bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of the proteolytic signature in CVB3-infected cells
Authors: Vlok Marli , Solis Nestor , Sadasivan Jibin , Mohamud Yasir , Warsaba Reid , Kizhakkedathu Jayachandran , Luo Honglin , Overall Christopher M. , Jan Eric 
Published: July 2024

ABSTRACT

Coxsackievirus B3 (CVB3) encodes proteinases that are essential for processing of the translated viral polyprotein. Viral proteinases also target host proteins to manipulate cellular processes and evade innate antiviral responses to promote replication and infection. While some host protein substrates of the CVB3 3C and 2A cysteine proteinases have been identified, the full repertoire of targets is not known. Here, we utilize an unbiased quantitative proteomics-based approach termed terminal amine isotopic labeling of substrates (TAILS) to conduct a global analysis of CVB3 protease-generated N-terminal peptides in both human HeLa and mouse cardiomyocyte (HL-1) cell lines infected with CVB3. We identified >800 proteins that are cleaved in CVB3-infected HeLa and HL-1 cells including the viral polyprotein, known substrates of viral 3C proteinase such as PABP, DDX58, and HNRNPs M, K, and D and novel cellular proteins. Network and GO-term analysis showed an enrichment in biological processes including immune response and activation, RNA processing, and lipid metabolism. We validated a subset of candidate substrates that are cleaved under CVB3 infection and some are direct targets of 3C proteinase
in vitro
. Moreover, depletion of a subset of TAILS-identified target proteins decreased viral yield. Characterization of two target proteins showed that expression of 3C
pro
-targeted cleaved fragments of emerin and aminoacyl-tRNA synthetase complex-interacting multifunctional protein 2 modulated autophagy and the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathway, respectively. The comprehensive identification of host proteins targeted during virus infection provides insights into the cellular pathways manipulated to facilitate infection.

IMPORTANCE
RNA viruses encode proteases that are responsible for processing viral proteins into their mature form. Viral proteases also target and cleave host cellular proteins; however, the full catalog of these target proteins is incomplete. We use a technique called terminal amine isotopic labeling of substrates (TAILS), an N-terminomics to identify host proteins that are cleaved under virus infection. We identify hundreds of cellular proteins that are cleaved under infection, some of which are targeted directly by viral protease. Revealing these target proteins provides insights into the host cellular pathways and antiviral signaling factors that are modulated to promote virus infection and potentially leading to virus-induced pathogenesis.
Comprehensive proteomic analysis of HCoV-OC43 virions and virus-modulated extracellular vesicles
Authors: Joharinia Negar , Bonneil Éric , Grandvaux Nathalie , Thibault Pierre , Lippé Roger 
Published: July 2024

ABSTRACT

Viruses are obligate parasites that depend on the cellular machinery for their propagation. Several viruses also incorporate cellular proteins that facilitate viral spread. Defining these cellular proteins is critical to decipher viral life cycles and delineate novel therapeutic strategies. While numerous studies have explored the importance of host proteins in coronavirus spread, information about their presence in mature virions is limited. In this study, we developed a protocol to highly enrich mature HCoV-OC43 virions and characterize them by proteomics. Recognizing that cells release extracellular vesicles whose content is modulated by viruses, and given our ability to separate virions from these vesicles, we also analyzed their protein content in both uninfected and infected cells. We uncovered 69 unique cellular proteins associated with virions including 31 high-confidence hits. These proteins primarily regulate RNA metabolism, enzymatic activities, vesicular transport, cell adhesion, metabolite interconversion, and translation. We further discovered that the virus had a profound impact on exosome composition, incorporating 47 novel cellular proteins (11 high confidence) and excluding 92 others (61 high confidence) in virus-associated extracellular vesicles compared to uninfected cells. Moreover, a dsiRNA screen revealed that 11 of 18 select targets significantly impacted viral yields, including proteins found in virions or extracellular vesicles. Overall, this study provides new and important insights into the incorporation of numerous host proteins into HCoV-OC43 virions, their biological significance, and the ability of the virus to modulate extracellular vesicles.

IMPORTANCE
In recent years, coronaviruses have dominated global attention, making it crucial to develop methods to control them and prevent future pandemics. Besides viral proteins, host proteins play a significant role in viral propagation and offer potential therapeutic targets. Targeting host proteins is advantageous because they are less likely to mutate and develop resistance compared to viral proteins, a common issue with many antiviral treatments. In this study, we examined the protein content of the less virulent biosafety level 2 HCoV-OC43 virus as a stand-in for the more virulent SARS-CoV-2. Our findings reveal that several cellular proteins incorporated into the virion regulate viral spread. In addition, we report that the virus extensively modulates the content of extracellular vesicles, enhancing viral dissemination. This underscores the critical interplay between the virus, host proteins, and extracellular vesicles.
Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission
Authors: Benlarbi Mehdi , Ding Shilei , Bélanger Étienne , Tauzin Alexandra , Poujol Raphaël , Medjahed Halima , El Ferri Omar , Bo Yuxia , Bourassa Catherine , Hussin Julie , Fafard Judith , Pazgier Marzena , Levade Inès , Abrams Cameron , Côté Marceline , Finzi Andrés 
Published: July 2024

ABSTRACT

The continued evolution of severe acute respiratory syndrome 2 (SARS-CoV-2) requires persistent monitoring of its subvariants. Omicron subvariants are responsible for the vast majority of SARS-CoV-2 infections worldwide, with XBB and BA.2.86 sublineages representing more than 90% of circulating strains as of January 2024. To better understand parameters involved in viral transmission, we characterized the functional properties of Spike glycoproteins from BA.2.75, CH.1.1, DV.7.1, BA.4/5, BQ.1.1, XBB, XBB.1, XBB.1.16, XBB.1.5, FD.1.1, EG.5.1, HK.3, BA.2.86 and JN.1. We tested their capacity to evade plasma-mediated recognition and neutralization, binding to angiotensin-converting enzyme 2 (ACE2), their susceptibility to cold inactivation, Spike processing, as well as the impact of temperature on Spike-ACE2 interaction. We found that compared to the early wild-type (D614G) strain, most Omicron subvariants' Spike glycoproteins evolved to escape recognition and neutralization by plasma from individuals who received a fifth dose of bivalent (BA.1 or BA.4/5) mRNA vaccine and improve ACE2 binding, particularly at low temperatures. Moreover, BA.2.86 had the best affinity for ACE2 at all temperatures tested. We found that Omicron subvariants’ Spike processing is associated with their susceptibility to cold inactivation. Intriguingly, we found that Spike-ACE2 binding at low temperature was significantly associated with growth rates of Omicron subvariants in humans. Overall, we report that Spikes from newly emerged Omicron subvariants are relatively more stable and resistant to plasma-mediated neutralization, present improved affinity for ACE2 which is associated, particularly at low temperatures, with their growth rates.

IMPORTANCE
The persistent evolution of SARS-CoV-2 gave rise to a wide range of variants harboring new mutations in their Spike glycoproteins. Several factors have been associated with viral transmission and fitness such as plasma-neutralization escape and ACE2 interaction. To better understand whether additional factors could be of importance in SARS-CoV-2 variants’ transmission, we characterize the functional properties of Spike glycoproteins from several Omicron subvariants. We found that the Spike glycoprotein of Omicron subvariants presents an improved escape from plasma-mediated recognition and neutralization, Spike processing, and ACE2 binding which was further improved at low temperature. Intriguingly, Spike-ACE2 interaction at low temperature is strongly associated with viral growth rate, as such, low temperatures could represent another parameter affecting viral transmission.
Exploring Barmah Forest virus pathogenesis: molecular tools to investigate non-structural protein 3 nuclear localization and viral genomic determinants of replication
Authors: Omler Ailar , Mutso Margit , Vaher Mihkel , Freitas Joseph R. , Taylor Adam , David Cassandra T. , Moseley Gregory W. , Liu Xiang , Merits Andres , Mahalingam Suresh 
Published: July 2024

ABSTRACT

Barmah Forest virus (BFV) is a mosquito-borne virus that causes arthralgia with accompanying rash, fever, and myalgia in humans. The virus is mainly found in Australia and has caused outbreaks associated with significant health concerns. As the sole representative of the Barmah Forest complex within the genus
Alphavirus
, BFV is not closely related genetically to other alphaviruses. Notably, basic knowledge of BFV molecular virology has not been well studied due to a lack of critical investigative tools such as an infectious clone. Here we describe the construction of an infectious BFV cDNA clone based on Genbank sequence and demonstrate that the clone-derived virus has
in vitro
and
in vivo
properties similar to naturally occurring virus, BFV field isolate 2193 (BFV2193-FI). A substitution in nsP4, V1911D, which was identified in the Genbank reference sequence, was found to inhibit virus rescue and replication. T1325P substitution in nsP2 selected during virus passaging was shown to be an adaptive mutation, compensating for the inhibitory effect of nsP4-V1911D. The two mutations were associated with changes in viral non-structural polyprotein processing and type I interferon (IFN) induction. Interestingly, a nuclear localization signal, active in mammalian but not mosquito cells, was identified in nsP3. A point mutation abolishing nsP3 nuclear localization attenuated BFV replication. This effect was more prominent in the presence of type I interferon signaling, suggesting nsP3 nuclear localization might be associated with IFN antagonism. Furthermore, abolishing nsP3 nuclear localization reduced virus replication in mice but did not significantly affect disease.

IMPORTANCE
Barmah Forest virus (BFV) is Australia’s second most prevalent arbovirus, with approximately 1,000 cases reported annually. The clinical symptoms of BFV infection include rash, polyarthritis, arthralgia, and myalgia. As BFV is not closely related to other pathogenic alphaviruses or well-studied model viruses, our understanding of its molecular virology and mechanisms of pathogenesis is limited. There is also a lack of molecular tools essential for corresponding studies. Here we describe the construction of an infectious clone of BFV, variants harboring point mutations, and sequences encoding marker protein. In infected mammalian cells, nsP3 of BFV was located in the nuclei. This finding extends our understanding of the diverse mechanisms used by alphavirus replicase proteins to interact with host cells. Our novel observations highlight the complex synergy through which the viral replication machinery evolves to correct mutation errors within the viral genome.
Structural and Magnetic Transformations from CuCl to Cu2Cl(OH)3 Induced by H2O and CuCl2
Authors: Pimentel D. P. 
Published: July 2024

This study explores the oxidation dynamics of “pure” CuCl during prolonged environmental exposure through X-ray diffraction and temperature-dependent magnetization assessments. While CuCl is traditionally considered diamagnetic, our investigation reveals the emergence of an antiferromagnetic transition at 4.7 K. This anomaly is potentially induced by the integration of water molecules into the CuCl matrix. The hydration process initiates a series of oxidation reactions, ultimately transmuting CuCl into Cu2Cl(OH)3. Over time, the distinctive diffraction pattern peaks corresponding to CuCl diminish, concurrently with the appearance and intensification of those ascribed to Cu2Cl(OH)3, culminating in a complete phase transition as confirmed by X-ray analysis. Correspondingly, magnetization measurements clearly discern magnetic transitions at 6.4 and 16 K, intensifying with the sample’s exposure duration. These findings illuminate the stark potential for probing the magnetic intricacies of Cu2Cl(OH)3, a subject that remains a compelling and unresolved intrigue within the field.
What does good care look like to people living with congenital heart disease in the 21st century? Qualitative online, asynchronous discussion forums
Authors: Wray Jo , Pagel Christina , Coats Louise , Chester Adrian H , Kennedy Fiona , Crowe Sonya 
Published: July 2024

ObjectivesAs part of a wider study, our aim was to elicit perspectives of people with congenital heart disease (CHD) and/or their parents/carers about their experiences of healthcare and what is important to them when receiving care.Design and settingA qualitative study involving a series of closed, asynchronous, online discussion forums underpinned by an interpretivist framework and set up and moderated by three patient charities via their Facebook pages.ParticipantsPeople with CHD and parents/carers of people with CHD from the UK.ResultsFive forums were run for 12–24 weeks across the three charities, and 343 participants signed up to the forums. Four linked themes related to processes of care were identified following thematic analysis of the transcripts: relationships and communication; access and coordination; experience of discrete episodes of care and psychological support. These impacted how care was experienced and, for some patients, outcomes of CHD and its treatment as well as broader health outcomes. In addition, context relating to stages of the patient journey was described, together with patient-related factors such as patients’ knowledge and expertise in their own condition.ConclusionsPeople with CHD and their parents/carers want individualised, person-centred care delivered within an appropriately resourced, multidisciplinary service. Although examples of excellent care were provided it is evident that, from the perspective of patients and parents/carers, some National Health Service Standards for people with CHD were not being met.
Pancreatic STAT5 activation promotes Kras
G12D
-induced and inflammation-induced acinar-to-ductal metaplasia and pancreatic cancer
Authors: Lin Yuli , Pu Shaofeng , Wang Jun , Wan Yaqi , Wu Zhihao , Guo Yangyang , Feng Wenxue , Ying Ying , Ma Shuai , Meng Xiang Jun , Wang Wenquan , Liu Liang , Xia Qing , Yang Xuguang 
Published: July 2024

Objective
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy because it is often diagnosed at a late-stage. Signal transducer and activator of transcription 5 (STAT5) is a transcription factor implicated in the progression of various cancer types. However, its role in KRAS-driven pancreatic tumourigenesis remains unclear.

Design

We performed studies with
LSL-Kras
G12D
;
Ptf1a-Cre
ERT
(KC
ERT
) mice or LSL-Kras
G12D
;

LSL-Trp53
R172H

;
Pdx1-Cre
(KPC) mice crossed with conditional disruption of STAT5 or completed deficiency interleukin (IL)-22. Pancreatitis was induced in mice by administration of cerulein. Pharmacological inhibition of STAT5 on PDAC prevention was studied in the orthotopic transplantation and patient-derived xenografts PDAC model, and KPC mice.

Results
The expression and phosphorylation of STAT5 were higher in human PDAC samples than control samples and high levels of STAT5 in tumour cells were associated with a poorer prognosis. The loss of STAT5 in pancreatic cells substantially reduces the KRAS mutation and pancreatitis-derived acinar-to-ductal metaplasia (ADM) and PDAC lesions. Mechanistically, we discovered that STAT5 binds directly to the promoters of ADM mediators, hepatocyte nuclear factor (HNF) 1β and HNF4α. Furthermore, STAT5 plays a crucial role in maintaining energy metabolism in tumour cells during PDAC progression. IL-22 signalling induced by chronic inflammation enhances KRAS-mutant-mediated STAT5 phosphorylation. Deficiency of IL-22 signalling slowed the progression of PDAC and ablated STAT5 activation.

Conclusion
Collectively, our findings identified pancreatic STAT5 activation as a key downstream effector of oncogenic KRAS signalling that is critical for ADM initiation and PDAC progression, highlighting its potential therapeutic vulnerability.
Intergenerational transmission of health inequalities: towards a life course approach to socioeconomic inequalities in health – a review
Authors: Houweling Tanja A J , Grünberger Ilona 
Published: July 2024

Adult health inequalities are a persistent public health problem. Explanations are usually sought in behaviours and environments in adulthood, despite evidence on the importance of early life conditions for life course outcomes. We review evidence from a broad range of fields to unravel to what extent, and how, socioeconomic health inequalities are intergenerationally transmitted.We find that transmission of socioeconomic and associated health (dis)advantages from parents to offspring, and its underlying structural determinants, contributes substantially to socioeconomic inequalities in adult health. In the first two decades of life—from conception to early adulthood—parental socioeconomic position (SEP) and parental health strongly influence offspring adult SEP and health. Socioeconomic and health (dis)advantages are largely transmitted through the same broad mechanisms. Socioeconomic inequalities in the fetal environment contribute to inequalities in fetal development and birth outcomes, with lifelong socioeconomic and health consequences. Inequalities in the postnatal environment—especially the psychosocial and learning environment, physical exposures and socialisation—result in inequalities in child and adolescent health, development and behavioural habits, with health and socioeconomic consequences tracking into adulthood. Structural factors shape these mechanisms in a socioeconomically patterned and time-specific and place-specific way, leading to distinct birth-cohort patterns in health inequality.Adult health inequalities are for an important part intergenerationally transmitted. Effective health inequality reduction requires addressing intergenerational transmission of (dis)advantage by creating societal circumstances that allow all children to develop to their full potential.
Regional inequalities in excess mortality and its community determinants during the early COVID-19 pandemic in South Korea
Authors: Kim Eunah , Lee Woojoo , Cho Sung-Il 
Published: July 2024

BackgroundExcess mortality during the COVID-19 pandemic provides a comprehensive measure of disease burden, and its local variation highlights regional health inequalities. We investigated local excess mortality in 2020 and its determinants at the community level.MethodsWe collected data from 250 districts in South Korea, including monthly all-cause mortality for 2015–2020 and community characteristics from 2019. Excess mortality rate was defined as the difference between observed and expected mortality rates. A Seasonal Autoregressive Integrated Moving Average model was applied to predict the expected rates for each district. Penalized regression methods were used to derive relevant community predictors of excess mortality based on the elastic net.ResultsIn 2020, South Korea exhibited significant variation in excess mortality rates across 250 districts, ranging from no excess deaths in 46 districts to more than 100 excess deaths per 100 000 residents in 30 districts. Economic status or the number of medical centres in the community did not correlate with excess mortality rates. The risk was higher in ageing, remote communities with limited cultural and sports infrastructure, a higher density of welfare facilities, and a higher prevalence of hypertension. Physical distancing policies and active social engagement in voluntary activities protected from excess mortality.ConclusionSubstantial regional disparities in excess mortality existed within South Korea during the early stages of COVID-19 pandemic. Weaker segments of the community were more vulnerable. Local governments should refine their preparedness for future novel infectious disease outbreaks, considering community circumstances.
Mortality and cancer incidence in a population exposed to TCDD after the Seveso, Italy, accident (1976–2013)
Authors: Consonni Dario , Rognoni Magda , Cavalieri d'Oro Luca , Pesatori Angela Cecilia 
Published: July 2024

ObjectivesThe Seveso accident (1976) caused the contamination with 2,3,7,8-tetrachlorodibenzo-para-dioxin (TCDD) in an area north of Milan, Italy. We report the results of the update of mortality and cancer incidence in the exposed population through 2013.MethodsThe study cohort includes subjects living in three contaminated zones with decreasing TCDD soil concentrations (zone A, B and R) and in a surrounding uncontaminated territory (reference). Poisson models stratified/adjusted for gender, age and period were fitted to calculate rate ratios (RRs) and 95% CIs.ResultsIn zone A in males, we found elevated mortality from circulatory diseases in the first decade after the accident (17 deaths, RR 2.00, 95% CI 1.24 to 3.23). In females, mortality from diabetes mellitus was increased, with a positive trend across zones. Incidence of soft tissue sarcoma was increased in males in zone R in the first decade (6 cases, RR 2.62, 95% CI 1.01 to 6.83). In females in zone B, there was an excess of non-Hodgkin’s lymphoma after 30 years (6 cases, RR 2.87, 95% CI 1.14 to 7.23). Multiple myeloma was increased in the second decade in females in zone B (4 cases, RR 5.09, 95% CI 1.82 to 14.2) and in males in zone R (11 cases, RR 2.15, 95% CI 1.08 to 4.26). In males in zone R, there was a leukaemia excess after 30 years (23 cases, RR 2.02, 95% CI 1.04 to 3.93).ConclusionsAlthough with different patterns across gender, zone and time, we confirmed previous results of increased cardiovascular diseases, diabetes, soft tissue sarcoma, and lymphatic and haematopoietic cancers.