bluuebunny/crossref_metadata_2025 huggingface dataset:
Xanthan- and Rice Cereal-Based Thickeners in Infants: A Multidisciplinary Single-Center Experience
Authors: Abdulezer Andrea , Mooney Patrick , Besner Marie-Eve , Laniel Sophie , Milton Sarah , Labelle Christine , Sant’Anna Guilherme M. , Sant’Anna Ana
Published: April 2022

Background:

Some infants aspirate thin liquids and must be fed thickened liquids in order to protect the lungs. However, thickeners have not been fully studied for safety. Xanthan-based thickeners have been implicated in the development of necrotizing enterocolitis and rice cereal-based thickeners have been associated with constipation and excessive weight gain. The aim of this study was to compare rates of adverse events between both thickeners.

Methods:

Single-center retrospective chart review conducted at a tertiary pediatric care center between January 2013 and July 2017. All infants deemed unsafe for oral feeding and treated with xanthan- or rice cereal-based milk thickeners were included. Data were extracted from the medical records and patients categorized according to the type of thickener. Primary outcome was the occurrence of diarrhea, constipation, overweight, and obesity at 3–6 and 6–12 months after thickener initiation. Appropriate statistical tests were used. In addition, an e-mail was sent to 14 level III Canadian Pediatric hospitals inquiring about their practice.

Results:

We identified 53 patients to be included in the study; 20 used xanthan-based- and 33 used rice cereal-based milk thickeners. Rates of diarrhea, constipation, overweight, and obesity at 3–6 and 6–12 months after initiation were not different between thickeners. Important variability concerning thickening practices was reported by the 8 centers that responded.

Conclusions:

In infants treated with milk thickeners, xanthan-based or rice cereal-based thickeners may have similar safety profiles that require further investigation including a larger number of patients.
Sarcopenia and Fat Mass in Children With Chronic Liver Disease and Its Impact on Liver Transplantation
Authors: Kyrana Eirini , Williams Jane E. , Wells Jonathan C. , Dhawan Anil
Published: April 2022

Background:

In adults, weight loss and sarcopenia are prognostic indicators of poor outcomes for patients awaiting liver transplant (LT). We tested the hypothesis that sarcopenia in children awaiting LT was related to poor outcomes.

Methods:

Children with end-stage chronic liver disease undergoing assessment for LT were recruited into an observational longitudinal study. Anthropometry and body composition (BC; whole-body dual-energy x-ray absorptiometry scan) were assessed before and, on average, 1 year after LT.

Results:

Eleven children (6 females:5 males) were assessed (4.7 to 17.2 years; median, 9.9) at baseline. Nine children went on to have an LT. The aspartate aminotransferase-to-platelet ratio index had a significant positive correlation with trunk lean mass and trunk lean mass index (LMI) SD score (SDS). At baseline, 4 patients were sarcopenic with appendicular LMI SDS less than −1.96. All fat mass and fat mass index (FMI) SDSs were within the normal range (above −1.96). There was a strong negative correlation between FMI SDS and height SDS. After transplant, there was a significant reduction in trunk LMI from 1.20 to −0.51 (95% CI, 1.03-2.4; P < 0.01). Body mass index SDS had a negative correlation with days to discharge after transplant. The majority of patients discharged after 16 days were sarcopenic. One year after transplantation, all patients were alive with normal graft function regardless of BC before LT.

Conclusion:

FMIs were normal regardless of LMIs and correlated negatively with height. BC was related to days to discharge after LT but not to outcomes a year after LT.
Trajectories of Depression Symptoms From Pregnancy Through 24 months Postpartum Among Kenyan Women Living With HIV
Authors: Larsen Anna M. , Osborn Lusi , Ronen Keshet , Richardson Barbra A. , Jiang Wenwen , Chohan Bhavna , Matemo Daniel , Unger Jennifer A. , Drake Alison L. , Kinuthia John , John-Stewart Grace
Published: April 2022

Background:

We examined longitudinal patterns and cofactors of depressive symptoms among pregnant and postpartum women living with HIV (WLWH).

Methods:

This study used data from a randomized trial of a text messaging intervention. WLWH were serially assessed for depressive symptoms from pregnancy through 24 months postpartum at 6 time points (pregnancy, 6 weeks, and 6, 12, 18, and 24 months postpartum). Depressive symptoms were assessed using Patient Health Questionnaire-9 and longitudinal patterns using group-based trajectory modeling. Moderate-to-severe depressive symptoms (MSD) correlates were assessed using generalized estimating equations.

Results:

Among 824 enrolled women, 14.6% ever had MSD during pregnancy or postpartum; 8.6% of WLWH had MSD in pregnancy and 9.0% any postpartum MSD. MSD was associated with abuse [RR: 3.8, 95% confidence interval (CI): 2.6 to 5.4], stigma (RR: 4.4, 95% CI: 3.1 to 6.3), and food insecurity (RR: 2.7, 95% CI: 1.9 to 3.8). Unintended pregnancy (RR: 1.6, 95% CI: 1.1 to 2.3) and recent HIV diagnosis (RR: 1.8, 95% CI: 1.2 to 2.6) were associated with higher MSD risk, whereas HIV status disclosure to partner (RR: 0.3, 95% CI: 0.2 to 0.6) and social support (RR: 0.97, 95% CI: 0.96 to 0.98) were associated with lower risk. Trajectory modeling identified 4 phenotypes of peripartum depressive symptoms: persistent no/low symptoms (38.5%), mild symptoms resolving postpartum (12.6%), low symptoms increasing slightly in postpartum (47.9%), and persistent moderate–severe symptoms throughout (1.1%).

Conclusions:

WLWH attending PMTCT services had varied patterns of depressive symptoms, which were associated with stressors (recent diagnosis and food insecurity) and factors reflecting low social power (abuse, stigma, and unintended pregnancy). Women experiencing concurrent abuse, stigma, and food insecurity should be prioritized for interventions to prevent persistent depression.
Effectiveness of Intraoperative Versus Dedicated Islet Cell Laboratory Isolation for Total Pancreatectomy With Islet Autotransplant
Authors: Navas Christopher M. , Smith Kerrington D. , Chaidarun Sushela S. , Fischer Dawn A. , Gardner Timothy B.
Published: April 2022

Background.

Total pancreatectomy with islet autotransplantation (TPIAT) requires a complex islet isolation process of the explanted pancreas. Islet isolation has historically required a specialized laboratory to perform islet isolation. We report our experience with a novel technique of intraoperative islet isolation that does not require a specialized islet laboratory, thereby making the isolation process simpler, more accessible, and less costly.

Methods.

We performed a retrospective, comparative effectiveness analysis of 50 adult patients who underwent TPIAT from 2012 to 2020 (TPIAT with remote isolation [n = 20] versus intraoperative isolation of islet cells [n = 30]). The primary outcome was islet equivalents per body weight (IEQ/kg) for patients in each group.

Results.

Mean IEQ/kg‘s (4294 remote group versus 3015 intraoperative group, P = 0.06) and 1-y postoperative C-peptide levels (1.51 ng/mL remote group versus 0.91 ng/mL intraoperative group, P = 0.10) were not different between groups. Mean 1-y HbA1c levels (7.7% in the remote group versus 7.1% intraoperative group, P = 0.67) and 1-y insulin requirements (P = 0.31) were not statistically different. Lower average cost of hospitalization was seen in the intraoperative group, although this was not statistically significant ($104 398 remote versus $78 986 intraoperative, P = 0.81).

Conclusions.

Intraoperative islet isolation has similar effectiveness in regard to glycemic outcomes compared with the use of a dedicated islet cell isolation laboratory at a lower cost.
Outcomes in Adult Liver Transplant Recipients Using Pediatric Deceased Donor Liver Grafts
Authors: Vargas Paola A. , Wang Haowei , Dalzell Christina , Argo Curtis , Henry Zachary , Su Feng , Stotts Matthew J. , Northup Patrick , Oberholzer Jose , Pelletier Shawn , Goldaracena Nicolas
Published: April 2022

Background.

The use of pediatric grafts for liver transplantation (LT) into adult recipients is rare, and reported outcomes are conflicting. The aim of this study is to evaluate the outcomes in adult recipients following LT with grafts from deceased pediatric donors.

Methods.

A retrospective study identifying adult LT between 2010 and 2020 using pediatric deceased donor liver grafts was conducted. Adults undergoing LT with deceased donor pediatric grafts (age ≤ 12) were identified and matched 1:2 with adults receiving adult grafts (age ≥ 18) based on recipient age (±10 y), model for end-stage liver disease (MELD) score at transplant (±5 points) and etiology of liver disease. To assess real liver size differences between the pediatric-donor and adult-donor groups, patients receiving a graft from a donor between 13 and 17 y were excluded from the main analysis and studied independently. Outcomes between the groups were compared. Complication rates were identified and graded using Clavien–Dindo classification. Graft and patient survival were assessed by Kaplan–Meier curves.

Results.

Twelve adult LT recipients with whole liver grafts from deceased pediatric donors were matched with 24 adult recipients of adult donors. Recipient age and MELD score were similar between groups. Recipients of pediatric grafts were more likely to be female (66.7% versus 16.7%, P = 0.007) and leaner (body mass index = 24.4 versus 29.9, P = 0.013). Alcohol-related cirrhosis was the most prevalent liver disease etiology in both groups (P = 0.96). There was no significant difference in length of stay, readmissions, early complications, or major complications between groups. Vascular and biliary complication rates were similar. Actuarial graft and patient survival at 1, 3, and 5 y were 100/100/100 versus 96/96/96 (P = 0.48).

Conclusions.

Excellent patient and graft survival is achievable with LT using young pediatric deceased donor grafts in smaller adult recipients. Outcomes are comparable with recipients of age and MELD-matched adult donors. Careful donor MELD-score recipient matching and close monitoring for potential biliary and vascular complications are crucial to achieve acceptable outcomes.
Early Experience Using Donor-derived Cell-free DNA for Surveillance of Rejection Following Simultaneous Pancreas and Kidney Transplantation
Authors: Williams Michael D. , Fei Mingwei , Schadde Erik , Hollinger Edward F. , Chan Edie Y. , Olaitan Oyedolamu
Published: April 2022

Background.

Allograft biopsy is the gold standard for diagnosing graft rejection following simultaneous pancreas and kidney (SPK) transplant. Intraperitoneal biopsies are technically challenging and can be burdensome to patients and the healthcare system. Donor-derived cell-free DNA (dd-cfDNA) is well-studied in kidney transplant recipients; however, it has not yet been studied in the SPK population.

Methods.

We hypothesized that dd-cfDNA could be utilized for rejection surveillance following SPK transplant. We prospectively collected dd-cfDNA in 46 SPK patients at a single institution.

Results.

There were 10 rejection events, 5 of which were confirmed with biopsy. The other 5 were treated based on dd-cfDNA and clinical data alone with favorable outcomes. Among all patients who did not have rejection, 97% had dd-cfDNA <0.5%. Dd-cfDNA may also help differentiate rejection from graft injury (ie, pancreatitis) with median values in rejection 2.25%, injury 0.36%, and quiescence 0.18% (P = 0.0006).

Conclusions.

Similar to kidneys, dd-cfDNA shows promise for rejection surveillance in SPK transplant recipients.
Cryptic aspergillosis: a rare entity and a diagnostic challenge
Authors: R. Lavanya , Ninan Marilyn M. , Kurien Regi , N. A Fouzia , Sahni Rani D. , Michael Joy S.
Published: April 2022

Introduction. Cryptic aspergillosis, caused by cryptic species of Aspergillus, is increasingly reported in humans and causes significant morbidity and mortality in immunocompromised individuals. The main aim of this study was to describe the occurrence of this entity at a large tertiary care centre and analyse the challenges in identifying them in a routine diagnostic laboratory.

Methods. This was a retrospective case review of all patients diagnosed with cryptic Aspergillus species from April 2019 to February 2020. The isolates were identified using conventional microbiological techniques, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI- TOF MS), 28S rRNA and internal transcribed spacer (ITS) sequencing.

Results. The species identified were Aspergillus tamarii, Aspergillus lentulus and Aspergillus sydowii. Identification by MALDI- TOF MS and sequencing was concordant for all except A. sydowii, with MALDI- TOF MS misidentifying it as Aspergillus thermomutans. All isolates showed low minimum inhibitory concentrations (MICs) for the panel of antifungal drugs.

Conclusion. Aspergillosis caused by cryptic Aspergillus species presents a diagnostic challenge. This study confirms the importance of molecular methods for accurate identification.
Proteiniclasticum aestuarii sp. nov., isolated from tidal flat sediment, and emended descriptions of the genus Proteiniclasticum and Proteiniclasticum ruminis
Authors: Namirimu Teddy , Yang Jhung-Ahn , Yang Sung-Hyun , Yu Jihyun , Kim Yun Jae , Kwon Kae Kyoung
Published: April 2022

A novel bacterium, designated SCR006T, was isolated from tidal flat sediment from Suncheon Bay, Republic of Korea. Cells of strain SCR006T were strictly anaerobic, motile cocci, Gram-reaction-negative, and catalase- and oxidase-negative. Growth was observed at 4–41 °C (optimum, 34–37 °C), at pH 6.5–10.0 (optimum, pH 7.0–7.5) and in presence of 0–8 % NaCl (optimum, 0–2 %). Fermentation products of peptone–yeast–glucose medium were acetate and ethanol. Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SCR006T had high sequence similarity to

Proteiniclasticum ruminis

D3RC-2T (97.9 %), followed by

Youngiibacter multivorans

DSM 6139T (95.9 %) and

Youngiibacter fragilis

232.1T (95.0 %). The average nucleotide identity value between strain SCR006T and

P. ruminis

DSM 24773T was 72.7 %, which strongly supported that strain SCR006T reresents a novel species within the genus

Proteiniclasticum

. The major cellular fatty acids are iso-C15 : 0 (27.2 %) and anteiso-C15 : 0 (16.9 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unidentified phospholipids, an unidentified aminolipid and five unidentified lipids. The genomic size was 3.2 Mb with genomic DNA G+C content of 45.6 mol%. The results of 16S rRNA-based and genome-based phylogenetic tree analyses indicated that SCR006T should be assigned to the genus

Proteiniclasticum

. Strain SCR006T could be distinguished from

P. ruminis

D3RC-2T by its growth conditions, cell morphology and genomic characteristics. Based on the phenotypic, phylogenetic, genomic and chemotaxonomic features, strain SCR006T represents a novel species, for which the name Proteiniclasticum aestuarii sp. nov. is proposed, with the type strain SCR006T (=KCTC 25245T= JCM 34531T)
Proteasome inhibition enhances myeloma oncolytic reovirus therapy by suppressing monocytic anti-viral immune responses
Authors: Dona Ada Alice , Caserta Enrico , Singer Mahmoud , Tandoh Theophilus , Nigam Lokesh , Winchester Janet , Chowdhury Arnab , Zhu Yinghui , Murtadha Mariam , Pozhitkov Alex , Sanchez James F , Vahed Hawa , Coffey Matt , Marcucci Guido , Krishnan Amrita , Nuovo Gerard , Sborov Douglas W. , Hofmeister Craig C , Pichiorri Flavia
Published: April 2022

Reovirus is an oncolytic virus with natural tropism for cancer cells. We previously showed that reovirus intravenous administration in myeloma patients was safe, but disease control associated with viral replication in the cancer cells was not observed. Here we show that ex vivo proteasome inhibitors (PIs) potentiate reovirus replication in circulating classical monocytes, increasing viral delivery to myeloma cells. We found that the anti-viral signals in monocytes primarily rely on the NF-kB activation and that this effect is impaired by the addition of PIs. Conversely, PIs improved reovirus-induced monocyte and T cell activation against cancer cells. Based on these preclinical data, we conducted a phase 1b trial of the reovirus Pelareorep together with the PI carfilzomib in 13 heavily pretreated bortezomib-resistant MM patients. Objective responses associated with reovirus active replication in MM cells, T cell activation and monocytic expansion were noted in 70% of patients.
Exploring the use of UmbiFlow™ to assess the impact of heat stress on fetoplacental blood flow in field studies
Authors: Bonell Ana , Vannevel Valerie , Sonko Bakary , Mohammed Nuredin , Vicedo-Cabrera Ana M. , Haines Andy , Maxwell Neil S , Hirst Jane , Prentice Andrew M
Published: April 2022

Objective

To evaluate the impact of heat stress on umbilical artery resistance index (RI) measured by UmbiFlow™ in field settings and the implications for pregnancy outcomes.

Methods

This feasibility study was conducted in West Kiang, The Gambia, West Africa; a rural area with increasing exposure to extreme heat. We recruited women with singleton fetuses who performed manual tasks (such as farming) during pregnancy. The umbilical artery RI was measured at rest, during and at the end of a typical working shift in women ≥ 28 weeks’ gestation. Adverse pregnancy outcomes (APO) were classified as stillbirth, preterm birth, low birth weight, or small for gestational age, and all other outcomes as normal.

Results

A total of 40 participants were included; 23 normal births and 17 APO. Umbilical artery RI demonstrated a nonlinear relationship to heat stress, with indication of a potential threshold value for placental insufficiency around 32ºC by universal thermal climate index. Preliminary evidence suggests the fetoplacental circulation response to heat stress differs in APO versus normal outcome.

Conclusions

The Umbiflow™ device proved to be an effective field method for assessing placental function. Dynamic changes in RI may begin to explain the association between extreme heat and APO.

Funding

The Wellcome Trust (216336/Z/19/Z)

Synopsis

Extreme heat exposure is increasing and a low-cost umbilical artery doppler device, UmbiFlow™, can aid understanding of fetoplacental function under heat stress conditions.
Non-cancer stem cell-derived Fibromodulin activates Integrin-dependent Notch signaling in endothelial cells to promote tumor angiogenesis and growth
Authors: Sengupta Shreoshi , Mondal Mainak , Prasasvi Kaval Reddy , Mukherjee Arani , Magod Prerna , Urbach Serge , Friedmann-Morvinski Dinorah , Marin Philippe , Somasundaram Kumaravel
Published: April 2022

Cancer stem cells alone can initiate and maintain tumors, but the function of non-cancer stem cells that form the tumor bulk remains poorly understood. Proteomic analysis showed a higher abundance of the extracellular matrix small leucine-rich proteoglycan Fibromodulin (FMOD) in the conditioned medium of non-cancer stem cells (DGCs; differentiated glioma cells) of glioma compared to that of glioma stem-like cells (GSCs). DGCs silenced for FMOD fail to cooperate with co-implanted GSCs to promote tumor growth. FMOD downregulation neither affects GSC growth and differentiation nor DGC growth and reprogramming in vitro. DGC-secreted FMOD promotes angiogenesis by activating Integrin-dependent Notch signaling in endothelial cells. Furthermore, conditional silencing of FMOD in newly generated DGCs in vivo inhibits the growth of GSC-initiated tumors due to poorly developed vasculature and increases mouse survival. Collectively, these findings demonstrate that DGC-secreted FMOD promotes glioma tumor angiogenesis and growth through paracrine signaling in endothelial cells and identifies a DGC-produced protein as a potential therapeutic target in glioma.
Effect of Heat inactivation and bulk lysis on Real-Time Reverse Transcription PCR Detection of the SARS-COV-2: An Experimental Study
Authors: Leta Dereje , Gutema Gadissa , Hagos Gebremedhin Gebremichael , Diriba Regasa , Bulti Gutema , Sura Tolawak , Ayana Desta , Chala Dawit , Lenjiso Boki , Bulti Jaleta , Abdella Saro , Tola Habteyes Hailu
Published: April 2022

The outbreak of the severe acute respiratory syndrome coronavirus - 2 has quickly turned into a global pandemic. Real-time reverse transcription Polymerase chain reaction is commonly used to diagnose as “gold standard”. Many coronaviruses are sensitive to heat and chemicals. Heat and chemical inactivation of samples is considered a possible method to reduce the risk of transmission, but the effect of heating and chemical treatment on the measurement of the virus is still unclear. Thus, this study aimed to investigate the effect of heat inactivation and chemical bulklysis on virus detection. The laboratory-based experimental study design was conducted in Ethiopian Public Health Institute from August to November 2020 on the samples referred to the laboratory for Coronavirus disease-19 testing. Tests were performed on eighty Nasopharyngeal/Oropharyngeal swab samples using the Abbott Real-time severe acute respiratory syndrome coronavirus - 2 assays, a test for the qualitative detection of virus in the sample. Data were analyzed and described by mean and standard deviation. Repeated measurement analysis of variance was used to assess the mean difference between the three temperatures and bulk lysis on viral detection. Post-hock analysis was employed to locate the place of significant differences. P-values less than 0.05 was used to declare statistical significance. About 6.2% (5/80) of samples were changed to negative results in heat inactivation at 60°C and 8.7% (7/80) of samples were changed to negative in heat inactivation at 100°C. The Cyclic threshold values of heat-inactivated samples (at 60°C, at 100°C, and bulk lysis) were significantly different from the temperature at 56°C. The efficacy of heat-inactivation varies greatly depending on temperature and duration. Therefore, local validation and verification of heat-inactivation are essential.
Drinking water chlorination impact on fecal carriage of extended-spectrum beta-lactamase-producing Enterobacteriaceae in Bangladeshi children in a double-blind, cluster-randomized controlled trial
Authors: Montealegre Maria Camila , Greenwood Esther E. , Teichmann Lisa , Nadimpalli Maya L. , Caduff Lea , Swarthout Jenna M. , Nydegger Tabea , Sultana Sonia , Islam Mohammad Aminul , Lanza Val F. , Luby Stephen P. , Pickering Amy J. , Julian Timothy R.
Published: April 2022

Background

Water, sanitation, and hygiene (WASH) services have the potential to interrupt transmission of antimicrobial-resistant bacteria and reduce the need for antibiotics, thereby reducing selection for resistance. However, evidence of WASH impacts on antimicrobial resistance (AMR) is lacking.

Methods

We evaluated extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and ESBL-KESC (Klebsiella spp., Enterobacter spp., Serratia spp., and Citrobacter spp.) carriage in the feces of 479 Bangladeshi children under 5 years of age enrolled in a double-blind, cluster-randomized controlled trial of in-line drinking water chlorination in two low-income urban communities in Bangladesh. We additionally assessed the intervention’s impact on circulating beta-lactamase genes in fecal metagenomes and in genomes of fecal ESBL-E. coli isolates.

Findings

We detected ESBL-E. coli in 65% (n = 309) and ESBL-KESC in 12% (n = 56) of enrolled children. We observed no effect of the intervention on the prevalence of ESBL-E. coli (relative risk [95% confidence interval] = 0.98 [0.78, 1.23]) when controlling for study site and age. Although ESBL-KESC (0.76 [0.44, 1.29]) was lower among children in the intervention group, the relative risk was not significant. Concentrations of ESBL-E. coli (log10 CFU/g-wet) were on average [95% confidence interval] 0.13 [-0.16, 0.42] higher in the intervention group and ESBL-KESC (log10 CFU/g-wet) were 0.10 [-0.22, 0.02], lower in the intervention group, when controlling for study site and age. Furthermore, the distribution of ESBL-E.coli sequence types, type of beta-lactamase-encoding genes in ESBL-E. coli isolates, and the presence and relative abundance of beta-lactamase-encoding genes in children’s fecal metagenomes did not differ significantly between the intervention and control children.

Interpretation

One year of in-line drinking water chlorination in communities did not meaningfully impact the carriage of ESBL-E. coli among children in an area of high ESBL-E. coli carriage. While ESBL-KESC was at lower prevalence than ESBL-E. coli, in the intervention group, limited study power prevented a clear interpretation of treatment effect. Development and evaluation of effective interventions to reduce AMR carriage are needed to support calls for WASH embedded in current National and Global AMR Action Plans.
Protist diversity and metabolic strategy in freshwater lakes are shaped by trophic state and watershed land use at a continental scale
Authors: Garner Rebecca E. , Kraemer Susanne A. , Onana Vera E. , Huot Yannick , Gregory-Eaves Irene , Walsh David A.
Published: April 2022

Protists play key roles in aquatic food webs as primary producers, predators, nutrient recyclers, and symbionts. Yet, a comprehensive view of protist diversity in freshwaters has been challenged by the immense environmental heterogeneity among lakes worldwide. We assessed protist diversity in the surface waters of 366 freshwater lakes across a north temperate to subarctic extent covering nearly 8.4 million km2 of Canada. Sampled lakes represented broad gradients in size, trophic state, and watershed land use. Hypereutrophic lakes contained the least diverse and most distinct protist communities relative to nutrient-poor lakes. Greater taxonomic variation among eutrophic lakes was mainly a product of heterotroph and mixotroph diversity, whereas phototroph assemblages were more similar under high- nutrient conditions. Overall, local physicochemical factors, particularly ion and nutrient concentrations, elicited the strongest responses in community structure, far outweighing the effects of geographic gradients. Despite their contrasting distribution patterns, obligate phototroph and heterotroph turnover was predicted by an overlapping set of environmental factors, while the metabolic plasticity of mixotrophs may have made them less predictable. Notably, protist diversity was associated with variation in watershed soil pH and agricultural crop coverage, pointing to human impact on the land-water interface that has not been previously identified in studies at smaller scales. Our study exposes the importance of both within-lake and external watershed characteristics in explaining protist diversity and biogeography, critical information in further developing an understanding of how freshwater lakes and their watersheds are impacted by anthropogenic stressors.

Importance

Freshwater lakes are experiencing rapid changes under accelerated anthropogenic stress and a warming climate. Microorganisms underpin aquatic food webs, yet little is known about how freshwater microbial communities are responding to human impact. Here, we assessed the diversity of protists and their myriad ecological roles in lakes varying in size across watersheds experiencing a range of land use pressures by leveraging data from a continental-scale survey of Canadian lakes. We found evidence of human impact on protist assemblages through an association with lake trophic state and extending to agricultural activity and soil characteristics in the surrounding watershed. Furthermore, trophic state appeared to explain the distributions of phototrophic and heterotrophic protists in contrasting ways. Our findings highlight the vulnerability of lake ecosystems to increased land use and the importance of assessing terrestrial interfaces to elucidate freshwater ecosystem dynamics.
Evidence of attack deflection suggests adaptive evolution of wing tails in butterflies
Authors: Chotard Ariane , Ledamoisel Joséphine , Decamps Thierry , Herrel Anthony , Chaine Alexis , Llaurens Violaine , Debat Vincent
Published: April 2022

Predation is a powerful selective force shaping many behavioural and morphological traits in prey species. The deflection of predator attacks from vital parts of the prey usually involves the coordinated evolution of prey body shape and colour. Here, we test the deflection effect of hindwing tails in the swallowtail butterflyIphiclides podalirius. In this species, hindwings display long tails associated with a conspicuous colour pattern. By surveying the wings within a wild population ofI. podalirius, we observed that wing damage was much more frequent on the tails. We then used a standardised behavioural assay employing dummy butterflies with realI. podaliriuswings to study the location of attacks by great titsParus major. Wing tails and conspicuous coloration of the hindwings were struck more often than the rest of the body by birds. Finally, we characterised the mechanical properties of fresh wings and found that the tail vein was more fragile than the others, suggesting facilitated escape ability of butterflies attacked at this location. Our results clearly support the deflective effect of hindwing tails and suggest that predation is an important selective driver of the evolution of wing tails and colour pattern in butterflies.
Overexpression of TopBP1 leads to transformation with a TP53 mutation of non-tumorigenic breast epithelial cells
Authors: Umesh Rintu M , Lahiri Mayurika
Published: April 2022

DNA topoisomerase IIβ - binding protein 1 (TopBP1) is a mediator protein that regulates the cell cycle checkpoint signaling pathway. A plethora of studies suggests high TopBP1 levels are positively associated with various cancers. Although TopBP1 transcript, as well as protein expression levels, are high in breast cancers, its role in breast tumorigenesis is not yet explored. In our studies, we observed that TopBP1 levels are high in premalignant and malignant cells of the MCF10A cancer progression series compared to the non-tumorigenic MCF10A cells. In order to establish the role of TopBP1 in tumorigenesis, TopBP1 overexpression in non-tumorigenic MCF10A, and stable knock-down in malignant MCF10CA1a cells were performed and grown in Matrigel™ as breast spheroids.

Overexpression of TopBP1 in MCF10A spheroids induced hyperproliferation, disruption of polarity and cell-cell junctions. Moreover, TopBP1 overexpressing 3D dissociated cells exhibited EMT-like phenotype and tumorigenic properties such as increased cell migration, invasion, colony formation capabilitiy and anchorage-independent growth, indicating acquisition of cellular transformation. Finally, we demonstrated TopBP1 overexpressing cells to form tumors in athymic mice thereby confirming their tumorigenic potential. We also confirmed that overexpression of TopBP1 led to a mutation in TP53 and other genomic insults. To summarise, we observed that ectopic expression of TopBP1 transforms MCF10A breast epithelial cells. These transformed cells harbour phenotypic and genotypic characteristics similar to that of malignant cells.
Flagellar Motility During E. Coli Biofilm Formation Provides a Competitive Disadvantage Which Recedes in the Presence of Co-Colonizers
Authors: Ben Youssef Wafa , Deforet Maxime , Monmeyran Amaury , Henry Nelly
Published: April 2022

In nature, bacteria form biofilms in very diverse environments, involving a range of specific properties and exhibiting competitive advantages for surface colonization. However, the underlying mechanisms are difficult to decipher. In particular, the contribution of cell flagellar motility to biofilm formation remains unclear. Here, we examined the ability of motile and nonmotile E. coli cells to form a biofilm in a well-controlled geometry, both in a simple situation involving a single-species biofilm and in the presence of co-colonizers. Using a millifluidic channel, we determined that motile cells have a clear disadvantage in forming a biofilm, exhibiting a long delay as compared to nonmotile cells. By monitoring biofilm development in real time, we observed that the decisive impact of flagellar motility on biofilm formation consists in the alteration of surface access time. Implementing a simple mathematical model to calculate surface access velocity for both motile (diffusion) and nonmotile (settling) cells, we discovered that the competitive advantage strongly depends on the geometry of the environment to be colonized. Interestingly, this advantage reverts for the smallest geometries, with a crossover at a height of 100 μm. We also report that the difference between and nonmotile cells in the ability to form a biofilm diminishes in the presence of cocolonizers, which could be due to motility inhibition through the consumption of key resources by the co-colonizers. We conclude that the impact of flagellar motility on surface colonization closely depends on the environment geometry and the population features, suggesting a unifying vision of the role of cell motility in surface colonization and biofilm formation.
Myosin Heavy Chain Converter Domain Mutations Drive Early-Stage Changes in Extracellular Matrix Dynamics in Hypertrophic Cardiomyopathy
Authors: Hsieh Jeanne , Becklin Kelsie , Givens Sophie , Komosa Elizabeth R. , Abrahante Lloréns Juan E. , Kamdar Forum , Moriarity Branden S. , Webber Beau R. , Singh Bhairab N. , Ogle Brenda M.
Published: April 2022

More than 60% of hypertrophic cardiomyopathy (HCM)-causing mutations are found in the gene loci encoding cardiac myosin-associated proteins including myosin heavy chain (MHC) and myosin binding protein C (MyBP-C). Moreover, patients with more than one independent HCM mutation may be at increased risk for more severe disease expression and adverse outcomes. However detailed mechanistic understanding, especially at early stages of disease progression, is limited. To identify early-stage HCM triggers, we generated single (MYH7 c.2167C>T [R723C] with a known pathogenic significance in the MHC converter domain) and double (MYH7 c.2167C>T [R723C]; MYH6 c.2173C>T [R725C] with unknown significance) myosin gene mutations in human induced pluripotent stem cells (hiPSCs) using a base-editing strategy. Cardiomyocytes (CMs) derived from hiPSCs with either single or double mutation exhibited phenotypic characteristics consistent with later-stage HCM including hypertrophy, multinucleation, altered calcium handling, metabolism and arrhythmia. We then probed mutant CMs at time points prior to the detection of known HCM characteristics. We found MYH7/MYH6 dual mutation dysregulated extracellular matrix (ECM) remodeling, altered integrin expression, and interrupted cell-ECM adhesion by limiting the formation of focal adhesions. These results point to a new phenotypic feature of early-stage HCM and reveal novel therapeutic avenues aimed to delay or prohibit disease onset.
Extracellular Vesicle Antibody Microarray for Multiplexed Inner and Outer Protein Analysis
Authors: Martel Rosalie , Shen Molly L. , DeCorwin-Martin Philippe , de Araujo Lorenna Oliveira Fernandes , Juncker David
Published: April 2022

Proteins are found both outside and inside of extracellular vesicles (EVs) and govern the properties and functions of EVs, while also constituting a signature of the cell of origin and of biological function and disease. Outer proteins on EVs can be directly bound by antibodies to either enrich EVs, or probe the expression of a protein on EVs, including in a combinatorial manner. However, co-profiling of inner proteins remains challenging. Here, we present the high-throughput, multiplexed analysis of extracellular vesicle inner and outer proteins (EVPio). We describe the optimization of fixation and heat-induced protein epitope retrieval for EVs, along with oligo-barcoded antibodies and branched DNA signal amplification for sensitive, multiplexed and high-throughput assays. We captured 4 subpopulations of EVs from colorectal cancer cell lines HT29 and SW403 based on EpCAM, CD9, CD63 and CD81 expression, and quantified the co-expression of 8 outer (integrins and tetraspanins) and 4 inner (heat shock, endosomal and inner leaflet) proteins. The differences in co-expression patterns were consistent with the literature and known biological function. In conclusion, EVPio analysis can simultaneously detect multiple inner and outer proteins in EVs immobilized on a surface, opening the way to extensive combinatorial protein profiles for both discovery and clinical translation.
Barcoding genetically distinctPlasmodium falciparumstrains for comparative assessment of fitness and antimalarial drug resistance
Authors: Carrasquilla Manuela , Drammeh Ndey Fatou , Rawat Mukul , Sanderson Theo , Zenonos Zenon , Rayner Julian C , Lee Marcus CS
Published: April 2022

The repeated emergence of antimalarial drug resistance inPlasmodium falciparum, including to the current frontline antimalarial artemisinin, is a perennial problem for malaria control. Nextgeneration sequencing has greatly accelerated the identification of polymorphisms in resistance-associated genes, but has also highlighted the need for more sensitive and accurate laboratory tools to profile current and future antimalarials, and to quantify the impact of drug resistance acquisition on parasite fitness. The interplay of fitness and drug response is of fundamental importance in understanding why particular genetic backgrounds are better at driving the evolution of drug resistance in natural populations, but the impact of parasite fitness landscapes on the epidemiology of drug resistance has typically been laborious to accurately quantify in the lab, with assays being limited in accuracy and throughput. Here we present a scalable method to profile fitness and drug response of genetically distinctP. falciparumstrains with well-described sensitivities to several antimalarials. We leverage CRISPR/Cas9 genome-editing and barcode sequencing to track unique barcodes integrated into a non-essential gene (pfrh3). We validate this approach in multiplex competitive growth assays of three strains with distinct geographical origins. Furthermore, we demonstrate that this method can be a powerful approach for tracking artemisinin response as it can identify an artemisinin resistant strain within a mix of multiple parasite lines, suggesting an approach for scaling the laborious ring-stage survival assay (RSA) across libraries of barcoded parasite lines. Overall, we present a novel high-throughput method for multiplexed competitive growth assays to evaluate parasite fitness and drug response
RNA decay defines the response to transcriptional perturbation in leukaemia
Authors: Todorovski Izabela , Feran Breon , Fan Zheng , Gadipally Sreeja , Yoannidis David , Kong Isabella Y , Bjelosevic Stefan , Zethoven Magnus , Hawkins Edwin D , Simpson Kaylene J , Arnau Gisela Mir , Papenfuss Anthony T , Johnstone Ricky W , Vervoort Stephin J
Published: April 2022

Therapeutic targeting of dysregulated transcriptional programs has arisen as a promising strategy for the treatment of leukaemias. The therapeutic response to small molecule inhibitors of Bromodomain-Containing Proteins (BRD), such as BRD2 and BRD4, P300/cAMP-response element binding protein (CBP) and Cyclin Dependent Kinases (CDKs), is generally attributed to the selective disruption of oncogenic gene expression networks driven by enhancers, super-enhancers (SEs) and lineage-specific transcription factors (TFs), including thec-MYConcogene. Using technologies such as thiol (SH)-linked alkylation for the metabolic sequencing of RNA sequencing (SLAM-seq) to profile messenger RNA (mRNA) decay and production rates, we demonstrate that gene intrinsic properties largely govern the selectivity associated with transcriptional inhibition, where total mRNA response signatures are dominated with genes that have short transcript half-lives, including those regulated by SEs and oncogenic TFs. Further highlighting that gene sensitivities only occur in the context of short transcript half-lives, stabilisation of thec-MYCtranscript through changes in the 3’ UTR rendered it insensitive to transcriptional targeting. However, this was not sufficient to rescuec-MYCtarget gene transcription and anti-leukaemia effects following transcriptional inhibition. Importantly, long-lived mRNAs encoding essential genes that evade transcriptional targeting can be rendered sensitive via modulation of mRNA decay kinetics through inhibition of the RNA Binding Protein (RBP), ELAV Like RNA binding protein 1 (ELAVL1)/ Human Antigen R (HuR). Taken together, these data demonstrate that mRNA decay shapes the therapeutic response to transcriptional perturbation and can be modulated for novel therapeutic outcomes using transcriptional agents in leukaemia.
Functional plasticity and recurrent cell states of malignant B cells in follicular lymphoma
Authors: Attaf Noudjoud , Dong Chuang , Gil Laurine , Cervera-Marzal Inãki , Gharsalli Tarek , Navarro Jean-Marc , Mboumba Diana-Laure , Chasson Lionel , Lemonnier François , Gaulard Philippe , Roulland Sandrine , Spinelli Lionel , Nadel Bertrand , Milpied Pierre
Published: April 2022

Follicular lymphoma (FL) derives from malignant transformation of germinal center (GC) B cells. FL malignant B cells are heterogeneous and diverge from their GC B cell-of-origin, but the diversity, function, and location of malignant B cell states remain to be addressed. Based on integrative single-cell RNA-seq, we identified and studied recurrent FL malignant B cell states and dynamics. Most FL B cells spanned a continuum of states from proliferating GC-like to quiescent memory (Mem)-like cell states. That GC-to-Mem axis was the main source of intra-tumor transcriptional heterogeneity. While FL B cell states were independent from subclonal B cell receptor genetics divergence, T follicular helper (TFH) cell-derived signals controlled the transition from Mem-like to GC-like states. GC-like, TFH-activated and Mem-like FL B cells tended to occupy distinct niches within and around tumor follicles. Our study characterizes novel malignant cell states recurrent in B cell lymphomas, and highlights the functional plasticity of malignant B cells.
SOX9 binds TCFs to mediate Wnt/β-catenin target gene activation
Authors: Ramakrishnan Aravinda-Bharathi , Burby Peter E. , Adiga Kavya , Cadigan Ken M.
Published: April 2022

Activation of the Wnt/β-catenin pathway regulates gene expression by promoting the formation of a β-catenin-TCF complex on target gene chromatin. The transcription factor SOX9 antagonises Wnt signalling in many contexts through its ability to down-regulate β-catenin protein levels. Here, we find that SOX9 promotes the proliferation of Wnt-driven colorectal cancer (CRC) cells. We identify multiple enhancers activated by SOX9 working in concert with the Wnt pathway. These enhancers are co-occupied by TCFs and SOX9 and contain TCF and SOX9 binding sites that are necessary for transcriptional activation. In addition, we identify a physical interaction between the DNA-binding domains of TCFs and SOX9 and show that TCF-SOX9 interactions are important for target gene regulation and CRC cell growth. Our work demonstrates a highly context-dependent effect of SOX9 on Wnt targets, with activation or repression being dependent on the presence or absence of SOX9 binding sites on Wnt-regulated enhancers respectively.
Pharmacological inhibition of titan-like cells formation suggests that accumulation of endogenous free radicals that correlate with mitochondrial changes are required to induce this transition inCryptococcus neoformans
Authors: García-Barbazán Irene , García-Rodas Rocío , Sachse Martin , Luque Daniel , Megías Diego , Zaragoza Oscar
Published: April 2022

Cryptococcus neoformansis an encapsulated yeast able to cause disease (mainly meningoencephalitis) among immunosuppressed patients, mostly HIV+. This yeast can form the so-called titan cellsin vivo, which are cells of an abnormal larger size due to an increase in both the capsule and the cell body size (total size reaching between 50-70 microns). This phenomenon can be partially reproducedin vitroto obtain cells of an intermediate size (25-30 um), which have been denominated titan-like cells. In this work, we have screened 1,520 compounds from the Prestwick Chemical Library and identified off-patent drugs that inhibited titan-like cell formationin vitro. We developed an automated fluorescence-based microscopy assay and identified 64 compounds as possible inhibitors of titan-like cellsin vitro. We chose 10 of these compounds to confirm their inhibitory effect and confirmed them as inhibitors of titan-like cells with dose-response curves. Several of the compounds identified had antioxidant properties (i.e., retinoic acid), indicating a possible role of free radicals during titan cell formation. Using fluorescent probes, we found that there was an endogenous accumulation of ROS during cell growth, which was inhibited in the presence of retinoic acid. Furthermore, we found that during titanization, there were significant changes in the mitochondria, which is the main organelle where ROS are produced. We hypothesize that an intracellular increase of free radicals at the mitochondria might be a triggering signal to induce titanization.

Importance

Cryptococcus neoformansis an excellent model to investigate fungal pathogenesis. This yeast can produce “titan cells”, which are cells of an abnormal larger size that contribute to the persistence of the yeast in the host. In this work, we have used a new approach to characterize them, which is identifying drugs that inhibit this process. We have used a repurposing off- patent drug library, combined with an automatic method to image and analyse fungal cell size. In this way, we have identified many compounds that inhibit this transition. Interestingly, several compounds were antioxidants, allowing us to confirm that endogenous ROS and mitochondrial changes are important for titan cell formation. This work provides new evidences of the mechanisms required for titanization. Furthermore, the future characterization of the inhibitory mechanisms of the identified compounds by the scientific community will contribute to better understand the role of titan cells in virulence.
Cytoneme-mediated transport of active Wnt5b/Ror2 complexes in zebrafish gastrulation
Authors: Zhang Chengting , Brunt Lucy , Rogers Sally , Scholpp Steffen
Published: April 2022

Chemical signaling is the primary means by which cells communicate in the embryo. The underlying principle refers to a group of ligand-producing cells and a group of cells that respond to this signal because they express the appropriate receptors. In the zebrafish embryo, Wnt5b binds to the receptor Ror2 to trigger the Wnt/Planar Cell Polarity (Wnt/PCP) signaling pathway to regulate tissue polarity and cell migration. However, it is still unclear how this lipophilic ligand is transported from the source cells through the aqueous extracellular space to the target tissue. Here we show that Wnt5b, together with Ror2, is loaded on long protrusions. The active Wnt5b/Ror2 complexes are handed over from these cytonemes to the receiving cell to trigger Wnt/PCP signaling, regardless of whether the cell expresses functional receptors. On the tissue level, we show that cytoneme-dependent spreading of active Wnt5b/Ror2 affects convergence and extension in the zebrafish gastrula.