bluuebunny/crossref_metadata_2025 huggingface dataset:
Pseudomonas aeruginosacontracts mucus to form biofilms in tissue-engineered human airways
Authors: Rossy Tamara , Distler Tania , Pezoldt Joern , Kim Jaemin , Talà Lorenzo , Bouklas Nikolaos , Deplancke Bart , Persat Alexandre
Published: May 2022

The opportunistic pathogenPseudomonas aeruginosacauses antibiotic-recalcitrant pneumonia by forming biofilms in the respiratory tract. Despite extensivein vitroexperimentation, howP. aeruginosaforms biofilms at the airway mucosa is unresolved. To investigate the process of biofilm formation in realistic conditions, we developed AirGels: 3D, optically-accessible tissue-engineered human lung models that emulate the airway mucosal environment. AirGels recapitulate important factors that mediate host-pathogen interactions including mucus secretion, flow and air-liquid interface, while accommodating high resolution live microscopy. With AirGels, we investigated the contributions of mucus toP. aeruginosabiofilm biogenesis inin vivo-like conditions. We found thatP. aeruginosaforms mucus-associated biofilms within hours by contracting luminal mucus early during colonization. Mucus contractions facilitates aggregation, thereby nucleating biofilms. We show thatP. aeruginosaactively contracts mucus using retractile filaments called type IV pili. Our results therefore suggest that, while protecting epithelia, mucus constitutes a breeding ground for biofilms.
Distinct cell states define the developmental trajectories of mucinous appendiceal neoplasms towards pseudomyxoma metastases
Authors: Ayala Carlos , Sathe Anuja , Bai Xiangqi , Grimes Susan M. , Shen Jeanne , Poultsides George A. , Lee Byrne , Ji Hanlee P.
Published: May 2022

Appendiceal mucinous neoplasms(AMN)are rare tumors of the gastrointestinal tract. They metastasize with widespread abdominal dissemination leading to pseudomyxoma peritonei(PMP), a disease with poor prognosis. The cellular features of origin, differentiation and progression in AMN and PMP remain largely unknown. We characterized the distinct cell states of AMN and PMP using single-cell RNA-sequencing in 31 samples including AMNs, PMP metastases and matched normal tissues. We identified previously undescribed cellular features and heterogeneity in AMN and PMP. We discovered developmental cell states in tumor epithelial cells that ranged from progenitor phase to goblet cell differentiation, which was accompanied by elevated mucin gene expression. Metastatic PMP cells had a distinct cell state with increased mTOR and RAS signaling pathways and a series of upregulated cancer genes. We observed heterogeneity in a single PMP tumor as well as PMP metastases from the same patient. We validated our findings with immunohistochemistry, mass spectrometry on malignant ascites from PMP patients and gene expression data from an independent set of 63 PMPs.
Substantial differences in soil viral community composition within and among four Northern California habitats
Authors: Durham Devyn M. , Sieradzki Ella T. , ter Horst Anneliek M. , Santos-Medellín Christian , Bess C. Winston A. , Geonczy Sara E. , Emerson Joanne B.
Published: May 2022

Viruses contribute to food web dynamics and nutrient cycles in diverse ecosystems, yet the biogeographical patterns that underlie these viral dynamics are poorly understood, particularly in soil. Here, we identified trends in soil viral community composition in relation to habitat, moisture content, and physical distance. We generated 30 soil viromes from four distinct habitats (wetlands, grasslands, woodlands, and chaparral) by selectively capturing virus-sized particles prior to DNA extraction, and we recovered 3,432 unique viral ‘species’ (vOTUs). Viral communities differed significantly by soil moisture content, with viral richness generally higher in wet compared to dry soil habitats. However, vOTUs were rarely shared between samples, including replicates <10 m apart, suggesting that soil viruses may not disperse well and that future soil viral community sampling strategies may need to account for extreme community differences over small spatial scales. Of the 19% of vOTUs detected in more than one sample, 93% were from the same habitat and site, suggesting greater viral community similarity in closer proximity and under similar environmental conditions. Within-habitat differences indicate that extensive sampling would be required for rigorous cross-habitat comparisons, and results belie emerging paradigms of higher viral activity in wet soils and soil viral community spatial heterogeneity.
Identification of a bile acid-binding transcription factor in Clostridioides difficile using chemical proteomics
Authors: Forster ER , Yang X , Hang HC , Shen A
Published: May 2022

Clostridioides difficile is a Gram-positive anaerobic bacterium that is the leading cause of hospital-acquired gastroenteritis in the US. In the gut milieu, C. difficile encounters microbiota-derived bile acids capable of inhibiting its growth, which are thought to be a mechanism of colonization resistance. While the levels of certain bile acids in the gut correlate with susceptibility to C. difficile infection, their molecular targets in C. difficile remain unknown. In this study, we sought to use chemical proteomics to identify bile acid-interacting proteins in C. difficile. Using photoaffinity bile acid probes and chemical proteomics, we identified a previously uncharacterized MerR family protein, CD3583 (now BapR), as a putative bile acid-sensing transcription regulator. Our data indicate that BapR binds and is stabilized by lithocholic acid (LCA) in C. difficile. Although loss of BapR did not affect C. difficile’s sensitivity to LCA, ΔbapR cells elongated more in the presence of LCA compared to wild-type cells. Transcriptomics revealed that BapR regulates the expression of the gene clusters mdeA-cd3573 and cd0618-cd0616, and cwpV, with the expression of the mdeA-cd3573 locus being specifically de-repressed in the presence of LCA in a BapR-dependent manner. Electrophoretic mobility shift assays revealed that BapR directly binds to the mdeA promoter region. Since mdeA is involved in amino acid-related sulfur metabolism and the mdeA-cd3573 locus encodes putative transporters, we propose that BapR senses a gastrointestinal tract-specific small molecule, LCA, as an environmental cue for metabolic adaptation.
Epidemiology and role of SARS-CoV-2 Linkage in Paediatric Inflammatory Multisystem Syndrome (PIMS): A Canadian Paediatric Surveillance Program National Prospective Study
Authors: Tal Tala El , Morin Marie-Paule , Morris Shaun K. , Farrar Daniel S. , Berard Roberta A , Kakkar Fatima , Hepburn Charlotte Moore , Baerg Krista , Beaufils Camille , Bennett Terri-Lyn , Benseler Susanne M , Beaudoin-Bussières Guillaume , Chan Kevin , Cyr Claude , Dahdah Nagib , Donner Elizabeth J. , Drouin Olivier , Edjoc Rojiemiahd , Eljaouhari Maryem , Embree Joanne E. , Farrell Catherine , Finzi Andrés , Forgie Sarah , Giroux Ryan , Kang Kristopher T. , King Melanie , Thibodeau Melanie Laffin , Lang Bianca , Laxer Ronald M. , Luu Thuy Mai , McCrindle Brian W. , Orkin Julia , Papenburg Jesse , Pound Catherine M. , Price Victoria E. , Proulx-Gauthier Jean-Philippe , Purewal Rupeena , Sadarangani Manish , Salvadori Marina l. , Thibeault Roseline , Top Karina A. , Viel-Thériault Isabelle , Haddad Elie , Scuccimarri Rosie , Yeung Rae S. M.
Published: May 2022

Background

Paediatric inflammatory multisystem syndrome (PIMS) is a rare but serious condition temporally associated with SARS-CoV-2 infection. Using the Canadian Paediatric Surveillance Program (CPSP), a national surveillance system, we aimed to 1) study the impact of SARS-CoV-2 linkage on clinical and laboratory characteristics, and outcomes in hospitalized children with PIMS across Canada 2) identify risk factors for ICU admission, and 3) establish the minimum national incidence of hospitalizations due to PIMS and compare it to acute COVID-19.

Methods

Weekly online case reporting was distributed to the CPSP network of more than 2800 pediatricians, from March 2020 to May 2021. Comparisons were made between cases with respect to SARS-CoV-2 linkage. Multivariable modified Poisson regression was used to identify risk factors for ICU admission and Minimum incidence proportions were calculated.

Findings

In total, 406 PIMS cases were analyzed, of whom 202 (49· 8%) had a positive SARS-CoV-2 linkage, 106 (26· 1%) had a negative linkage, and 98 (24· 1%) had an unknown linkage. The median age was 5· 4 years (IQR 2· 5–9· 8), 60% were male, and 83% had no identified comorbidities. Compared to cases with a negative SARS-CoV-2 linkage, children with a positive SARS-CoV-2 linkage were older (8· 1 years [IQR 4· 2–11· 9] vs. 4· 1 years [IQR 1· 7–7· 7]; p<0· 001), had more cardiac involvement (58· 8% vs. 37· 4%; p<0· 001), gastrointestinal symptoms (88· 6% vs. 63· 2%; p<0· 001), and shock (60· 9% vs. 16· 0%; p<0· 001). At–risk groups for ICU admission include children ≥ 6 years and those with a positive SARS-CoV-2 linkage. No deaths were reported. The minimum incidence of PIMS hospitalizations during the study period was 5· 6 hospitalizations per 100,000 population <18 years.

Interpretation

While PIMS is rare, almost 1 in 3 hospitalized children required ICU admission and respiratory/hemodynamic support, particularly those ≥ 6 years and with a positive SARS-CoV-2 linkage.

Funding

Financial support for the CPSP was received from the Public Health Agency of Canada.
Association between Self-reported Masking Behavior and SARS-CoV-2 Infection Wanes from Pre-Delta to Omicron-Predominant Periods — North Carolina COVID-19 Community Research Partnership
Authors: Tjaden Ashley H. , Gibbs Michael , Runyon Michael , Weintraub William S. , Taylor Yhenneko J. , Edelstein Sharon L. ,   the COVID-19 Community Research Partnership Study Group
Published: May 2022

We assessed the association between self-reported mask use during non-household interactions and COVID-19 infection during three pandemic periods. Odds of infection for those who did not always compared to those who always wore a mask was 66% higher during pre-Delta, 53% higher during Delta, declining to 16% higher during Omicron.
Predictive signs and symptoms of Bacterial Meningitis isolates in Northern Ghana
Authors: Weyori Enoch Weikem , Bernard Nkrumah , Abdul-Karim Abass , Eleeza John Bertson , Abubakari Braimah Baba , Kosi Abiwu Hilarius Asiwome , Eugene Kuugbee Dogkotenge , Yidaana Adadow , Ziblim Shamsu-Deen , Nuertey Benjamin , Weyori Benjamin Asubam , Yakubu Etowi Boye , Azure Stebleson , Abdul-Muizz Muktar , Cheba Valentine Koyiri , Kojo Adatsi Richard
Published: May 2022

Background

Cerebrospinal meningitis (CSM) is a public health burden in Ghana that causes up to 10% mortality of the disease annually. About 20% of those who survive cerebrospinal meningitis suffer permanent sequelae. The study sought to understand the predictive signs and symptoms of bacterial meningitis implicated in its outcomes.

Method

Retrospective data from the Public Health Division, Ghana Health Service on bacterial meningitis from 2015 to 2019 used for this study. A pre-tested data extraction form was used to collect patients’ information from case-based forms kept at the Disease Control Unit from 2015 to 2019. Data were transcribed from the case-based forms into a pre-designed Microsoft Excel template. The data was cleaned and imported into SPSS version 26 for analysis.

Results

Between 2015-2019, a total of 2,446 CSM cases were reported. Out of these, 842 were confirmed. Among the confirmed cases, males constituted 55.3%. Children below 14 years of age were most affected (51.4%). The pathogens commonly responsible for bacterial meningitis wereNeisseria meningitidisandStreptococcus pneumoniaewith their respective strains especiallyNm W135, Nm X, Spn St. 1, andSpn St. 12F/12A/12B/44/4being responsible for most of the confirmed cases. The most predictive sign and symptom for bacterial meningitis was fever (X2=5.738a;p <0.05; AOR=1.303). Identified signs that were associated but less likely to cause disease were abdominal pain (X2=12.038a;p <0.05; AOR=0.597), neck stiffness (X2=6.447a;p <0.05; AOR=0.788), altered consciousness (X2=15.438a;p <0.05; AOR=0.673), and convulsion (X2=15.084a;p <0.05; AOR=0.678).

Conclusion

The confirmed cases of bacterial meningitis from 2015 to 2019 had fever as the main predictive symptom. It is therefore noticed that abdominal pain, neck stiffness, altered consciousness and convulsion did not associate with CSM within the study period.
Demographic and professional risk factors of COVID-19 infections among physicians in low- and middle-income settings; findings from a representative survey in two Brazilian states
Authors: Russo Giuliano , Cassenote Alex , de Oliveira Bruno Luciano Carneiro Alves , Scheffer Mario
Published: May 2022

Abstract

Introduction

Health workers (HWs) are a key resource for health systems worldwide, and have been affected heavily by the COVID-19 pandemic. Evidence is consolidating on incidence and associated drivers of infections, predominantly in high-income settings. It is however still unclear what the risk factors may be for specific health professions, particularly in low- and middle-income countries (LMICs).

Methods

We conducted a cross-sectional survey in a representative sample of 1,183 medical doctors registered with Brazil’s Federal Council of Medicine in one developed (São Paulo) and one disadvantaged state (Maranhão). Between February-June 2021, we administered a telephone questionnaire to collect data on physicians’ demographics, deployment to services, vaccination status, and self-reported COVID-19 infections. We performed descriptive, univariate, and multilevel clustered analysis to explore the association between physicians’ infection rates, and their sociodemographic and employment characteristics. A generalized linear mixed model with a binomial distribution was used to estimate the adjusted odds ratio.

Results

We found that 35.8% of physicians in our sample were infected with COVID-19 in the first year of the pandemic. The infection rate in Maranhão (49.2%) [95% CI 45.0-53.4] was almost twice that in São Paulo (24.1%) [95% CI 20.8-27.5]. Being a physician in Maranhão [95% CI 2.08-3.57], younger than 50 years [95% CI 1.41-2.89], and having worked in a COVID-19 ward [95% CI 1.28-2.27], were positively associated with the probability of infections. Conversely, working with diagnostic services [95% CI 0.53-0.96], in administrative functions [95% CI 0.42-0.80], or in teaching and research [95% CI 0.48-0.91] was negatively associated.

Conclusions

Based on data from Brazil, COVID-19 infections in LMICs may be more likely in those health systems with lower physician-to-patient ratios, and younger doctors working in COVID-19 wards may be infected more frequently. Such findings may be used to identify policies to mitigate COVID-19 effects on HWs in LMICs.
The Role of Mitochondrial genome abundance in Alzheimer’s Disease
Authors: Harerimana Nadia V. , Paliwali Devashi , Romero-Molina Carmen , Bennett David A. , Pa Judy , Goate Alison , Swerdlow Russell H. , Andrews Shea J.
Published: May 2022

Mitochondrial dysfunction is an early and prominent feature of Alzheimer’s disease (AD), with impaired energy metabolism preceding the onset of clinical symptoms. Here we propose an update to the mitochondrial dysfunction hypothesis of AD based on recent results examining the role of mitochondrial genome abundance in AD. In a large post-mortem study, we show that lower brain mitochondrial genome abundance is associated with a greater odds of AD neuropathological change and worse cognitive performance. We hypothesize that lower mitochondrial genome abundance impairs mitochondrial function by reducing mitochondrial bioenergetics, thereby impacting neuronal and glial cell function. However, it remains to be determined if mitochondrial dysfunction causes, mediates, or is a by-product of AD pathogenesis. Additional support for this hypothesis will be generated by linking peripheral blood mitochondrial genome abundance to AD and establishing clinical trials of compounds that upregulate total mitochondrial genome abundance or boost mitochondrial mass.

RESEARCH IN CONTEXT

Systematic Review

The authors used PubMed to review the literature on mitochondrial genomics in Alzheimer’s disease (AD) using the following search term:mitochondria* AND (“copy number” OR heteroplasmy OR haplogroup*) AND“Alzheimer’s disease”. The accumulated evidence suggested that increased mitochondrial genome abundance is neuroprotective, but found conflicting evidence for the association of mitochondrial heteroplasmy or specific haplogroups with AD.

Interpretation

We found that higher mtDNA abundance was robustly associated with reduced AD neuropathology burden and higher neurocognitive performance. Given these findings, we propose an updated hypothesis for mitochondrial dysfunction in AD: that mitochondrial genome abundance is a relevant mechanism in AD pathogenesis. We postulate that baseline mtDNA abundance itself contributes to baseline mitochondrial function and lifetime risk, and that propensity and sensitivity to mtDNA depletion further modulate risk, histopathology, and clinical decline.

Future directions

Using statistical genetics approaches, examining the association of peripheral mtDNA abundance with AD, and upregulating mtDNA abundance, would further strengthen the evidence of a causal role for mtDNA abundance and mitochondrial dysfunction in AD pathogenesis
Bacterial contamination of Healthcare workers’ mobile phones in Africa: a systematic review and meta-analysis
Authors: Zenbaba Demisu , Sahiledengle Biniyam , Beressa Girma , Desta Fikreab , Teferu Zinash , Nugusu Fikadu , Atlaw Daniel , Shiferaw Zerihun , Mamo Ayele , Negash Wogane , Negash Getahun , Mama Mohammedaman , Nigussie Eshetu , Chattu Vijay Kumar
Published: May 2022

Background

Mobile phones are potential reservoirs for pathogens and sources of healthcare-associated illnesses. More microbes can be found on a mobile phone than on a man’s lavatory seat, the sole of a shoe, or a door handle. When examining patients, frequent handling of mobile phones can spread bacteria and provide a suitable breeding environment for numerous microorganisms. Nevertheless, evidence of bacterial contamination of mobile phones among healthcare workers in Africa was not conclusive. Thus, this meta-analysis and systematic review was conducted to estimate the pooled prevalence of bacterial contamination of mobile phones used by healthcare workers and the most frequent bacterial isolates in Africa.

Methods

We systematically retrieved relevant studies using PubMed/MEDLINE, Scopus, POPLINE, HINARI, Science Direct, Cochrane Library databases, and Google Scholar from 2009 to 2021 publication year. We included observational studies that reported the prevalence of bacterial contamination of mobile phones among healthcare workers. Two independent authors assessed the quality of the studies. The DerSimonian-random Laird’s effect model was used to calculate effect estimates for the pooled prevalence of bacterial contamination in mobile phones, as well as a 95% confidence interval (CI).

Results

Among 3882 retrieved studies, 23 eligible articles with a total sample size of 2,623 study participants were included in the meta-analysis. The pooled prevalence of mobile phones bacterial contamination among healthcare workers was 83.9% (95% CI: 80.6, 87.2%; I2= 98%, p-value < 0.001). The most dominant type of bacteria isolated in this review wascoagulase-negative staphylococci(CONS) which accounted for 44.5% of the pooled contamination rate of mobile phones used by healthcare workers, followed byStaphylococcus aureus(32.3%), andEscherichia coli(8.4%).

Conclusion

The review indicated that the contamination with a different bacterial isolate of mobile phones used by health care workers was high. The most dominant bacterial isolates wereCoagulase-negative staphylococci, Staphylococcus aureus, andEscherichia coli. Hence, these findings would have implications for policymakers and resource allocation for preventive measures initiatives.
Pilot study to evaluate hypercoagulation and inflammation using rotational thromboelastometry and calprotectin in COVID-19 patients
Authors: Stanford S.N. , Roy A. , Rea C. , Harris Ben , Ashton A. , Mangles S. , Everington T. , Taher R. , Burns D. , Arbuthnot E. , Cecil T.
Published: May 2022

Introduction

Abnormal coagulation and inflammation are hallmarks of SARs-COV-19. Stratifying affected patients on admission to hospital may help identify those who are risk of developing severe disease early on. ROTEM is a point of care test that can be used to measure abnormal coagulation and calprotectin is a measure of inflammation.

Aim

Assess if ROTEM can measure hypercoagulability on admission and identify those who will develop severe disease early on. Assess if calprotectin can measure inflammation and if there is a correlation with ROTEM and calprotectin.

Methods

COVID-19 patients were recruited on admission and ROTEM testing was undertaken daily for a period of 7 days. Additionally inflammatory marker calprotectin was also tested.

Results

33 patients were recruited to the study out of which 13 were admitted to ITU and 20 were treated on the ward. ROTEM detected a hypercoagulable state on admission but did not stratify between those admitted to a ward or escalated to ITU. Calprotectin levels were raised but there was no statistical difference (p=0.73) between groups. Significant correlations were observed between FIBA5 (p<0.00), FIBCFT (p<0.00), FIBMCF (p<0.00) and INMCF (p<0.00) and calprotectin.

Conclusion

COVID19 patients were hypercoagulable in admission. The correlations between ROTEM and calprotectin underline the interactions between inflammation and coagulation.
The cost-effectiveness of small-quantity lipid-based nutrient supplements for prevention of child death and malnutrition and promotion of healthy development: modeling results for Uganda
Authors: Adams Katherine P , Vosti Stephen A , Arnold Charles D , Engle-Stone Reina , Prado Elizabeth L , Stewart Christine P , Wessells K Ryan , Dewey Kathryn G
Published: May 2022

Objective

Recent meta-analyses demonstrate that small-quantity lipid-based nutrient supplements (SQ-LNS) for young children significantly reduce child mortality, stunting, wasting, anemia and adverse developmental outcomes. Cost considerations should inform policy decisions. We developed a modeling framework to estimate the cost and cost-effectiveness of SQ-LNS and apply the framework in the context of rural Uganda.

Design

We adapted costs from a costing study of micronutrient powder (MNP) in Uganda, and based effectiveness estimates on recent meta-analyses and Uganda-specific estimates of baseline mortality and the prevalence of stunting, wasting, anemia, and developmental disability.

Setting

Rural Uganda.

Participants

Not applicable.

Results

Providing SQ-LNS daily to all children in rural Uganda (>1 million) for 12 months (from 6-18 months of age) via the existing Village Health Team system would cost ∼$52 per child (2020 US dollars), or ∼$58.7 million annually. Annually, SQ-LNS could avert an average of >242,000 disability adjusted life years (DALYs) as a result of preventing 3,689 deaths, >160,000 cases of moderate or severe anemia, and ∼6,000 cases of developmental disability. The estimated cost per DALY averted is $242, which is considered “very cost effective” relative to the Uganda per capita GDP of $822.

Conclusions

In this context, SQ-LNS may be more cost-effective than other options such as MNP or the provision of complementary food, although the total cost for a program including all age-eligible children would be high. Strategies to reduce costs, such as targeting to the most vulnerable populations and the elimination of taxes on SQ-LNS, may enhance financial feasibility.
The Glycan-Specificity of the Pineapple Lectin AcmJRL and its Carbohydrate-Dependent Binding of the SARS-CoV-2 Spike Protein
Authors: Meiers Joscha , Dastbaz Jan , Adam Sebastian , Rasheed Sari , Kirsch Susanne H. , Meiser Peter , Gross Peter , Müller Rolf , Titz Alexander
Published: May 2022

The current SARS-CoV-2 pandemic has become one of the most challenging global health threats, with over 530 million reported infections by May 2022. In addition to vaccines, research and development have also been directed towards novel drugs. Since the highly glycosylated spike protein of SARS-CoV-2 is essential for infection, it constitutes a prime target for antiviral agents. The pineapple-derived jacalin-related lectin (AcmJRL) is present in the medication bromelain in significant quantities and has previously been described to bind mannosides. Here, we elucidated its ligand specificity by glycan array analysis, quantified the interaction with carbohydrates and validated high-mannose glycans as preferred ligands. Because the SARS-CoV-2 spike protein was previously reported to carry a high proportion of high-mannose N-glycans, we tested the binding of AcmJRL to recombinantly produced spike protein. We could demonstrate that AcmJRL binds the spike protein with a low micromolar KDin a carbohydrate-dependent fashion, suggesting its use as a potential SARS-CoV-2 neutralising agent.
Tumor-intrinsic PRC2 inactivation drives a context-dependent immune-desert tumor microenvironment and confers resistance to immunotherapy
Authors: Yan Juan , Chen Yuedan , Patel Amish J. , Warda Sarah , Nixon Briana G. , Wong Elissa W.P. , Miranda-Román Miguel A. , Lee Cindy J. , Yang Ning , Wang Yi , Sher Jessica , Giff Emily , Tang Fanying , Khurana Ekta , Singer Sam , Liu Yang , Galbo Phillip M. , Maag Jesper L. , Koche Richard P. , Zheng Deyou , Deng Liang , Antonescu Cristina R. , Li Ming , Chen Yu , Chi Ping
Published: May 2022

Immune checkpoint blockade (ICB) has demonstrated clinical success in “inflamed” tumors with significant T-cell infiltrates, but tumors with an immune-desert tumor microenvironment (TME) fail to benefit. The tumor cell-intrinsic molecular mechanisms of the immune-desert phenotype remain poorly understood. Here, we demonstrate that inactivation of the Polycomb-repressive complex 2 (PRC2) core components, EED or SUZ12, a prevalent genetic event in malignant peripheral nerve sheath tumor (MPNST) and sporadically in other cancer types, drives a context-dependent immune-desert TME. PRC2 inactivation reprograms the chromatin landscape that leads to a cell-autonomous shift from primed baseline signaling-dependent cellular responses (e.g., interferon γ) to PRC2-regulated development and cellular differentiation transcriptional programs. Further, PRC2 inactivation reprograms the TME, leads to diminished tumor immune infiltrates and immune evasion through reduced chemokine production and impaired antigen presentation and T-cell priming, and confers ICB primary resistance through blunted T-cell recruitment in vivo. We demonstrate that strategies that enhancing innate immunity via intratumoral delivery of inactivated modified vaccinia virus Ankara (MVA) leads to increased tumor immune infiltrates and sensitizes PRC2-loss tumors to ICB. Our results provide novel molecular mechanisms of context-dependent dysfunctional epigenetic reprogramming that underline the immune-desert phenotype in MPNST and other cancers with PRC2 inactivation. Importantly, our findings highlight genetic-inactivation of PRC2 as a novel context-dependent ICB therapeutic resistance biomarker in cancer, and caution that therapeutic strategies that non-selectively target PRC2 in the host may lead to undesirable context-dependent immune evasion and ICB resistance in tumors. Our studies also point to intratumoral delivery of immunogenic therapeutic viruses as an initial strategy to modulate the immune-desert TME and capitalize on the clinical benefit of ICB.
Exploring Xylem Anatomical Adaptations Associated with Crassulacean Acid Metabolism and Hydraulic Capacitance in Clusia Leaves: Lessons for CAM Bioengineering
Authors: Leverett Alistair , Ferguson Kate , Winter Klaus , Borland Anne M.
Published: May 2022

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Background and Aims

Many succulent species are characterised by the presence of crassulacean acid metabolism (CAM) and/or elevated bulk hydraulic capacitance (CFT). Both CAM and elevated CFT substantially reduce the rate at which water moves through transpiring leaves. However, little is known about how these physiological adaptations are coordinated with leaf vascular architecture and xylem anatomy.

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Methods

The genus Clusia contains species spanning the entire C3-CAM continuum, and also is known to have > 5-fold interspecific variation in CFT. We used this highly diverse genus to explore how interspecific variation in vein density and xylem vessel dimensions are coordinated with CAM and CFT.

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Key Results

We found that constitutive CAM phenotypes were associated with lower vein length per leaf area (VLA) and vein termini density (VTD), compared to C3 or facultative CAM species. However, when vein densities were standardised by leaf depth, this value was higher in CAM than C3 species, which is likely an adaptation to overcome apoplastic hydraulic resistance in deep chlorenchyma tissue. In contrast, CFT did not correlate with any xylem anatomical trait measured, suggesting CAM has a greater impact on leaf hydraulic physiology than CFT.

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Conclusions

Our findings strongly suggest that CAM photosynthesis is coordinated with leaf vein densities. The link between CAM and vascular anatomy will be important to consider when attempting to bioengineer CAM into C3 crops.
PAF1 and FACT cooperate with MLL-AF4 to drive enhancer activity in leukemia
Authors: Crump Nicholas T. , Smith Alastair , Godfrey Laura , Jackson Nicole , Rice Siobhan , Kim Jaehoon , Basrur Venkatesha , Fermin Damian , Elenitoba-Johnson Kojo , Roeder Robert G. , Allis C. David , Roberts Irene , Roy Anindita , Milne Thomas A.
Published: May 2022

Aberrant enhancer activation has been identified as a key mechanism driving oncogene expression in many cancers. Here we use TOPmentation (Transcription factor-OPtimized ChIPmentation) to probe enhancer usage in primary MLL-rearranged acute lymphoblastic leukemia. We find that MLL-AF4, commonly held to promote transcription by binding to gene promoters, is also present at many active enhancers, where it assembles a complex of transcriptional co-activators normally found in the gene body. This includes DOT1L, ENL, PAF1, and a newly identified interaction with the histone chaperone FACT. By chemical degradation, we demonstrate that PAF1 and FACT are required for enhancer activity, including maintaining histone H3K27 acetylation, enhancer RNA transcription and enhancer-promoter interactions. This work identifies novel roles for PAF1 and FACT in enhancer function, and reveals an enhancer-targeting mechanism by which MLL-AF4 upregulates transcription, recruiting transcription machinery through a network of multivalent interactions to control enhancer activity and gene expression in acute leukemias.
New Vista into Origins of Viruses from a Prototypic ssDNA Phage
Authors: Kejzar Nejc , Laanto Elina , Rissanen Ilona , Abrishami Vahid , Selvaraj Muniyandi , Moineau Sylvain , Ravantti Janne , Sundberg Lotta-Riina , Huiskonen Juha T.
Published: May 2022

Viruses play a central role in all ecological niches; the origin of viruses, however, remains an open question. While phylogenetic analysis of distantly related viruses is hampered by a lack of detectable sequence similarity, structural biology can reveal conserved capsid protein structures that facilitate the study of distant evolutionary relationships. Here, we characterize the lipid-containing ssDNA temperate bacteriophage ΦCjT23, which is infecting Flavobacterium sp. (Bacteroidetes). We further detected ΦCjT23-like sequences in the genome of strains belonging to several Flavobacterium species. The virion structure determined by cryogenic electron microscopy revealed similarities to members of the viral kingdom Bamfordvirae that currently consists solely of dsDNA viruses. Common to these viruses, infecting hosts from all domains of life, is a major capsid protein composed of two upright β-sandwiches. The minimalistic structure of ΦCjT23 suggests that this phage serves as a model for the last common ancestor between ssDNA and dsDNA viruses in the Bamfordvirae. Both ΦCjT23 and the related phage FLiP infect Flavobacterium species found in several environments, suggesting that these types of viruses have a global distribution and shared evolutionary origin. Detailed comparisons to related, more complex viruses not only expand our knowledge about this group of viruses but also provide a rare glimpse into early virus evolution.
Bacterial capsular polysaccharides with antibiofilm activity share common biophysical and electrokinetic properties
Authors: Bayard-Bernal Joaquín , Thiebaud Jérôme , Brossaud Marina , Beaussart Audrey , Caillet Celine , Waldvogel Yves , Travier Laetitia , Létoffé Sylvie , Fontaine Thierry , Rokbi Bachra , Talaga Philippe , Beloin Christophe , Mistretta Noelle , Duval Jérôme F.L. , Ghigo Jean-Marc
Published: May 2022

Bacterial biofilms are surface-attached communities that are difficult to eradicate due to a high tolerance to antimicrobial agents. The use of non-biocidal surface-active compounds to prevent the initial adhesion and aggregation of bacterial pathogens is a promising alternative to antibiotic treatments and several antibiofilm compounds have been identified, including some capsular polysaccharides released by various bacteria. However, the lack of chemical and mechanistic understanding of the activity of these high-molecular-weight polymers limits their use for control of biofilm formation. Here, we screened a collection of 32 purified capsular polysaccharides and identified seven new compounds with non-biocidal activity against biofilms formed by Escherichia coli and/or Staphylococcus aureus. We analyzed the polysaccharide mobility under applied electric field conditions and showed that active and inactive polysaccharide polymers display distinct electrokinetic properties and that all active macromolecules shared high intrinsic viscosity features. Based on these characteristics, we identified two additional antibiofilm capsular polysaccharides with high density of electrostatic charges and their permeability to fluid flow. Our study therefore provides insights into key biophysical properties discriminating active from inactive polysaccharides. This characterization of a specific electrokinetic signature for polysaccharides displaying antibiofilm activity opens new perspectives to identify or engineer non-biocidal surface-active macromolecules to control biofilm formation in medical and industrial settings.

Significance statement

Some bacteria produce non-biocidal capsular polysaccharides that reduce the adhesion of bacterial pathogens to surfaces. Due to a lack of molecular and structural definition, the basis of their antiadhesion activity is unknown, thus hindering their prophylactic use for biofilm control. Here, we identified nine new active compounds and compared their composition, structure and biophysical properties with other inactive capsular polysaccharides. Despite the absence of specific molecular motif, we demonstrate that all active polysaccharides share common electrokinetic properties that distinguish them from inactive polymers. This characterization of the biophysical properties of antibiofilm bacterial polysaccharide provides key insights to engineer non-biocidal and bio-inspired surface-active compounds to control bacterial adhesion in medical and industrial settings.
In vivo reprogramming leads to premature death due to hepatic and intestinal failure
Authors: Parras Alberto , Vílchez-Acosta Alba , Desdín-Micó Gabriela , Mrabti Calida , Rechsteiner Cheyenne , Battiston Fabrice , Branchina Clémence , Pérez Kevin , Sempoux Christine , Ocampo Alejandro
Published: May 2022

The induction of cellular reprogramming by forced expression of the transcription factors OCT4, SOX2, KLF4, and C-MYC (OSKM) has been shown to allow the dedifferentiation of somatic cells and ameliorate age-associated phenotypes in multiple tissues and organs. Yet to date, the benefits of in vivo reprogramming are limited by the occurrence of detrimental side-effects. Here, using complementary genetic approaches, we demonstrated that continuous in vivo induction of the reprogramming factors leads to hepatic and intestinal dysfunction resulting in decreased body weight and premature death. By generating a novel transgenic reprogrammable mouse strain, which avoids OSKM expression in both liver and intestine, we drastically reduced the early lethality and adverse effects associated with in vivo reprogramming. This new reprogramming mouse allows safe and long-term continuous induction of OSKM and might enable a better understanding of in vivo reprogramming as well as maximize its potential effects on rejuvenation and regeneration.
Smartphone-Operated Affordable PCR Thermal Cycler for the Detection of Antimicrobial Resistant Bacterial Genes
Authors: Pudasaini Sanam , Thapa Garima , Marasini Bishnu P. , Giri Basant
Published: May 2022

Objectives

Antimicrobial resistance (AMR) is a global public health threat. Surveillance of AMR requires affordable, rapid, and user-friendly diagnostic method. Our aim was to develop a low-cost thermocycler to perform polymerase chain reaction (PCR).

Methods

We developed a smartphone-operated PCR thermal cycler using locally available recycled materials. The thermal cycler was used for the amplification for three bacterial genes - bla-TEM and bla-CTXM and 16s rRNA in human urine samples. The performance of custom-built thermal cycler was compared with the commercial one.

Results

The thermal cycler was portable (<1kg weight), required 12 V power supply, 25 µL of solution, and cost only USD50.0. Temperature and time conditions were instructed using a custom-built smartphone application. The ramping rate of was 0.23°C for heating and 0.43°C for cooling, set temperatures were within ± 0.5 °C of target showing a good thermal stability. The antibiotic sensitivity test of human urine samples showed they were highly resistance and multi-resistant. Nearly 46 % (n=54) E. coli isolates were positive in ESBL screening test. The custom-built thermocycler was able to accurately predict the presence of bla-TEM and bla-CTXM genes (n=6).

Conclusions

We developed and demonstrated a portable, low-cost, easy-to-use, and smartphone-operated PCR thermal cycler. Since it is portable, it can be used in remote location and field settings, including places without stable power supply. The use of the thermal cycler system can be extended, beyond the detection of AMR genes, e.g., in clinical diagnosis, genetics, forensic analysis, and environmental protection.
Zur and Zinc Increase Expression ofE. coliRibosomal Protein L31 Through RNA-Mediated Repression of the Repressor L31p
Authors: Rasmussen Rebecca A. , Camarillo Jeannie M. , Sosnowski Victoria , Cho Byoung-Kyu , Goo Young Ah , Lucks Julius B. , O’Halloran Thomas V.
Published: May 2022

Bacteria can adapt in response to numerous stress conditions. One such stress condition is zinc depletion. The zinc-sensing transcription factor Zur regulates the way enteric bacteria respond to severe changes in zinc availability. Under zinc sufficient conditions, Zn-loaded Zur (Zn2-Zur) is well-known to repress transcription of genes encoding zinc uptake transporters and paralogues of a few ribosomal subunits. Here, we report the discovery and mechanistic basis for the ability of Zur to up-regulate expression of the ribosomal protein L31 in response to zinc inE. coli. Through genetic mutations and reporter gene assays, we find that Zur achieves the up-regulation of L31 through a double repression cascade by which Zur first represses the transcription of L31p, a zinc-lacking paralogue of L31, which in turn represses the translation of L31. Mutational analyses show that translational repression by L31p requires an RNA hairpin structure within thel31mRNA and involves the N-terminus of the L31p protein. This work uncovers a new genetic network that allows bacteria to respond to host-induced nutrient limiting conditions through a sophisticated ribosomal protein switching mechanism.

Graphical Abstract
Polyamines shift expression of macrophage L-arginine metabolism related-genes during Leishmania amazonensis infection
Authors: Zanatta Jonathan Miguel , Acuña Stephanie Maia , Bento Camilla de Almeida , Stolf Beatriz Simonsen , Muxel Sandra Marcia
Published: May 2022

Polyamines are molecules involved in macrophage activation and polarization in response to pathogens. The interaction with Leishmania promotes modulation of macrophage immune response to favor arginine deviation to polyamines production, leading to parasite survival. Polyamine levels are a potential modulator of growth factors, driving cells to proliferation, wound healing, oxidative stress, or regulating translation. Here, we investigate the impact of L-arginine and polyamines in the transcriptional regulation of genes involved in arginine metabolization and pro-inflammatory response to L. amazonensis in murine BALB/c macrophages. We found that supplementation with L-arginine is insufficient to modulate macrophage gene expression and infection. Polyamine supplementation altered nitric oxide synthase (Nos2) and nitric oxide (NO) production, as well as other macrophage enzymes. Putrescine supplementation increased transcript levels of polyamine metabolism-related genes Arginase 2 (Arg2), Spermidine synthase (SpdS), and Spermine synthase (SpmS) in both uninfected and L. amazonensis infected macrophages. Putrescine increased Nos2 expression without leading to NO production, while L-arginine plus spermine led to production of NO in uninfected macrophages. Besides, L-arginine supplementation reduced the levels of Il-1b during infection, and L-arginine or L-arginine plus putrescine increased Mcp1 at 24h of infection. The percentage of infected macrophages was lower after putrescine, spermidine, and spermine supplementation than L-arginine supplementation. Our data showed that the polyamines shift L-arginine-metabolism related-genes on BALB/c macrophages and affect infection by L. amazonensis.
A small DNA virus initiates replication with no more than three genome copies per cell
Authors: Ren Ruifan , Zheng Limin , Han Junping , Carvalho Camila Perdoncini , Miyashita Shuhei , Zhang Deyong , Qu Feng
Published: May 2022

Cellular organisms purge lethal mutations as they occur (in haploids), or as soon as they become homozygous (in sexually reproducing diploids), thus making the mutation-carrying genomes the sole victims of lethality. How lethal mutations in viruses are purged remains an unresolved question because numerous viral genomes could potentially replicate in the same cell, sharing their encoded proteins, hence shielding lethal mutations from selection. Previous investigations by us and others suggest that viruses with plus strand (+) RNA genomes may compel such selection by bottlenecking the replicating genome copies in each cell to low single digits. However, it is unclear if similar bottlenecks also occur in cells invaded by DNA viruses. Here we investigated whether tomato yellow leaf curl virus (TYLCV), a small virus with a single-stranded DNA genome, underwent population bottlenecking in cells of its host plants. We engineered the TYLCV genome to produce two replicons that express green fluorescent protein and mCherry, respectively, in a replication-dependent manner. We found that less than 65% of cells penetrated by both replicons replicated both, whereas at least 35% of cells replicated either of them alone, illustrating an intracellular population bottleneck size of no more than three. Furthermore, sequential inoculations unveiled strong mutual exclusions of these two replicons in most cells. Collectively our data demonstrated for the first time that DNA viruses like TYLCV are subject to stringent intracellular population bottlenecks, suggesting that such population bottlenecks may be a virus-encoded, evolutionarily conserved trait that assures timely elimination of lethal mutations.

Significance statement

An important unresolved issue in virus life cycles is how natural selection acts on individual virus copies in the same cells. Unlike cellular organisms in which genome copies with lethal or advantageous mutations usually share their hosts with no more than one homologous genome copy, viruses could potentially reproduce with numerous sister genomes per cell, permitting sharing of protein products, thereby greatly diminishing phenotypic impacts of otherwise eventful mutations. Previous investigations suggest that (+) RNA viruses solve this problem by bottlenecking the number of replicating genome copies to low single digits. The current study reveals strikingly similar intracellular population bottlenecks for a DNA virus. Further mechanistic interrogations could avail the virus-encoded bottleneck-enforcing apparatus as targets for antiviral therapy and prevention.
SAXSDOG: open software for real-time azimuthal integration of 2D scattering images
Authors: Burian Max , Meisenbichler Christian , Naumenko Denys , Amenitsch Heinz
Published: May 2022

In situ small- and wide-angle scattering experiments at synchrotrons often result in massive quantities of data within just seconds. Especially during such beamtimes, processing of the acquired data online, without appreciable delay, is key to obtaining feedback on the failure or success of the experiment. This had led to the development of SAXSDOG, a Python-based environment for real-time azimuthal integration of large-area scattering images. The software is primarily designed for dedicated data pipelines: once a scattering image is transferred from the detector onto the storage unit, it is automatically integrated and pre-evaluated using integral parameters within milliseconds. The control and configuration of the underlying server-based processes is achieved via a graphical user interface, SAXSLEASH, which visualizes the resulting 1D data together with integral classifiers in real time. SAXSDOG further includes a portable `take-home' version for users that runs on standalone computers, enabling its use in laboratories or at the preferred workspace.
Robust approaches for model-free small-angle scattering data analysis
Authors: Bender Philipp , Honecker Dirk , Bersweiler Mathias , Costo Rocio , Kahmann Tamara , Ludwig Frank , Leiner Jon , Jochum Johanna K.
Published: May 2022

The small-angle neutron scattering data of nanostructured magnetic samples contain information regarding their chemical and magnetic properties. Often, the first step to access characteristic magnetic and structural length scales is a model-free investigation. However, due to measurement uncertainties and a restricted q range, a direct Fourier transform usually fails and results in ambiguous distributions. To circumvent these problems, different methods have been introduced to derive regularized, more stable correlation functions, with the indirect Fourier transform being the most prominent approach. Here, the indirect Fourier transform is compared with the singular value decomposition and an iterative algorithm. These approaches are used to determine the correlation function from magnetic small-angle neutron scattering data of a powder sample of iron oxide nanoparticles; it is shown that with all three methods, in principle, the same correlation function can be derived. Each method has certain advantages and disadvantages, and thus the recommendation is to combine these three approaches to obtain robust results.