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Frequent dissemination and carriage of an SCC mec-mecC hybrid in methicillin-resistant Mammaliicoccus sciuri in farm animals from Tunisia

Objectives: In this study, we aimed to assess the extent of dissemination of methicillin-resistant Mammaliicoccus sciuri in animal farms in Tunisia and evaluate the distribution of virulence and methicillin resistance genes in the M. sciuri population.Methods: Staphylococci and mammaliicocci isolated from unhealthy animals and healthy humans from adjacent farms in Tunisia were characterized for antimicrobial susceptibility, biofilm formation, agglutination, and hemolysis abilities. Mammaliicoccus sciuri relatedness and content in antibiotic resistance and virulence genes were analyzed by whole-genome sequencing (WGS).Results: Mammaliicoccus sciuri was the most prevalent species (46.2%), showing the highest resistance rates to fusidic acid (94.6%), oxacillin (73%), penicillin (40.5%), clindamycin (37%), ciprofloxacin (27%), and cefoxitin (24.3%). Some isolates carried genes encoding resistance to nine different antibiotic classes. mecA was found in 35% of M. sciuri and mecC in 16.2%. All isolates carrying mecC were of S. sciuri subspecies carnaticus and carried the hybrid element SCC mec-mecC. Mammaliicoccus sciuri were able to produce strong biofilm (27%) and have clumping ability (16%). Additionally, they carried genes for capsule production ( cap8 , 100%), iron-regulated surface determinants ( isdE , 24%; isdG , 3%), and virulence regulation ( clpC and clpP , 100%). Single nucleotide polymorphisms (SNPs) analysis showed that 17 M. sciuri cross-transmission events probably occurred between different animal species and farms. Moreover, SCC mec was estimated to have been acquired five times by S. sciuri subsp. carnaticus.Conclusion: Multidrug resistant and pathogenic M. sciuri were frequently disseminated between different animal species within the farm environment. mecA and mecC can be disseminated by both frequent acquisition of the SCC mec element and clonal dissemination.(c) 2022 The Authors. Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. This is an open access article under the CC BY-NC-ND license ( )
Brown JA, Sanidad KZ, Lucotti S, Lieber CM, Cox RM, Ananthanarayanan A, Basu S, Chen J, Shan MR, Amir M, Schmidt F, Weisblum Y, Cioffi M, Li TT, Rowdo FM, Martin ML, Guo CJ, Lyssiotis C, Layden BT, Dannenberg AJ, Bieniasz PD, Lee B, Inohara N, Matei I, Plemper RK, Zeng MY
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Gut microbiota-derived metabolites confer protection against SARS-CoV-2 infection

GUT MICROBES 2022 DEC 31; 14(1):? Article 2105609
The gut microbiome is intricately coupled with immune regulation and metabolism, but its role in Coronavirus Disease 2019 (COVID-19) is not fully understood. Severe and fatal COVID-19 is characterized by poor anti-viral immunity and hypercoagulation, particularly in males. Here, we define multiple pathways by which the gut microbiome protects mammalian hosts from SARS-CoV-2 intranasal infection, both locally and systemically, via production of short-chain fatty acids (SCFAs). SCFAs reduced viral burdens in the airways and intestines by downregulating the SARS-CoV-2 entry receptor, angiotensin-converting enzyme 2 (ACE2), and enhancing adaptive immunity via GPR41 and 43 in male animals. We further identify a novel role for the gut microbiome in regulating systemic coagulation response by limiting megakaryocyte proliferation and platelet turnover via the Sh2b3-Mpl axis. Taken together, our findings have unraveled novel functions of SCFAs and fiber-fermenting gut bacteria to dampen viral entry and hypercoagulation and promote adaptive antiviral immunity.
Mansisidor AR, Risca VI
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Chromatin accessibility: methods, mechanisms, and biological insights

NUCLEUS 2022 DEC 31; 13(1):236-276
Access to DNA is a prerequisite to the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and DNA repair. How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. Over the past decade, genome-wide assays and new imaging approaches have enabled a greater understanding of how access to the genome is regulated by nucleosomes and associated proteins. Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation - processes that are beginning to be understood. Here, we review the ongoing development of accessibility measurements, we summarize the different molecular and structural mechanisms that shape the accessibility landscape, and we detail the many important biological functions that are linked to chromatin accessibility.
Clamp loaders are pentameric AAA+ assemblies that use ATP to open and close circular DNA sliding clamps around DNA. Clamp loaders show homology in all organisms, from bacteria to human. The eukaryotic PCNA clamp is loaded onto 3 ' primed DNA by the replication factor C (RFC) hetero-pentameric clamp loader. Eukaryotes also have three alternative RFC-like clamp loaders (RLCs) in which the Rfc1 subunit is substituted by another protein. One of these is the yeast Rad24-RFC (Rad17-RFC in human) that loads a 9-1-1 heterotrimer clamp onto a recessed 5 ' end of DNA. Recent structural studies of Rad24-RFC have discovered an unexpected 5 ' DNA binding site on the outside of the clamp loader and reveal how a 5 ' end can be utilized for loading the 9-1-1 clamp onto DNA. In light of these results, new studies reveal that RFC also contains a 5 ' DNA binding site, which functions in gap repair. These studies also reveal many new features of clamp loaders. As reviewed herein, these recent studies together have transformed our view of the clamp loader mechanism.
Wolfisberg R, Thorselius CE, Salinas E, Elrod E, Trivedi S, Nielsen L, Fahnoe U, Kapoor A, Grakoui A, Rice CM, Bukh J, Holmbeck K, Scheel TKH
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Neutralization and receptor use of infectious culture-derived rat hepacivirus as a model for HCV

HEPATOLOGY 2022 NOV; 76(5):1506-1519
Background and Aims Lack of tractable immunocompetent animal models amenable to robust experimental challenge impedes vaccine efforts for HCV. Infection with rodent hepacivirus from Rattus norvegicus (RHV-rn1) in rats shares HCV-defining characteristics, including liver tropism, chronicity, and pathology. RHV in vitro cultivation would facilitate genetic studies on particle production, host factor interactions, and evaluation of antibody neutralization guiding HCV vaccine approaches. Approach and Results We report an infectious reverse genetic cell culture system for RHV-rn1 using highly permissive rat hepatoma cells and adaptive mutations in the E2, NS4B, and NS5A viral proteins. Cell culture-derived RHV-rn1 particles (RHVcc) share hallmark biophysical characteristics of HCV and are infectious in mice and rats. Culture adaptive mutations attenuated RHVcc in immunocompetent rats, and the mutations reverted following prolonged infection, but not in severe combined immunodeficiency (SCID) mice, suggesting that adaptive immune pressure is a primary driver of reversion. Accordingly, sera from RHVcc-infected SCID mice or the early acute phase of immunocompetent mice and rats were infectious in culture. We further established an in vitro RHVcc neutralization assay, and observed neutralizing activity of rat sera specifically from the chronic phase of infection. Finally, we found that scavenger receptor class B type I promoted RHV-rn1 entry in vitro and in vivo. Conclusions The RHV-rn1 infectious cell culture system enables studies of humoral immune responses against hepacivirus infection. Moreover, recapitulation of the entire RHV-rn1 infectious cycle in cell culture will facilitate reverse genetic studies and the exploration of tropism and virus-host interactions.
Shih T, De D, Daveluy SD, Hogeling M, Lowes MA, Sayed C, Shi VY, Hsiao JL
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Real-World Considerations of Candidacy for Biologics in Hidradenitis Suppurativa

AMERICAN JOURNAL OF CLINICAL DERMATOLOGY 2022 NOV; 23(6):749-753 Article s40257-022-00711-1
Hidradenitis suppurativa (HS) is a chronic, progressive inflammatory skin disease that is often recalcitrant to multiple treatments. In determining biologic candidacy for patients with HS, we propose a paradigm shift away from Hurley staging and towards consideration of other variables. Biologics represent a long-term treatment option for HS that may serve as a disease-modifying agent. These medications are typically initiated in patients with moderate to severe disease, which, based on inclusion criteria in clinical trials, is often defined as Hurley stage II or III disease, at which point irreversible tissue damage has already occurred. In real-world clinical settings, these considerations include treatments tried and failed, predicted disease trajectory, disease characteristics beyond lesion type, impact of disease on patients' functional status and quality of life, and patient comorbidities, venturing away from the limitations of Hurley stage designations. Future clinical trials may benefit from inclusion of recalcitrant Hurley stage I patients, which may then re-shape treatment guidelines and insurance coverage and improve patient access to biologic treatments.
Hashemi-Arend A, Vasquez KS, Guishard D, Naji M, Ronning A, George-Alexander G, Vasquez D, Sylvester C, Pagano W, Khalida C, Coffran C, Ezeonu T, Fofana K, Bielopolski D, Vaughan R, Qureshi A, Tobin JN, Kost RG
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Implementing DASH-Aligned Meals and Self-Measured Blood Pressure to Reduce Hypertension at Senior Centers: A RE-AIM Analysis

NUTRIENTS 2022 NOV; 14(22):? Article 4890
Low-income, minority seniors face high rates of hypertension that increase cardiovascular risk. Senior centers offer services, including congregate meals, that can be a valuable platform to reach older adults in underserved communities. We implemented two evidence-based interventions not previously tested in this setting: DASH-aligned congregate meals and Self-Measured Blood Pressure (SMBP), to lower blood pressure (BP) at two senior centers serving low-income, racially diverse communities. The study enrolled congregate meal program participants, provided training and support for SMPB, and nutrition and BP education. DASH-aligned meals delivered 40% (lunch) or 70% (breakfast and lunch) of DASH requirements/day. Primary outcomes were change in BP, and BP control, at Month 1. Implementation data collected included client characteristics, menu fidelity, meal attendance, SMBP adherence, meal satisfaction, input from partner organizations and stakeholders, effort, and food costs. We used the RE-AIM framework to analyze implementation. Study Reach included 94 older, racially diverse participants reflecting neighborhood characteristics. Effectiveness: change in systolic BP at Month 1 trended towards significance (-4 mmHg, p = 0.07); change in SMBP reached significance at Month 6 (-6.9 mmHg, p = 0.004). We leveraged existing community-academic partnerships, leading to Adoption at both target sites. The COVID pandemic interrupted Implementation and Maintenance and may have attenuated BP effectiveness. DASH meals served were largely aligned with planned menus. Meal attendance remained consistent; meal satisfaction was high. Food costs increased by 10%. This RE-AIM analysis highlights the acceptability, feasibility, and fidelity of this DASH/SMBP health intervention to lower BP at senior centers. It encourages future research and offers important lessons for organizations delivering services to older adults and addressing cardiovascular risk among vulnerable populations.