bluuebunny/crossref_metadata_2025_split huggingface dataset:
A conserved protein inhibitor brings under check the activity of RNase E in cyanobacteria
Authors: Liu Su-Juan , Lin Gui-Ming , Yuan Yu-Qi , Chen Wenli , Zhang Ju-Yuan , Zhang Cheng-Cai 
Published: November 2023

Abstract
The bacterial ribonuclease RNase E plays a key role in RNA metabolism. Yet, with a large substrate spectrum and poor substrate specificity, its activity must be well controlled under different conditions. Only a few regulators of RNase E are known, limiting our understanding on posttranscriptional regulatory mechanisms in bacteria. Here we show that, RebA, a protein universally present in cyanobacteria, interacts with RNase E in the cyanobacterium Anabaena PCC 7120. Distinct from those known regulators of RNase E, RebA interacts with the catalytic region of RNase E, and suppresses the cleavage activities of RNase E for all tested substrates. Consistent with the inhibitory function of RebA on RNase E, depletion of RNase E and overproduction of RebA caused formation of elongated cells, whereas the absence of RebA and overproduction of RNase E resulted in a shorter-cell phenotype. We further showed that the morphological changes caused by altered levels of RNase E or RebA are dependent on their physical interaction. The action of RebA represents a new mechanism, potentially conserved in cyanobacteria, for RNase E regulation. Our findings provide insights into the regulation and the function of RNase E, and demonstrate the importance of balanced RNA metabolism in bacteria.
Biochemical and cellular insights into the Baz2B protein, a non-catalytic subunit of the chromatin remodeling complex
Authors: Breindl Matthias , Spitzer Dominika , Gerasimaitė Rūta , Kairys Visvaldas , Schubert Thomas , Henfling Ramona , Schwartz Uwe , Lukinavičius Gražvydas , Manelytė Laura 
Published: November 2023

Abstract
Baz2B is a regulatory subunit of the ATP-dependent chromatin remodeling complexes BRF1 and BRF5, which control access to DNA during DNA-templated processes. Baz2B has been implicated in several diseases and also in unhealthy ageing, however limited information is available on the domains and cellular roles of Baz2B. To gain more insight into the Baz2B function, we biochemically characterized the TAM (Tip5/ARBP/MBD) domain with the auxiliary AT-hook motifs and the bromodomain (BRD). We observed alterations in histone code recognition in bromodomains carrying cancer-associated point mutations, suggesting their potential involvement in disease. Furthermore, the depletion of Baz2B in the Hap1 cell line resulted in altered cell morphology, reduced colony formation and perturbed transcriptional profiles. Despite that, super-resolution microscopy images revealed no changes in the overall chromatin structure in the absence of Baz2B. These findings provide insights into the biological function of Baz2B.
DELTEX E3 ligases ubiquitylate ADP-ribosyl modification on nucleic acids
Authors: Zhu Kang , Suskiewicz Marcin J , Chatrin Chatrin , Strømland Øyvind , Dorsey Bryan W , Aucagne Vincent , Ahel Dragana , Ahel Ivan 
Published: November 2023

Abstract
Although ubiquitylation had traditionally been considered limited to proteins, the discovery of non-proteinaceous substrates (e.g. lipopolysaccharides and adenosine diphosphate ribose (ADPr)) challenged this perspective. Our recent study showed that DTX2 E3 ligase efficiently ubiquitylates ADPr. Here, we show that the ADPr ubiquitylation activity is also present in another DELTEX family member, DTX3L, analysed both as an isolated catalytic fragment and the full-length PARP9:DTX3L complex, suggesting that it is a general feature of the DELTEX family. Since structural predictions show that DTX3L possesses single-stranded nucleic acids binding ability and given the fact that nucleic acids have recently emerged as substrates for ADP-ribosylation, we asked whether DELTEX E3s might catalyse ubiquitylation of an ADPr moiety linked to nucleic acids. Indeed, we show that DTX3L and DTX2 are capable of ubiquitylating ADP-ribosylated DNA and RNA synthesized by PARPs, including PARP14. Furthermore, we demonstrate that the Ub-ADPr-nucleic acids conjugate can be reversed by two groups of hydrolases, which remove either the whole adduct (e.g. SARS-CoV-2 Mac1 or PARP14 macrodomain 1) or just the Ub (e.g. SARS-CoV-2 PLpro). Overall, this study reveals ADPr ubiquitylation as a general function of the DELTEX family E3s and presents the evidence of reversible ubiquitylation of ADP-ribosylated nucleic acids.
Amazonian avian biogeography: Broadscale patterns, microevolutionary processes, and habitat-specific models revealed by multidisciplinary approaches
Authors: Capurucho João Marcos Guimarães , Musher Lukas J , Lees Alexander , Rego Marco A , Del-Rio Glaucia , Aleixo Alexandre , Luzuriaga-Aveiga Vanessa E , Ferreira Mateus , Ribas Camila C , Thom Gregory 
Published: November 2023

Abstract
Our understanding of Amazonian biogeography is quickly increasing, catalyzed by the growing use of genomic datasets, improved knowledge of species distributions, and the accumulation of new data on the geological and climatic history of the region. The high number of species in Amazonia and their intricate patterns of geographic distribution triggered the development of many diversification hypotheses that shaped historical biogeography as a discipline. Here, we present a historical overview of avian biogeographic studies in Amazonia, their recent advances, outstanding questions, and future directions. We focus on how new approaches have led to novel understandings of the distribution patterns and diversification processes that underpin avian diversity. We show how genomic tools are being used to establish new hypotheses about the drivers of diversification and highlight the importance of recent studies of birds in previously overlooked environments, such as floodplains and open vegetation enclaves. We emphasize the importance of gene flow, species traits, and habitat affinities in studying diversification processes to fully acknowledge the complexity of Amazonian ecosystems and their history. We then discuss the current gaps in Amazonian taxonomic and biogeographic knowledge, with a focus on the issues that we believe hinder our understanding of the field. Amazonia has been facing increasing levels of forest loss due to agricultural expansion, infrastructure development, mining, climate change, and illegal activities catalyzed by weak governance. To halt biodiversity loss, it is crucial to increase our knowledge of the natural history and biogeography of Amazonian species. We suggest increasing incentives for research and training at institutions based in the region, as well as the establishment of partnerships with governments, local communities, NGOs, and international institutions to bring diverse communities together to address crucial questions.
The positive and negative emotion functions related to loneliness: a systematic review of behavioural and neuroimaging studies
Authors: Luo Qianyi , Shao Robin 
Published: November 2023

Abstract
Loneliness is associated with high prevalences of major psychiatric illnesses such as major depression. However, the underlying emotional mechanisms of loneliness remained unclear. We hypothesized that loneliness originates from both decreases in positive emotional processing and increases in negative emotion processing. To test this, we conducted a systematic review of 29 previous studies (total participants n = 19 560, mean age = 37.16 years, female proportion = 59.7%), including 18 studies that included questionnaire measures of emotions only, and 11 studies that examined the brain correlates of emotions. The main findings were that loneliness was negatively correlated with general positive emotions and positively correlated with general negative emotions. Furthermore, limited evidence indicates loneliness exhibited negative and positive correlations with the brain positive (e.g. the striatum) and negative (e.g. insula) emotion systems, respectively, but the sign of correlation was not entirely consistent. Additionally, loneliness was associated with the structure and function of the brain emotion regulation systems, particularly the prefrontal cortex, but the direction of this relationship remained ambiguous. We concluded that the existing evidence supported a bivalence model of loneliness, but several critical gaps existed that could be addressed by future studies that include adolescent and middle-aged samples, use both questionnaire and task measures of emotions, distinguish between general emotion and social emotion as well as between positive and negative emotion regulation, and adopt a longitudinal design that allows us to ascertain the causal relationships between loneliness and emotion dysfunction. Our findings provide new insights into the underlying emotion mechanisms of loneliness that can inform interventions for lonely individuals.
Pre-existing musculoskeletal pain and its association with mortality in newly diagnosed co-morbid conditions: an electronic health record cohort study
Authors: Marshall Michelle , Mason Kayleigh J , Edwards John J , Mamas Mamas A , Bailey James , Heron Neil , Achana Felix A , Frisher Martin , Huntley Alyson L , Mallen Christian D , Png May Ee , Tatton Stephen , White Simon , Jordan Kelvin P 
Published: November 2023

Abstract

Objective
Musculoskeletal pain is a common risk factor for co-morbid conditions and might increase the risk of poor outcomes. The objective was to determine whether patients with pre-existing musculoskeletal pain have an increased risk for mortality following a new diagnosis of a co-morbid condition.

Methods
Patients aged ≥45 years with a new diagnosis of acute coronary syndrome (ACS), stroke, cancer, dementia or pneumonia recorded in a UK electronic primary care database linked to hospital and mortality records were examined. The association of mortality with musculoskeletal pain (inflammatory conditions, OA and regional pain) was determined.

Results
The sample size varied from 128 649 (stroke) to 406 289 (cancer) by cohort, with 22–31% having pre-existing musculoskeletal conditions. In the ACS cohort, there was a higher rate of mortality for all musculoskeletal types. There were also higher unadjusted mortality rates in patients with inflammatory arthritis compared with those without musculoskeletal pain in the stroke, cancer and dementia cohorts and for patients with OA in the stroke and cancer cohorts. After adjustment for the number of prescribed medications and age, the increased risk of mortality remained only for patients with inflammatory arthritis in the ACS cohort (adjusted hazard ratio = 1.07; 95% CI 1.03, 1.10).

Conclusion
Older adults with inflammatory arthritis and OA have increased risk of mortality when they develop a new condition, which seems to be related to the prescription of multiple medicines. Pre-existing musculoskeletal pain is an indicator of a complex patient who is at risk of poorer outcomes at the onset of new illnesses.
Inaction, Silence, Focus, and Power: Identifying and Assessing Folk Theories of the Racism of Omission
Authors: Warren Evangeline , Valentino Lauren 
Published: November 2023

AbstractRecent scholarship has advanced a concept of racism operating through omission. Omission captures both inaction and action, highlighting how systems of oppression rely on inertia in addition to discriminatory action to perpetuate inequality. Yet little is known about how laypersons understand the role of omission in propagating racism in the United States. Building on this premise, we employ a mixed-methods approach to document and test folk theories of the racism of omission. We interview diverse individuals (N=40) about their appraisals of racism; we use these findings to design a vignette study which we fielded to a national sample (N=1,174). Interview data reveal that some Americans do understand omission to be a form of racism, highlighting (1) bystander inaction, (2) silencing of experiences of racism, (3) overfocus on White issues, and (4) disparities in positions of power as instances where inaction, exclusion, or inertia constitute a form of racism. Data show that Americans are most likely to consider overfocus and silencing as forms of omission-based racism, and that racism appraisals depend on the victim’s race. We find that political ideology, gender, income, race, and education shape appraisals of racism as omission. These findings have implications for measures of perceived racism and discrimination.
Seroprevalence of SARS-CoV-2 antibodies in pediatric hospital surgical unit: a lower-middle-income country perspective
Authors: Habib Murad , Javed Noshela , Burki Sadia Asmat , Ahmed Mansoor , Chaudhary Muhammad Amjad 
Published: November 2023

Abstract

Background
The objective of our study was to measure and give insight into the seropositivity of anti-SARS-CoV-2 antibodies in the patients in our pediatric hospital surgical unit in Pakistan.

Methods
A prospective cohort study was conducted at a tertiary care pediatric hospital surgical unit in Pakistan between 1 January 2021 and 1 June 2021 on the enrolled neonates and children aged 1 day to 13 years. All patients from three different pediatric strata [neonates (&lt;1 month), infants (1 to 12 months) and children (&gt;1 year)] were enrolled in the study.

Results
Six-hundred patients were enrolled, and 426 patients were included in the study. Among 426 patients, 234 (54.9%) were male, and 192 (45.1%) were female. Overall only 118 (27.7%) patients developed symptoms. The other 308 (72.3%) were asymptomatic of which 28 (9.1%) had fever, 28 (9.1%) had cough, 38 (12.33%) had body aches, 292 (94.8%) had vomiting/diarrhea, and only 28 (9.1%) developed loss of smell and taste. Our results showed seropositivity of 27.7% (n = 118), while 72.3% (n = 308) had negative antibody titers.

Conclusion
A much higher pediatric SARS-CoV-2 burden of 27.7% was found in our pediatric surgical unit than has previously been reported in the literature of 6.8% for children in pediatric hospitals or pediatric surgical units. Contrary to reporting early in the COVID-19 pandemic, this study determined that children experience a significant burden of COVID-19 infection. Thus, children appear very important in SARS-CoV-2 pandemic, from harboring the virus and further studies need to be done to find if they are transmitting the disease silently.
Mitochondrial Dynamics in Auditory Sensory Cells
Authors: Nuttall Alfred L , Foster Sarah , Wilson Teresa 
Published: November 2023

BackgroundThe auditory sensory hair cells convert sound vibrations into neuronal impulses. Excessive loud sound exposure can result in the overproduction of oxidative free radicals by the mitochondria in these cells. This can negatively impact hair cell function and viability leading to permanent loss of hearing sensitivity. The mechanisms that initiate this process are thought to include ischemia/reperfusion injury as well as metabolic overstimulation. Despite the importance of auditory hair cells, the basic physiology of the mitochondria in these cells is relatively unknown. Further, whether mitochondrial dynamics and spatial localization are altered to respond to increased energy needs of the cells with loud sound exposure has not been well‐characterized.ObjectiveIn this study, our goal was to characterize mitochondrial morphology and spatial distribution in auditory cells under normal and loud sound induced stress conditions.Methods and ResultsTo examine mitochondria in outer hair cells (OHCs), PhAMfloxed mice were crossed with prestin‐CreERT2 mice to generate mice that express a mitochondrial‐specific version of the Dendra2 fluorescent protein (mito‐Dendra2) in the mitochondria in OHCs. For examination of mitochondria in all organ of Corti cells, immunolabeling for the mitochondrial outer membrane protein Tom20 was performed. These mice were exposed to damaging levels of loud sound and the cochlea harvested at 24 and 48 hours following noise exposure. Airyscan and super resolution imaging of mito‐Dendra2 and Tom20 fluorescence showed primarily fragmented mitochondria in the OHCs and a mixture of punctate and short rod‐shaped mitochondria in the inner hair cells of normal control animals. Following noise exposure, the mitochondria of the organ of Corti cells were examined for alterations in spatial distribution, number, and morphology, and preliminary results demonstrated changes in the distribution of mitochondria in OHCs.ConclusionsMitochondria are highly dynamic organelles that are maintained by the conserved actions of mitochondrial division, fusion, motility, and tethering. The presence of excessive cellular stress typically results in attenuated fusion processes and increased mitochondrial fragmentation. The presence of fragmented mitochondria in OHCs suggests that the balance of fission and fusion processes are altered, potentially due to a higher oxidant environment being present in these cells.Support or Funding InformationSupported by grants 5R01DC000105 (ALN) and P30DC005983.
Stressor‐Enhanced Infectious Colitis is Due to Aberrant Colonic Epithelial Cell Signaling
Authors: Mackos Amy , Bailey Michael T 
Published: November 2023

It has been long known that exposure to psychological stressors can exacerbate gastrointestinal disease, however the mechanism by which this occurs has not yet been fully elucidated. One hypothesis is that disruptions in the indigenous microbiota of the intestine by psychological stressors contribute to the exacerbation of disease. Recently, our laboratory has shown that exposing mice to the social stressor, namely, social disruption (SDR) significantly alters the intestinal microbiota community structure, and reduces the levels of beneficial species like Lactobacillus reuteri. These stressor‐induced changes in the microbiota can lead to increased proinflammatory cytokines (e.g., TNF‐α) and chemokines (e.g., CCL2) in the colons of mice challenged with the colonic pathogen Citrobacter rodentium. Exaggerated expression of these pro‐inflammatory cytokines and chemokines can enhance inflammatory monocyte recruitment, leading to enhanced colonic tissue damage. Thus, identifying the cellular source(s) of colonic TNF‐α and CCL2 during stressor exposure has important health implications. Due to close proximity with the colonic microbiota, we hypothesized that colonic epithelial cells (CEC) from stressor‐exposed mice would have increased expression of TNF‐α and CCL2 as compared to CEC from naïve mice. To test this hypothesis mice were exposed to SDR, which involves repeated social defeat, for 2 hours a night for 6 consecutive nights. The morning following the last night of the stressor, mice were euthanized, colons were excised, and both CEC and lamina propria cells were isolated. Results demonstrated that CEC from SDR‐exposed mice had significant increases in both TNF‐α and CCL2 gene expression as compared to CEC isolated from non‐stressed controls. Conversely, TNF‐α and CCL2 gene expression was unchanged in lamina propria cells from stressor exposed mice when compared their control counterparts. Together, these data have led to the proposed model that stressor exposure can lead to aberrant inflammatory gene expression in colonic epithelial cells, which may prime the colon for an overzealous inflammatory response when challenged with an enteric pathogen following stressor exposure.Support or Funding InformationSupported by NIH grant AT006552‐01A1 (M.T.B).
Lactobacillus rhamnosus Isolated from “amabere amaruranu” Cultured Milk Modulated the Production of Inflammatory Cytokines in Caco‐2 Cells
Authors: Ngeny Beverly , Onyango E M 
Published: November 2023

Probiotic microorganisms have been shown to confer health benefits on the host when administered in adequate amounts. In the gastrointestinal tract, they promote host immunity, regulate immune signaling pathways and produce anti‐pathogenic factors. The immune effects resulting from interactions between intestinal epithelial cells and commensal bacteria have not yet been fully elucidated. This study examined the effects of a Lactobacillus rhamnosus isolate from “amabere amaruranu” a Kenyan traditional cultured milk, on the production of pro‐inflammatory cytokines (Interleukin 8 and Tumor Necrosis Factor‐α) and anti‐inflammatory cytokines (Interleukin 10 and Transforming Growth Factor‐β) in enterocytes. The L. rhamnosus isolate was cultured in de‐Mann Rogosa Sharpe media overnight, the broth was collected and filtered to obtain filtered spent broth (FSB). Cell pellets resuspended in PBS were sonicated and filtered to obtain cytoplasmic fraction (CF). Differentiated Caco‐2 cell monolayer in transwells, after 21 days post‐confluence were co‐cultured with live L. rhamnosus (MRS6AN) isolate or apically treated with PBS control or CF or FSB. After 6–36 hrs of incubation, cells were collected and lysed and cell supernatants were collected. Enzyme Linked Immunosorbent Assay was used to determine the cytokine content in the cell lysate, apical and basolateral supernatants. Effects of the various treatments (PBS Control, MRS6AN, CF and FSB) on Caco‐2 cell lysate levels of TGF‐β were 14.5, 191.6, 153.3 and 128.8 ng/ml, respectively; of IL10 were 7.1, 44, 33.6 and 31 pg/ml, respectively; of IL8 were 200, 1014, 1489.1 and 1659.6 pg/ml, respectively, and of TNF‐α were 4.1, 27.6, 33.1 and 30.1 pg/ml, respectively. There were very low levels of TGFβ, IL10, IL8 and TNFα cytokines in both the apical and basolateral supernatants. In conclusion, L. rhamnosus isolate and its cytoplasmic fraction or spent media seemed to cause a higher production of anti‐inflammatory TGF‐β and pro‐inflammatory IL8 cytokines by differentiated Caco‐2 cells.Support or Funding InformationEast Tennessee State University