bluuebunny/crossref_metadata_2025 huggingface dataset:
Cost savings in male circumcision post-operative care using two-way text-based follow-up in rural and urban South Africa
Authors: Su Yanfang , Mukora Rachel , Ndebele Felex , Pienaar Jacqueline , Khumalo Calsile , Xu Xinpeng , Tweya Hannock , Sardini Maria , Day Sarah , Sherr Kenneth , Setswe Geoffrey , Feldacker Caryl
Published: February 2023

Introduction

Voluntary medical male circumcision (VMMC) clients are required to attend multiple post-operative follow-up visits in South Africa. However, with demonstrated VMMC safety, stretched clinic staff in SA may conduct more than 400,000 unnecessary reviews for males without complications, annually. Embedded into a randomized controlled trial (RCT) to test safety of two-way, text-based (2wT) follow-up as compared to routine in-person visits among adult clients, the objective of this study was to compare 2wT and routine post-VMMC care costs in rural and urban South African settings.

Methods

Activity-based costing (ABC) estimated the costs of post-VMMC care, including counselling, follow-ups, and tracing in $US dollars. Transportation for VMMC and follow-up was provided for rural clients in outreach settings but not for urban clients in static sites. Data were collected from National Department of Health VMMC forms, RCT databases, and time-and-motion surveys. Sensitivity analysis presents different follow-up scenarios. We hypothesized that 2wT would save per-client costs overall, with higher savings in rural settings.

Results

VMMC program costs were estimated from 1,084 RCT clients: 537 in routine care and 547 in 2wT. On average, 2wT saved $3.56 per client as compared to routine care. By location, 2wT saved $7.73 per rural client and increased urban costs by $0.59 per client. 2wT would save $2.16 and $7.02 in follow-up program costs if men attended one or two post-VMMC visits, respectively.

Conclusion

Quality 2wT follow-up care reduces overall post-VMMC care costs by supporting most men to heal at home while triaging clients with potential complications to timely, in-person care. 2wT saves more in rural areas where 2wT offsets transportation costs. Minimal additional 2wT costs in urban areas reflect high care quality and client engagement, a worthy investment for improved VMMC service delivery. 2wT scale-up in South Africa could significantly reduce overall VMMC costs while maintaining service quality.
Apelin improves angiogenesis and blood flow reperfusion following lower limb ischemia in diabetic mice
Authors: Robillard Stéphanie , Trân Kien , Brazeau Tristan , Boisvert Elizabeth , Lizotte Farah , Auger-Messier Mannix , Boudreault Pierre-Luc , Marsault Éric , Geraldes Pedro
Published: February 2023

BACKGROUND

Peripheral artery disease (PAD) is a major risk factor for lower-extremity amputation in diabetic patients caused by an insufficient angiogenic response. Unfortunately, therapeutic angiogenesis using growth factors, such as the vascular endothelial growth factor (VEGF), are ineffective in diabetic conditions due to diabetes-induced growth factor resistance. The apelinergic system (APJ receptor/apelin) is highly upregulated under hypoxic condition and acts as an activator of angiogenesis. Apelin treatment has been shown to improve revascularization in nondiabetic models of ischemia, however, its role on angiogenesis in diabetic conditions remains poorly investigated. Thus, this study explored the impact of Pyr-apelin-13 in endothelial cell function and diabetic mouse model of hindlimb ischemia.

METHODS

Nondiabetic and diabetic mice underwent femoral artery ligation to induce lower limb ischemia. A group of diabetic mice was implanted subcutaneously with osmotic pumps delivering Pyr-apelin-13 for 28 days. Blood flow reperfusion was measured for 4 weeks post-surgery and exercise willingness was assessed in individual cages with voluntary wheels.In vitro, BAECs were exposed to normal (NG) or high glucose (HG) levels and hypoxia. Cell migration, proliferation and tube formation assays were performed following either VEGF or Pyr-apelin-13 stimulation.

RESULTS

Following limb ischemia, blood flow reperfusion, functional recovery of the limb and vascular density were improved in diabetic mice receiving Pyr-apelin-13 compared to untreated diabetic mice. In cultured BAECs, exposure to HG concentrations and hypoxia reduced VEGF proangiogenic actions, whereas apelin proangiogenic effects remained unaltered. Pyr-apelin-13 induced its proangiogenic actions through Akt/AMPK/eNOS and RhoA/ROCK signaling pathways under both NG or HG concentrations and hypoxia exposure.

CONCLUSIONS

Pyr-apelin-13 promoted endothelial cell function and angiogenesis in the ischemic limb despite diabetes and HG level exposure. Therefore, our results identified the apelinergic system as a potential therapeutic target for angiogenic therapy in diabetic patients with PAD.

Highlights

Sustained delivery of Pyr-apelin-13 improves blood flow reperfusion, functional recovery of the hindlimb and capillary density in diabetic mice following ischemia.

Unlike VEGF, signaling pathways and proangiogenic actions induced by apelin/APJ stimulation are not impaired by high glucose exposure.

Despite the presence of tissue ischemia, diabetes reduces the expression of apelin and APJ in the ischemic adductor muscle, an effect overcome by apelin administration.
Female gene networks are expressed in myofibroblast-like smooth muscle cells in vulnerable atherosclerotic plaques
Authors: Benavente Ernest Diez , Karnewar Santosh , Buono Michele , Mili Eloi , Hartman Robin J. G. , Kapteijn Daniek , Slenders Lotte , Daniels Mark , Aherrahrou Redouane , Reinberger Tobias , Mol Barend M. , de Borst Gert J. , de Kleijn Dominique P. V. , Prange Koen H. M. , Depuydt Marie A. C. , de Winther Menno P. J. , Kuiper Johan , Björkegren Johan L. M. , Erdmann Jeanette , Civelek Mete , Mokry Michal , Owens Gary K , Pasterkamp Gerard , den Ruijter Hester M.
Published: February 2023

Women presenting with coronary artery disease (CAD) more often present with fibrous atherosclerotic plaques, which are currently understudied. Phenotypically modulated smooth muscle cells (SMCs) contribute to atherosclerosis in women. How these phenotypically modulated SMCs shape female versus male plaques is unknown. Here, we show sex-stratified gene regulatory networks (GRNs) from human carotid atherosclerotic tissue. Prioritization of these networks identified two main SMC GRNs in late-stage atherosclerosis. Single-cell RNA-sequencing mapped these GRNs to two SMC phenotypes: a phenotypically modulated myofibroblast-like SMC network and a contractile SMC network. The myofibroblast-like GRN was mostly expressed in plaques that were vulnerable in females. Finally, mice orthologs of the female myofibroblast-like genes showed retained expression in advanced plaques from female mice but were downregulated in male mice during atherosclerosis progression. Female atherosclerosis is driven by GRNs that promote a fibrous vulnerable plaque rich in myofibroblast-like SMCs.
Functional comparisons of the virus sensor RIG-I from humans, the microbatMyotis daubentonii, and the megabatRousettus aegyptiacus, and their response to SARS-CoV-2 infection
Authors: Schoen Andreas , Hölzer Martin , Müller Marcel A. , Drosten Christian , Marz Manja , Lamp Benjamin , Weber Friedemann
Published: February 2023

Bats (orderChiroptera) are a major reservoir for emerging and re-emerging zoonotic viruses. Their tolerance towards highly pathogenic human viruses led to the hypothesis that bats may possess an especially active antiviral interferon (IFN) system. Here, we cloned and functionally characterized the virus RNA sensor, Retinoic Acid-Inducible Gene-I (RIG-I), from the “microbat”Myotis daubentonii(suborderYangochiroptera) and the “megabat”Rousettus aegyptiacus(suborder Yinpterochiroptera), and compared them to the human ortholog. Our data show that the overall sequence and domain organization is highly conserved and that all three RIG-I orthologs can mediate a similar IFN induction in response to viral RNA at 37° and 39°C, but not at 30°C. Like human RIG-I, bat RIG-Is were optimally activated by double stranded RNA containing a 5’-triphosphate end and required Mitochondrial Antiviral-Signalling Protein (MAVS) for antiviral signalling. Moreover, the RIG-I orthologs of humans and ofR. aegyptiacus, but not ofM. daubentonii, enable innate immune sensing of SARS-CoV-2 infection. Our results thus show that microbats and megabats express a RIG-I that is not substantially different from the human counterpart with respect to function, temperature dependency, antiviral signaling, and RNA ligand properties, and that human and megabat RIG-I are able to sense SARS-CoV-2 infection.

IMPORTANCE

A common hypothesis holds that bats (orderChiroptera) are outstanding reservoirs for zoonotic viruses because of a special antiviral interferon (IFN) system. However, functional studies about key components of the bat IFN system are rare. RIG-I is a cellular sensor for viral RNA signatures that activates the antiviral signalling chain to induce IFN. We cloned and functionally characterized RIG-I genes from representatives of the subordersYangochiropteraandYinpterochiroptera. The bat RIG-Is were conserved in their sequence and domain organization, and similar to human RIG-I in (i) mediating virus- and IFN-activated gene expression, (ii) antiviral signalling, (iii) temperature dependence, and (iv) recognition of RNA ligands. Moreover, RIG-I ofRousettus aegyptiacus(suborderYinpterochiroptera) and of humans were found to recognize SARS-CoV-2 infection. Thus, members of both bat suborders encode RIG-Is that are comparable to their human counterpart. The ability of bats to harbour zoonotic viruses therefore seems due to other features.
Effects of supervised exercises on pain and disability in patients with hip or knee osteoarthritis: A systematic review and meta-analysis
Authors: Mapinduzi Jean , Ndacayisaba Gérard , Mitchaϊ Penielle Mahutchegnon , Bonnechère Bruno , Oyéné Kossi
Published: February 2023

Background

Hip and knee osteoarthritis are among the most prevalent and disabling conditions affecting mainly older adults, with a risk of undergoing a total hip or knee replacement for the end stage. Increasing recommendations of conservative treatments have been reported as the first-line strategy for the initial management of this condition.

Objective

This review sought to investigate the effects of supervised exercises versus non-pharmacological conservative therapies to reduce pain and disability levels on patients with hip or knee osteoarthritis.

Methods

Three databases (PubMed, Cochrane Library, and ScienceDirect) were systematically searched for randomized-controlled trials published between 01-01-2001 and 31-10-2022. PEDro scale was used to assess the methodological quality of the included studies. The PRISMA guidelines were applied for this review.

Results

Twelve randomized-controlled trials of moderate-to-high quality were included in this review. The studies involved 1,049 participants with a mean age (SD) of 64 (6) years old. The duration of the intervention and follow-up varied from 2 weeks to 16 months. Supervised exercises for hip or knee osteoarthritis were significantly less effective in terms of pain reduction (SMD=-0.40 [95%CI 0.16, 0.65], p=0.001) compared to home-based exercises (active musculoskeletal therapies), but not in terms of disability reduction (SMD=-0.04[95%CI −0.43, 0.36], p=0.86). There was a non-significant difference of supervised exercises compared to passive musculoskeletal therapies in terms of disability (SMD=0.21[95%CI −0.09, 0.50], p=0.17), or pain reduction (SMD=-0.19; [95%CI −0.57, 0.19], p=0.33).

Conclusion

Supervised exercises were found to be less effective in reducing pain, but not in disability reduction when compared to home-based exercises.

Systematic review registration

Prospero CRD42021271912
Caloric restriction prevents inflammation and insulin dysfunction in middle-aged ovariectomized mice
Authors: Sapatini Leticia Roberta Leme , Calsa Bruno , Marim Lais Jorge , Helaehil Júlia Venturini , Chiarotto Gabriela Bortolança , Corezola do Amaral Maria Esméria
Published: February 2023

Loss of ovarian function is associated with increased visceral fat. In this study, we aimed to study the effects of caloric restriction (CR) on metabolism in ovariectomized mice. Female, 8–12-month-old mice were divided into three groups: OVX (ovariectomized mice), OVXR (40% CR) and Sham. CR increased insulin sensitivity and glucose tolerance. AMPK phosphorylation was observed in the liver of OVXR mice. CR also increased hepatic cholesterol and triglyceride levels. The reductions in the level of TBARS in the serum and liver and of H2O2 in the liver of OVXR mice suggested alterations in the redox state of the liver. Although expression of catalase protein was reduced by CR, expression of superoxide dismutase was not altered by CR. Although interleukin IL-6 and IL-10 levels in OVXR mice were similar to those in Sham mice, macrophage infiltration was reduced in OVXR mice. OVXR mice had increased sirtuin1 levels and decreased sirtuin3 levels in the liver. In conclusion, CR improved the condition of ovariectomized mice by reducing adiposity and increasing insulin sensitivity and glucose tolerance through a mechanism that may involve AMPK.
Racial Differences in FMD
Authors: Martinez Andrea , Okoh Alexis , Ko Yi-An , Wells Bryan
Published: February 2023

Background

Fibromuscular dysplasia (FMD) is a non-atherosclerotic arteriopathy associated with stenosis, aneurysm, and dissection. We aimed to characterize racial differences in clinical presentation and diagnosis among patients with FMD at our institution.

Methods

We utilized an ambulatory FMD database to review demographics, clinical presentation, and diagnostic assessments of patients diagnosed with FMD within a university-affiliated healthcare system. Patients were classified as White or Non-White based on self-identified race. We evaluated race-specific differences in diagnosis and disease manifestations.

Results

A total of 208 patients (White: n=160 (77%); Non-White; n=48 (23%)) were included in the analysis. The time from initial FMD symptom to diagnosis was longer in Non-Whites than Whites (5.5 vs. 1.5 yrs; p<0.001), yet time from diagnosis to Emory specialist center visit was longer in Whites (3.2 vs. 1.2 yrs; p=0.035). Whites were more likely to undergo ≥ 5 multi-imaging diagnostic assessments than Non-Whites (89% vs. 73%; p=0.002). History of hypertension, stroke, & chronic kidney disease were more common in Non-Whites. FMD involvement of the internal carotid artery and upper extremity vessels were more common in Non-Whites, while Whites had more renal artery involvement.

Conclusion

We found racial differences in the diagnosis of FMD. The time from symptom onset to diagnosis was longer in Non-White than White FMD patients. Multimodality diagnostic imaging was more often utilized in Whites than Non-Whites. Research is needed to investigate these racial differences.
Major depression, suicidal behaviors and neuroticism are pro-atherogenic states driven by lowered reverse cholesterol transport
Authors: Jirakran Ketsupar , Vasupanrajit Asara , Tunvirachaisakul Chavit , Kubera Marta , Maes Michael
Published: February 2023

Background

There are strong associations between major depressive disorder (MDD), metabolic syndrome (MetS) and cardiovascular disorder, which may be explained by increased atherogenicity and the microimmuneoxysome (Maes et al., 1994; 2011). The present study was conducted to determine if MDD, the severity of depression, suicidal behaviors, and neuroticism are associated with increased pro-atherogenic versus anti-atherogenic indices (PRO/ANTI-AI) and a reverse cholesterol transport (RCT) index.

Methods

This study included 34 healthy controls, 33 participants with MetS, and MDD patients with (n=31) and without (n=35) MetS, and measured total (TC) and free (FC) cholesterol, high (HDLc) and low (LDLc) density lipoprotein cholesterol, triglycerides (TG), apolipoprotein (ApoA), ApoB, cholesterol esterification rate (CER) and a composite (based on HDLc, ApoA and CER), reflecting RCT.

Results

In the combined MDD + MetS study group, no associations between MDD and lipids were detected. After the exclusion of all MetS participants, MDD is strongly associated with (a) increased FC, TG, ApoB, Castelli risk index 1, ApoB/ApoA, and (b) decreased HDLc, ApoA and the RCT index. In participants without MetS, there are significant associations between severity of depression, suicidal behaviors, and neuroticism and ApoB/ApoA, Castelli risk, and RCT indices.

Conclusions

Studies linking lipids to depressive subtypes can only be interpreted after MetS patients are excluded. The depression phenome, suicidal behaviors, and neuroticism are associated with a lowered RCT and increased atherogenicity, which are likely involved in the microimmuneoxidative pathophysiology of MDD. The RCT is a new drug target to treat and prevent MDD, neuroticism, and suicidal behaviors.
Epistatic Features and Machine Learning Improve Alzheimer’s Risk Prediction Over Polygenic Risk Scores
Authors: Hermes Stephen , Cady Janet , Armentrout Steven , O’Connor James , Carlson Sarah , Cruchaga Carlos , Wingo Thomas , Greytak Ellen McRae ,   The Alzheimer’s Disease Neuroimaging Initiative
Published: February 2023

Background

Polygenic risk scores (PRS) are linear combinations of genetic markers weighted by effect size that are commonly used to predict disease risk. For complex heritable diseases such as late onset Alzheimer’s disease (LOAD), PRS models fail to capture much of the heritability. Additionally, PRS models are highly dependent on the population structure of data on which effect sizes are assessed, and have poor generalizability to new data.

Objective

The goal of this study is to construct a paragenic risk score that, in addition to single genetic marker data used in PRS, incorporates epistatic interaction features and machine learning methods to predict lifetime risk for LOAD.

Methods

We construct a new state-of-the-art genetic model for lifetime risk of Alzheimer’s disease. Our approach innovates over PRS models in two ways: First, by directly incorporating epistatic interactions between SNP loci using an evolutionary algorithm guided by shared pathway information; and second, by estimating risk via an ensemble of machine learning models (gradient boosting machines and deep learning) instead of simple logistic regression. We compare the paragenic model to a PRS model from the literature trained on the same dataset.

Results

The paragenic model is significantly more accurate than the PRS model under 10-fold cross-validation, obtaining an AUC of 83% and near-clinically significant matched sensitivity/specificity of 75%, and remains significantly more accurate when evaluated on an independent holdout dataset. Additionally, the paragenic model maintains accuracy within APOE genotypes.

Conclusion

Paragenic models show potential for improving lifetime disease risk prediction for complex heritable diseases such as LOAD over PRS models.
Recruitment of apolipoprotein E facilitates Herpes simplex virus 1 attachment, entry, and release
Authors: Liu Lifeng , Thorsteinsson Konrad , Bano Fouzia , Jayaweera Sanduni Wasana , Avinens Damien , Conca Dario , Pace Hudson , Lövheim Hugo , Olofsson Anders , Bally Marta
Published: February 2023

Over two decades, epidemiological studies have revealed that interactions between human polymorphic apolipoprotein 4 (ApoE, isoform 4) and herpes simplex virus type 1 (HSV1) associate with higher risk of Alzheimer’s disease, a serious and increasing issue among elder populations worldwide. Nevertheless, little is known about the mechanisms behind ApoE-HSV1 interactions at molecular levels. Here, we investigate the effects of ApoE on the HSV1 infectious life cycle inin vitrocell experiments. Analysis of HSV1 growth curves shows that HSV1 production is promoted in presence of any of the three ApoE isoforms, with ApoE 3 or 4 demonstrating more proviral effects than ApoE 2. Quantification by qPCR reveals that the presence of ApoE 2, 3, or 4 leads to an increase of HSV1 extracellular release but unchanged levels of viral genome copies within cells or on the cell surface, indicating that virus replication, assembly, or transport to cell membrane are not affected. Further test of virus release directly demonstrates that HSV1 detachment from the cell surface is promoted by ApoE. Subsequent results reveal that ApoE is both present in purified HSV1 particles produced in ApoE-expressing cells after ultra-centrifugation and able to incorporate into HSV1 particles after purification, suggesting that harbouring ApoE may play a key role in the pro-viral effect of ApoE. Along these lines, we tested the infectious behaviour of ApoE-coated viruses and observed faster attachment kinetics and higher entry efficiencies of ApoE decorated HSV1. Our hypothesis that the association with ApoE leads to modified interactions of the virus with the cell membrane during entry and egress, was further validated in biophysical experiments. In such experiments, HSV1-membrane interaction kinetics and apparent affinity between HSV1 and native supported lipid bilayers (a plasma membrane mimic) were quantified using total internal reflection microscopy. HSV1 particles decorated with ApoE demonstrate both higher association (kon) and dissociation rate constants (koff), as well as less irreversible binding to the membrane, which is in line with the biological experiments. Overall, our results provide new insights into the roles of ApoE during HSV1 infections, which is worth to be considered when studying their involvement during Alzheimer’s disease development.
Rhizosphere bacterial colonization of beet occurs in discrete phases regardless of bioinoculation with the wild sea beet root community
Authors: Gołębiewski Marcin , Sikora Marcin , Mazur Justyna , Szymańska Sonia , Tyburski Jarosław , Hrynkiewicz Katarzyna , Ulrich Werner
Published: February 2023

Bioinoculation can increase crop yields under environmental stress. Plant colonization by microbes is an example of succession, with its distinct phases differing in community structure and diversity. This process needs to be studied to determine the optimal timing for bioinoculation and its effects. Haere, we show that, regardless of bio-inoculation, soil type and plant genotype, bacteria colonize the rhizosphere of axenic beets and tissues in two phases, differing in bacterial load, nestedness, community structure, diversity and assembly mechanism, and associated with taproot development. Communities remained stable after five weeks of growth in soil. The alpha diversity was greater and the bacterial load was lower in the late samples than in the early ones. Time, soil type and genotype determined community structure but not alpha diversity, bacterial load, nestedness or assembly mechanisms both in the rhizosphere and in the endosphere. Inoculation changed the community structure and members of Pseudomonadota and Bacillota of low abundance in the inoculant were recruited by beets.

Axenic beet colonization occurs through phases similar to other instances of microbial succession, and bacteria are recruited mostly randomly. The transition from the early to late phase involves a decrease in the bacterial load in plant tissues, which may be linked to plant growth and the arrest of bacterial cell division. Therefore, early inoculation seems to be favourable. Five weeks of growth in soil enabled formation of stable bacterial communities in both the rhizosphere and the endosphere. The influence of inoculation seems to be indirect, probably due to microbe-microbe interactions.
Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells
Authors: Jain Naveen , Goyal Yogesh , Dunagin Margaret C. , Cote Christopher J. , Mellis Ian A. , Emert Benjamin , Jiang Connie L. , Dardani Ian P. , Reffsin Sam , Raj Arjun
Published: February 2023

Pluripotency can be induced in somatic cells by the expression of the four “Yamanaka” factors OCT4, KLF4, SOX2, and MYC. However, even in homogeneous conditions, usually only a rare subset of cells admit reprogramming, and the molecular characteristics of this subset remain unknown. Here, we apply retrospective clone tracing to identify and characterize the individual human fibroblast cells that are primed for reprogramming. These fibroblasts showed markers of increased cell cycle speed and decreased fibroblast activation. Knockdown of a fibroblast activation factor identified by our analysis led to increased reprogramming efficiency, identifying it as a barrier to reprogramming. Changing the frequency of reprogramming by inhibiting the activity of LSD1 led to an enlarging of the pool of cells that were primed for reprogramming. Our results show that even homogeneous cell populations can exhibit heritable molecular variability that can dictate whether individual rare cells will reprogram or not.
Proteomic analysis across patient iPSC-based models and human post-mortem hippocampal tissue reveals early cellular dysfunction, progression, and prion-like spread of Alzheimer’s disease pathogenesis
Authors: Pomeshchik Yuriy , Velasquez Erika , Gil Jeovanis , Klementieva Oxana , Gidlöf Ritha , Sydoff Marie , Bagnoli Silvia , Nacmias Benedetta , Sorbi Sandro , Westergren-Thorsson Gunilla , Gouras Gunnar K. , Rezeli Melinda , Roybon Laurent
Published: February 2023

The hippocampus is a primary region affected in Alzheimer’s disease (AD). Because AD postmortem brain tissue is not available prior to symptomatic stage, we lack understanding of early cellular pathogenic mechanisms. To address this issue, we examined the cellular origin and progression of AD pathogenesis in patient-based model systems including iPSC-derived brain cells transplanted into the mouse brain hippocampus. Notably, proteomic analysis of the graft enabled the identification of proteomic alterations in AD patient brain cells, associated with increased levels of β-sheet structures and Aβ42 peptides. Interestingly, the host cells surrounding the AD graft also presented alterations in cellular biological pathways. Furthermore, proteomic analysis across human iPSC-based models and human post-mortem hippocampal tissue projected coherent longitudinal cellular changes indicative of disease progression from early to end stage AD. Our data showcase patient-based models to study the cellular origin, progression, and prion-like spread of AD pathogenesis.

Highlights

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AD patient iPSC-derived brain cells survive in the hippocampus of immunodeficient mice 6 months post-transplantation.

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Proteomic analysis of the grafts reveals profound alterations in cellular biological pathways in iPSC-derived hippocampal cells despite absence of senile plaques.

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Proteomic alterations within transplanted AD iPSC-derived hippocampal cells are reminiscent of early/prodromal AD.

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AD-grafted cells induce proteomic changes in host mouse cells.
Surface Energy and Viscoelastic Characteristics ofStaphylococcus epidermidisandCutibacterium acnesBiofilm on Commercial Skin Constructs versus agar
Authors: Razgaleh S. A. , Wrench Andrew , Jones A-Andrew D.
Published: February 2023

Biofilms are recalcitrant to both study and infectious disease treatment as it requires not only the study or management of single organism behavior, but also many dynamical interactions including but not limited to bacteria-bacteria, bacteria-host, bacteria-nutrients, and bacteria-material across multiple time scales. This study performs comparative and quantitative research of two materials used in biofilm research, TSA agar and skin epidermal, to reveal how adhesion effects viscoelastic properties of biofilms at long time scales. We show that the host surface stressors, such as wettability and surface energy, impact the biofilm’s mechanical integrity and viscoelastic properties. While it is known that the bacteria-material interface influences initial biofilm formation and external stress influences mature biofilm function, this study examines the influence of the bacteria-material interface on mature biofilms. These mechanical viscoelastic properties have the potential to determine metabolite and pathogenesis pathways which means that the platform researchers use to study impacts the outcome.
Attachment Stimuli Trigger Widespread Synchrony across Multiple Brains
Authors: Shimon-Raz Ortal , Yeshurun Yaara , Ulmer-Yaniv Adi , Levinkron Ayelet , Salomon Roy , Feldman Ruth
Published: February 2023

Infant stimuli elicit widespread neural and behavioral response in human adults and such massive allocation of resources attests to the evolutionary significance of the primary attachment. Here, we examined whether attachment-related cues also trigger cross-brain concordance, generating greater neural uniformity among individuals. Post-partum mothers were imaged twice in oxytocin/placebo administration design and stimuli included four ecological videos; two of infant/mother alone (Alone) and two mother-infant dyadic contexts (Social). Theory-driven analysis measured cross-brain synchrony in preregistered nodes of the parental caregiving network (PCN), which integrates subcortical structures underpinning mammalian mothering with cortical areas implicated in simulation, mentalization, and emotion regulation, and data--driven analysis assessed brain-wide concordance using whole brain parcellation. Results demonstrated widespread cross-brain synchrony in both the PCN and across the neuroaxis, from primary sensory and somatosensory areas, through insular-cingulate regions, to temporal and prefrontal cortices. TheSocialcontext yielded significantly more cross-brain concordance, with PCN’s striatum, parahipporcampal gyrus, superior temporal sulcus, anterior cingulate cortex (ACC), and prefrontal cortex displaying cross-brain synchrony only to mother-infant social cues. Moment-by-moment fluctuations in mother-infant social synchrony, ranging from episodes of gaze aversion to rhythmically-coordinated positive bouts, were tracked online by cross-brain concordance in the pre-registered ACC. Findings indicate that social attachment stimuli, representing evolutionary-salient universal cues that require no verbal narrative for immediate comprehension, trigger substantial inter-brain concordance and suggest that the mother-infant bond, an icon standing at the heart of human civilization, may function to glue brains into a unified experience and bind humans into social groups.

Significance Statement

Infant stimuli elicit widespread neural response in human adults, attesting to their evolutionary significance, but do they also trigger cross-brain concordance and induce neural uniformity among perceivers? We measured cross-brain synchrony to ecological mother-infant videos. We employed theory-driven analysis, measuring cross-brain concordance in the parenting network, and data-driven analysis, assessing brain-wide concordance using whole-brain parcellation. Attachment cues triggered widespread cross-brain concordance in both the parenting network and across the neuroaxis. Moment-by-moment fluctuations in behavioral synchrony were tracked online by cross-brain variability in ACC. Attachment reminders bind humans’ brains into a unitary experience and stimuli characterized by social synchrony enhance neural similarity among participants, describing one mechanism by which attachment bonds provide the neural template for the consolidation of social groups.
Aberrant activation of Wnt/β-Catenin signaling pathway drives the expression of poor prognosis-associated microRNAs in adrenocortical cancer with a major impact on miR-139-5p and its host gene PDE2A
Authors: Cristante Justine , El Sayed Soha Reda , Denis Josiane , Ragazzon Bruno , Hantel Constanze , Chabre Olivier , Guyon Laurent , Cherradi Nadia
Published: February 2023

Adrenocortical carcinoma (ACC) is a rare malignancy with dismal prognosis. Deregulated microRNA (miRNA) expression has been implicated in ACC aggressiveness. Nevertheless, the mechanisms underlying such deregulations remain unknown. Aberrant Wnt/β-Catenin signaling has been reported in about 40% of ACC and is associated with poor outcome. Here, we investigated the link between constitutive activation of Wnt/β-Catenin pathway and miRNA expression alterations in ACC. Inducible shRNA-mediated gene silencing of β-Catenin (β-Cat) was performed in ACC cells expressing constitutively active β-Catenin. The miRnome of ACC cells was analyzed using RNA-Sequencing. Selected miRNAs and mRNAs were validated using quantitative PCR and functional experiments with an emphasis on miR-139-5p, its host gene phosphodiesterase 2A (PDE2A) and its target gene N-Myc Downstream-Regulated Gene 4 (NDRG4). Prognostic values of Wnt/β-Catenin pathway components or mutational status and their correlations with miRNA/mRNA expressions were determined in COMETE-ENSAT and TCGA cohorts. We carried out the first miRnome analysis in β-Catenin-deficient (β-Cat-) ACC cells. Twelve upregulated miRNAs and 42 downregulated miRNAs among which miR-139-5p and miRNAs of the 14q32 locus were identified in β-Cat-cells. Downregulation of selected poor prognosis-associated miRNAs was confirmed using RT-qPCR. Remarkably, the expression of the intronic miR-139-5p was decreased by 90% in β-Cat-cells with a concomitant repression of its host gene PDE2A and upregulation of its target gene NDRG4. In ACC patients, miR-139-5p levels were highly correlated with the levels of PDE2A and anti-correlated with those of NDRG4. MiR-139-5p and PDE2A expressions were higher in patients with mutations in components of Wnt/β-Catenin signaling pathway or high expression of LEF1, with LEF1 proving a better predictor of prognosis than Wnt/β-Catenin signaling pathway mutational status. Our findings indicate that in addition to inducing protein-coding genes in ACC, constitutively active Wnt/β-Catenin signaling upregulates the expression of a subset of miRNAs involved in tumour aggressiveness and poor clinical outcome.
Acute stress modulates social approach and social maintenance in adult zebrafish
Authors: Cook Alex , Beckmann Holger , Azap Rutkay , Ryu Soojin
Published: February 2023

Stress alters social functioning in a complex manner. An important variable determining the final effects of stress is stressor intensity. However, the precise relationship between stressor intensity and social behavior is not well understood. Here we investigate the effects of varying acute stressor intensity exposure on social behavior using adult zebrafish. We first establish a novel test using adult zebrafish that allows distinguishing fish’s drive to approach a social cue and its ability to engage and maintain social interaction within the same behavioral paradigm. Next, we combined this test with a new method to deliver an acute stress stimulus of varying intensities. Our results show that both social approach and social maintenance are reduced in adult zebrafish upon acute stress exposure in an intensity-dependent manner. Interestingly, lower stress intensity reduces social maintenance without affecting the social approach, while a higher stress level is required to alter social approach. These results provide evidence for a direct correlation between acute stressor intensity and social functioning and suggest that distinct steps in social behavior are modulated differentially by the acute stress level.

SIGNIFICANCE STATEMENT

Acute stress exposure has a potent effect on social behavior in many animals including humans. However, so far the effect of different stressor intensity on distinct steps of social behavior has not been directly tested. Here, using zebrafish, we develop a new social behavior paradigm and a new graded acute stressor delivery method in order to test the relationship between acute stressor intensity and social behavior. Our results show that acute stress modulates both social approach and social maintenance in an intensity-dependent manner but social maintenance is affected at lower stress intensity than social approach. Thus, this work reveals that distinct steps in social behavior are differentially modulated by the acute stress level.
SARS-COV-2 NSP5 Antagonizes MHC II Expresion by Subverting Histone Deacetylase 2
Authors: Taefehshokr Nima , Lac Alex , Vrieze Angela M , Dickson Brandon H , Guo Peter N , Jung Catherine , Blythe Eoin N , Fink Corby , Aktar Amena , Dikeakos Jimmy D , Dekaban Gregory A , Heit Bryan
Published: February 2023

SARS-CoV-2 interferes with antigen presentation by downregulating MHC II on antigen presenting cells, but the mechanism mediating this process is unelucidated. Herein, analysis of protein and gene expression in human antigen presenting cells reveals that MHC II is downregulated by the SARS-CoV-2 main protease, NSP5. This suppression of MHC II expression occurs via decreased expression of the MHC II regulatory protein CIITA. This downregulation of CIITA is independent of NSP5’s proteolytic activity, but rather, NSP5 delivers HDAC2 to IRF3 at an IRF binding site within the CIITA promoter. Here, HDAC2 deacetylates and inactivates the CIITA promoter. This loss of CIITA expression prevents further expression of MHC II, with this suppression alleviated by ectopic expression of CIITA or knockdown of HDAC2. These results identify a mechanism by which SARS-CoV-2 limits MHC II expression, thereby delaying or weakening the subsequent adaptive immune response.

Importance

SARS-CoV-2 alters the expression of many immunoregulatory proteins to limit and delay the host antiviral response, thereby producing a more severe and longer-lasting infection. Preventing and limiting the activation of helper T cells by reducing MHC II expression on antigen presenting cells is one of these strategies, but while this mechanism was identified early in the pandemic, the mechanism allowing SARS-CoV-2 to limit MHC II expression has remained unclear. Herein, we demonstrate that this occurs via a tripartite interaction between viral NSP5 and host HDAC2 and IRF3, where a complex of NSP5 and HDAC2 is recruited to IRF3 bound to the promoter of CIITA—the master regulator of MHC II expression—with the delivery of HDAC2 then mediating the deacetylation of the CIITA promoter and the suppression of MHC II expression.
Neonatal Subarachnoid Hemorrhage Disrupts Multiple Aspects of Cerebellar Development
Authors: Butler David F. , Skibo Jonathan , Traudt Christopher M. , Millen Kathleen J.
Published: February 2023

Over the past decade, survival rates for extremely low gestational age neonates (ELGANs; <28 weeks gestation) has markedly improved. Unfortunately, a significant proportion of ELGANs will suffer from neurodevelopmental dysfunction. Cerebellar hemorrhagic injury (CHI) has been increasingly recognized in the ELGANs population and may contribute to neurologic dysfunction; however, the underlying mechanisms are poorly understood. To address this gap in knowledge, we developed a novel model of early isolated posterior fossa subarachnoid hemorrhage (SAH) in neonatal mice and investigated both acute and long-term effects. Following SAH on postnatal day 6 (P6), we found significant decreased levels of proliferation with the external granular layer (EGL), thinning of the EGL, decreased Purkinje cell (PC) density, and increased Bergmann glial (BG) fiber crossings at P8. At P42, CHI resulted in decreased PC density, decreased molecular layer interneuron (MLI) density, and increased BG fiber crossings. Results from both Rotarod and inverted screen assays did not demonstrate significant effects on motor strength or learning at P35-38. Treatment with the anti-inflammatory drug Ketoprofen did not significantly alter our findings after CHI, suggesting that treatment of neuro-inflammation does not provide significant neuroprotection post CHI. Further studies are required to fully elucidate the mechanisms through which CHI disrupts cerebellar developmental programming in order to develop therapeutic strategies for neuroprotection in ELGANs.
Helminth infection impacts hematopoiesis
Authors: Wijshake Tobias , Wang Jipeng , Rose Joseph , Marlar-Pavey Madeleine , Collins James J. , Agathocleous Michalis
Published: February 2023

Helminth infections are common in animals. However, the impact of a helminth infection on the function of hematopoietic stem cells (HSCs) and other hematopoietic cells has not been comprehensively defined. Here we describe the hematopoietic response to infection of mice withSchistosoma mansoni,a parasitic flatworm which causes schistosomiasis. We analyzed the frequency or number of hematopoietic cell types in the bone marrow, spleen, liver, thymus, and blood, and observed multiple hematopoietic changes caused by infection. Schistosome infection impaired bone marrow HSC function after serial transplantation. Functional HSCs were present in the infected liver. Infection blocked bone marrow erythropoiesis and augmented spleen erythropoiesis, observations consistent with the anemia and splenomegaly prevalent in schistosomiasis patients. This work defines the hematopoietic response to schistosomiasis, a debilitating disease afflicting more than 200 million people, and identifies impairments in HSC function and erythropoiesis.
cGAS-activating lupus autoantibody for cancer immunotherapy
Authors: Chen Xiaoyong , Tang Xiangjun , Cuffari Benedette J. , Tang Caroline , Gao Xingchun , Noble Philip W. , Young Melissa R. , Turk Olivia M. , Shirali Anupama , Gera Joseph , Nishimura Robert N. , Zhou Jiangbing , Hansen James E.
Published: February 2023

Cytoplasmic DNA triggers a cGAS-mediated signaling cascade that promotes an innate immune response and is potentially actionable in cancer immunotherapy. Here we show that a cytoplasmic-localizing lupus anti-DNA autoantibody activates cGAS and facilitates an immune-mediated prolongation of survival in orthotopic models of glioblastoma (GBM). Mechanistically, cellular penetration and blood-brain barrier crossing by the anti-DNA autoantibody is linked to nucleoside transport. Pulldown, knockdown, signaling, and cytotoxicity assays demonstrate autoantibody association with and activation of cGAS. In orthotopic GBM models, the autoantibody localizes to brain tumor, increases tumor CD8+ T cell content, and prolongs survival in immunocompetent but not immunodeficient mice. This work introduces the new concept of a cGAS-activating anti-DNA autoantibody, which impacts theories on mechanisms of autoimmunity and has translational applications in cancer immunotherapy.
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale
Authors: Mendelevich Asia , Gupta Saumya , Pakharev Aleksei , Teodosiadis Athanasios , Mironov Andrey A. , Gimelbrant Alexander A.
Published: February 2023

Motivation

Analysis of allele-specific expression is strongly affected by the technical noise present in RNA-seq experiments. Previously, we showed that technical replicates can be used for precise estimates of this noise, and we provided a tool for correction of technical noise in allele-specific expression analysis. This approach is very accurate but costly due to the need for two or more replicates of each library. Here, we develop a spike-in approach that is highly accurate at only a small fraction of the cost.

Results

We show that a distinct RNA added as a spike-in before library preparation reflects technical noise of the whole library and can be used in large batches of samples. We experimentally demonstrate the effectiveness of this approach using combinations of RNA from species distinguishable by alignment, namely, mouse, human, andC.elegans. Our new approach,controlFreq, enables highly accurate and computationally efficient analysis of allele-specific expression in (and between) arbitrarily large studies at an overall cost increase of ~ 5%.

Availability

Analysis pipeline for this approach is available at GitHub asRpackagecontrolFreq(github.com/gimelbrantlab/controlFreq).

Contact

agimelbrant@altius.org
Drug repurposing for Leishmaniasis with Hyperbolic Graph Neural Networks
Authors: Lau Yenson , Gutierrez Jahir M. , Volkovs Maksims , Zuberi Saba
Published: February 2023

Leishmanisis, a neglected tropical disease caused by protozoan parasites of the genusLeishmania, affects millions of individuals living in poverty across the world and is second to malaria in parasitic causes of death. Although current drugs for treating leishmaniasis exist, these are either highly toxic, ineffective, or expensive. For this reason, there is an urgent need to identify affordable, safer, and more effective treatments. Drug repurposing is a promising method for identifying existing molecules with the potential to treat leishmaniasis. Here, we present a deep learning model for drug repurposing based on hyperbolic graph neural networks. We leverage experimentally validated protein-drug interactions and molecular descriptors across three different parasites to train and validate our model. The final network model shows significant gains over the best baseline model, with an 11.6% increase in precision of the top scoring 0.5% protein-drug pairs. Finally, our model identified two experimental drugs that could target threeL. majorproteins involved in drug resistance and cell cycle regulation, which play an essential role in ensuring the parasite’s survival inside the host.

Author summary

Leishmanisis is a deadly and neglected tropical disease. Current treatments are ineffective, highly toxic, and unaffordable for the majority of affected individuals who live in extreme poverty. To accelerate the discovery and development of novel treatments against this disease, we develop a model that proposes existing drugs with the potential to treat leishmaniasis. Our methodology is based on hyperbolic graph neural networks, a class of deep learning models that can incorporate protein-drug interaction information from similar but well-studied parasites, in addition to utilizing chemical and molecular features. Empirically, this additional information leads to improved predictions of drug interactions withL. majorproteins. Overall, the protein-drug pairs predicted by our model suggests two existing drugs that could target essential pathways for growth and survival ofLeishmaniaparasites, which could be exploited either as a booster to increase the therapeutic effect of an existing anti-leishmaniasis drug, or as a novel chemotherapeutic treatment against the disease.