bluuebunny/crossref_metadata_2025 huggingface dataset:
A Novel Preservation Solution Containing Quercetin and Sucrose for Porcine Kidney Transplantation
Authors: Gochi Mikako , Kato Fuminori , Toriumi Asuka , Kawagoe Tomoko , Yotsuya Shuichi , Ishii Daisuke , Otani Masahide , Nishikawa Yuji , Furukawa Hiroyuki , Matsuno Naoto
Published: February 2021

Background.

In organ transplantation, the University of Wisconsin (UW) solution has been the gold standard for organ preservation. Quercetin (Que) has numerous antioxidant and anti-inflammatory activities, and sucrose (Suc) may be effective for cold storage (CS). This study aimed to investigate the in vitro protective effect of Que and Suc on cold injury to the kidney and to determine whether Que + Suc could improve ischemia-reperfusion injury during CS and hypothermic oxygenated perfusion (HOPE) in autologous transplantation models.

Methods.

BHK-21 cells were stored at 4°C for 3 days in UW solution for CS/machine perfusion (CS/MP-UW) with Que (33.1 μM, 3.3 μM, 0.33 μM) and Suc (0.1 M). In a porcine model of renal autologous transplantation, left kidney grafts were preserved under 3 conditions: group 1, CS preservation for 24 hours; group 2, CS preservation for 22 hours and HOPE with CS/MP-UW solution for 2 hours; and group 3, identical preservation as group 2, with Que and Suc added to the solution. Animals were euthanized on day 7 after autologous transplantation.

Results.

After 3 days of CS preservation, the CS/MP-UW solution with Que (33.1 μM, 3.3 μM) and Suc showed significant cell protection against cold injury. In the porcine model of renal autologous transplantation, the last blood Cre level and the blood lipid hydroperoxide on posttransplantation day 2 were significantly different between group 1 and group 3. Moreover, the total endothelial, glomerular, tubular, interstitial (EGTI) histology score in the kidney tissue was also significantly different. Regarding the change in renal resistance in HOPE, the decrease observed in group 3 was significantly larger than that in group 2.

Conclusions.

Our results suggest that the addition of Que and Suc to a UW solution can improve kidney preservation and could potentially enhance the outcome of kidney transplantation.
CD94 Ex Vivo Cultures in a Bone Marrow Transplantation Setting
Authors: Abrams Kraig , Graves Scott S. , Parker Maura H. , Storb Rainer
Published: February 2021

Background.

Complementary, marrow donor-derived peripheral blood T-lymphocyte infusions enable consistent hematopoietic engraftment in lethally irradiated dog leukocyte antigen (DLA)-haploidentical littermate recipients, but at the cost of severe graft versus host disease (GVHD). Here, we explored whether CD94-selected and in vitro-expanded natural killer (NK) cells could be substituted for T-lymphocytes for enhancing marrow engraftment without causing severe GVHD.

Methods.

Five dogs were conditioned with 700 cGy total body irradiation followed by infusion of DLA-haploidentical donor marrow and CD94-selected, in vitro-expanded NK cells. NK cells were infused at a median of 140 000 (range 78 000–317 000) cells/kg.

Results.

Four dogs rejected their marrow grafts, whereas 1 dog fully engrafted and developed GVHD. We observed an increase in peripheral blood NK cells after infusion of CD94-selected, ex vivo-expanded NK in 2 dogs. Peripheral blood lymphocyte counts peaked at day 7 or 8 posttransplant in the 4 rejecting dogs, whereas in the fully engrafted dog, lymphocyte counts remained stable at suboptimal levels.

Conclusions.

Our study indicates NK cells can be expanded in vitro and safely infused into DLA-haploidentical recipients. Within the range of CD94-selected and expanded cells infused we concluded that they failed to both uniformly promote engraftment and avert GVHD.
Differences in Liver Graft Survival by Recipient Sex
Authors: De Simone Alexia I. , Zhang Xun , Dahhou Mourad , Sapir-Pichhadze Ruth , Cardinal Heloise , Ng Vicky , Foster Bethany J.
Published: February 2021

Background.

We aimed to characterize patterns of differences in liver graft failure rates by recipient sex, accounting for the modifying effects of donor sex and recipient age.

Methods.

We evaluated 144 212 first deceased donor liver transplant recipients [1988–2019; Scientific Registry of Transplant Recipients (SRTR)]. We used multivariable time-varying Cox models, considering a recipient sex by donor sex by recipient age (0–12, 13–24, 25–44, ≥45 y) interaction.

Results.

Among recipients of male donors, females <45 y had higher graft failure rates than males of the same age, but none of these differences were statistically significant [0–12 y: adjusted hazard ratio (aHR) 1.17 (0.98, 1.40); 13–24 y: aHR 1.18 (0.96, 1.46); 25–44 y: aHR 1.11 (0.96, 1.28)]; there was no material or statistically significant difference between female and male recipients ≥45 y [aHR 1.01 (0.97, 1.06)]. When the donor was female, recipients <45 y showed no statistically significant differences in graft outcomes by recipient sex [0–12 y: aHR 0.91 (0.74, 1.11); 13–24 y: aHR 0.98 (0.77, 1.25); 25–44 y: aHR 0.86 (0.73, 1.01)], whereas female recipients ≥45 y had significantly lower graft failure rates [aHR 0.85 (0.81, 0.89)] than males of the same age.

Conclusions.

Among recipients of female donors, female recipients ≥45 y had significantly better outcomes than males of the same age; there were no clear differences by recipient sex in younger recipients. When the donor was male, there was no material or statistically significant difference in graft failure rates between males and females ≥45 y; among younger recipients point estimates suggested higher failure rates in females than males recipients, but confidence intervals were wide making firm conclusions impossible. Larger studies combining multiple datasets are needed.
Outcomes of Liver Transplantation in Treated Portopulmonary Hypertension Patients With a Mean Pulmonary Arterial Pressure ≥35 mm Hg
Authors: DuBrock Hilary M. , Runo James R. , Sadd Corey J. , Burger Charles D. , Cartin-Ceba Rodrigo , Rosen Charles B. , Taner Timucin , Nyberg Scott L. , Heimbach Julie K. , Findlay James Y. , Krowka Michael J.
Published: February 2021

Background.

Portopulmonary hypertension (POPH), pulmonary arterial hypertension (PAH) that develops in the setting of portal hypertension, affects 5%–6% of patients with liver disease and is associated with significant morbidity and mortality. A mean pulmonary arterial pressure (mPAP) threshold of 35 mm Hg is used to stratify perioperative risk and liver transplant eligibility in treated POPH patients but does not take into account the specific factors that contribute to the pressure elevation.

Methods.

In this case series, we describe the characteristics and posttransplant outcomes of patients with treated POPH and an mPAP ≥35 mm Hg and pulmonary vascular resistance (PVR) <250 dynes-s-cm−5 at or just before liver transplantation (LT). We also describe the effect of PAH therapy on pulmonary hemodynamics in patients with POPH.

Results.

Sixteen patients were included. All patients were on PAH therapy at the time of LT. PAH therapy resulted in a decrease of mPAP (median 18.4%; interquartile range [IQR] 8.9%–27.0%) with a reduction in PVR (median 50.5%; IQR, 45.4%–70.7%), and an increase in both cardiac output (CO) (median 28.1%; IQR 5.7%–63.8%) and PAWP (median 50.0%; IQR 16.7%–108.3%) before LT. One year posttransplant survival was 69% (11/16); however, only 1 death was attributed to POPH. At 1-year posttransplant, 63.6% (7/11) of patients were weaned off all PAH therapy with clinical and echocardiographic resolution of POPH.

Conclusions.

In treated POPH patients with an mPAP ≥35 mm Hg and PVR < 250 dynes-s-cm−5 before LT, 1-year posttransplant survival was 69% and the majority of patients were able to discontinue PAH therapy.
Ischemia-reperfusion Injury in the Transplanted Lung: A Literature Review
Authors: Talaie Tara , DiChiacchio Laura , Prasad Nikhil K. , Pasrija Chetan , Julliard Walker , Kaczorowski David J. , Zhao Yunge , Lau Christine L.
Published: February 2021

Lung ischemia-reperfusion injury (LIRI) and primary graft dysfunction are leading causes of morbidity and mortality among lung transplant recipients. Although extensive research endeavors have been undertaken, few preventative and therapeutic treatments have emerged for clinical use. Novel strategies are still needed to improve outcomes after lung transplantation. In this review, we discuss the underlying mechanisms of transplanted LIRI, potential modifiable targets, current practices, and areas of ongoing investigation to reduce LIRI and primary graft dysfunction in lung transplant recipients.
Hippocampal D1—but not D2—like dopamine receptors modulate the phosphorylation of ERK in food deprivation-induced reinstatement of morphine in extinguished rats
Authors: Mozafari Roghayeh , Karimi-Haghighi Saeideh , Hooshmandi Etrat , Ghasemi Rasoul , Koruji Morteza , Ahadi Reza , Haghparast Abbas
Published: February 2021

Reinstatement to drug abuse is the most challenging issue in the treatment of addiction. Thus, knowledge of the involved neurobiological mechanisms of reinstatement is a fundamental necessity. There is substantial and crucial evidence that dopamine is implicated in motivational processes such as relapse. Our behavioral results reported that the administration of dopamine receptor antagonists inhibited reinstatement of morphine in food-deprived rats. Previous studies have indicated that the ERK pathway plays a critical role in the cellular responses to stress and reward. Therefore, the purpose of the current study was to evaluate the effect of intra-dentate gyrus administration of dopamine receptor antagonists on the phosphorylation of hippocampal ERK in the reinstatement phase of morphine reward in food-deprived rats. All groups of animals passed conditioned place preference and were bilaterally given different doses of D1- or D2-like dopamine compounds (0.25, 1 and 4 μg/0.5 μl) into the dentate gyrus. Immediately after the reinstatement phase, each animal was euthanized, and the hippocampi were immediately dissected. Then, the p-ERK/ERK ratio was evaluated using Western blot analysis. The principal findings in this study demonstrated that intra-dentate gyrus administration of the highest dose of the D1-like receptor antagonist could enhance the hippocampal p-ERK/ERK ratio in food-deprived rats while the D2-Like receptor antagonist failed to change this ratio.
Time of day influences psychophysical measures in women with burning mouth syndrome
Authors: Sosa Janell S. Payano , Da Silva Joyce T. , Burrowes Shana A.B , Yoo Soo Y. , Keaser Michael L. , Meiller Timothy F. , Seminowicz David A.
Published: February 2021

Burning mouth syndrome (BMS) is a chronic orofacial pain condition that mainly affects postmenopausal women. BMS type I patients report little to no spontaneous pain in the morning and increases in pain through the day, peaking in the afternoon. Quantitative sensory testing (QST) findings from BMS type 1 patients are inconsistent as they fail to capture this temporal variation. We examined how QST in BMS type 1 compared to healthy participants was affected by time of day. QST of the face and forearm included warmth detection threshold (WDT), cold detection threshold (CDT), and heat pain thresholds (HPT), ratings of suprathreshold heat, and pressure pain thresholds (PPT), and was performed twice: once in the morning and once in the afternoon. BMS patients reported: no differences in morning and afternoon comparisons of the orofacial region between groups and no differences in PPTs in either orofacial or arm regions between groups; lower within group PPTs of the masseter in the afternoon; higher WDTs, and lower CDTs of the forearm in the morning compared to healthy participants; lower CDTs and higher pain intensity ratings to heat stimuli at low temperatures on the forearm in the afternoon compared to healthy participants. The findings indicate that compared to healthy participants, BMS Type I patients had altered thermal sensitivity, which depended on body area tested (forearm vs orofacial region), and higher pain sensitivity, which was slightly more pronounced in the afternoon plausibly due to a hypervigilance.

Perspective

Somatosensory profiles in BMS type 1 can be affected by time of day, possibly as an effect of spontaneous burning pain that increases throughout the day. Our findings highlight the cyclical effect of BMS pathophysiology across a day, which may further help clinicians choose appropriate treatment strategies for BMS patients.
WasR< 1 before the English lockdowns? On modelling mechanistic detail, causality and inference about Covid-19
Authors: Wood S. N. , Wit E. C.
Published: February 2021

Detail is a double edged sword in epidemiological modelling. The inclusion of mechanistic detail in models of highly complex systems has the potential to increase realism, but it also increases the number of modelling assumptions, which become harder to check as their possible interactions multiply. In a major study of the Covid-19 epidemic in England, Knock et al. (2020) fit an age structured SEIR model with added health service compartments to data on deaths, hospitalization and test results from Covid-19 in seven English regions for the period March to December 2020. The simplest version of the model has 684 states per region. One main conclusion is that only full lockdowns brought the pathogen reproduction number,R, below one, withR≫ 1 in all regions on the eve of March 2020 lockdown. We critically evaluate the Knock et al. epidemiological model, and the semi-causal conclusions made using it, based on an independent reimplementation of the model designed to allow relaxation of some of its strong assumptions. In particular, Knock et al. model the effect on transmission of both non-pharmaceutical interventions and other effects, such as weather, using a piecewise linear function,b(t), with 12 breakpoints at selected government announcement or intervention dates. We replace this representation by a smoothing spline with time varying smoothness, thereby allowing the form ofb(t) to be substantially more data driven, and we check that the corresponding smoothness assumption is not driving our results. We also reset the mean incubation time and time from first symptoms to hospitalisation, used in the model, to values implied by the papers cited by Knock et al. as the source of these quantities. We conclude that there is no sound basis for using the Knock et al. model and their analysis to make counterfactual statements about the number of deaths that would have occurred with different lockdown timings. However, if fits of this epidemiological model structure are viewed as a reasonable basis for inference about the time course of incidence andR, then without very strong modelling assumptions, the pathogen reproduction number was probably below one, and incidence in substantial decline, some days before either of the first two English national lockdowns. This result coincides with that obtained by more direct attempts to reconstruct incidence. Of course it does not imply that lockdowns had no effect, but it does suggest that other non-pharmaceutical interventions (NPIs) may have been more effective than Knock et al. imply, and that full lockdowns were probably not the cause ofRdropping below one.
Human islet expression levels of Prostaglandin E2synthetic enzymes, but not prostaglandin EP3 receptor, are positively correlated with markers of β-cell function and mass in non-diabetic obesity
Authors: Truchan Nathan A. , Fenske Rachel J. , Sandhu Harpreet K. , Weeks Alicia M. , Patibandla Chinmai , Wancewicz Benjamin , Pabich Samantha , Reuter Austin , Harrington Jeffrey M. , Brill Allison L. , Peter Darby C. , Nall Randall , Daniels Michael , Punt Margaret , Kaiser Cecilia E. , Cox Elizabeth D. , Ge Ying , Davis Dawn B. , Kimple Michelle E.
Published: February 2021

Elevated islet production of prostaglandin E2(PGE2), an arachidonic acid metabolite, and expression of Prostaglandin E2Receptor subtype EP3 (EP3) are well-known contributors to the β-cell dysfunction of type 2 diabetes (T2D). Yet, many of the same pathophysiological conditions exist in obesity, and little is known about how the PGE2production and signaling pathway influences non-diabetic beta-cell function. In this work, plasma arachidonic acid and PGE2metabolite levels were quantified in a cohort of non-diabetic and T2D human subjects to identify their relationship with glycemic control, obesity, and systemic inflammation. In order to link these findings to processes happening at the islet level, cadaveric human islets were subject to gene expression and functional assays. Interleukin-6 (IL-6) and cyclooxygenase-2 (COX-2) mRNA levels, but not those of EP3, positively correlated with donor body mass index (BMI). IL-6 expression also strongly correlated with the expression of COX-2 and other PGE2synthetic pathway genes. Insulin secretion assays using an EP3-specific antagonist confirmed functionallyrelevant up-regulation of PGE2production. Yet, islets from obese donors were not dysfunctional, secreting just as much insulin in basal and stimulatory conditions as those from non-obese donors as a percent of content. Islet insulin content, on the other hand, was increased with both donor BMI and islet COX-2 expression, while EP3 expression was unaffected. We conclude up-regulated islet PGE2production may be part of the β-cell adaption response to obesity and insulin resistance that only becomes dysfunctional when both ligand and receptor are highly expressed in T2D.
Macroscopic quantities of collective brain activity during wakefulness and anesthesia
Authors: Ponce-Alvarez Adrián , Uhrig Lynn , Deco Nikolas , Signorelli Camilo M. , Kringelbach Morten L. , Jarraya Béchir , Deco Gustavo
Published: February 2021

The study of states of arousal is key to understand the principles of consciousness. Yet, how different brain states emerge from the collective activity of brain regions remains unknown. Here, we studied the fMRI brain activity of monkeys during wakefulness and anesthesia-induced loss of consciousness. Using maximum entropy models, we derived collective, macroscopic properties that quantify the system’s capabilities to produce work, to contain information and to transmit it, and that indicate a phase transition from critical awake dynamics to supercritical anesthetized states. Moreover, information-theoretic measures identified those parameters that impacted the most the network dynamics. We found that changes in brain state and in state of consciousness primarily depended on changes in network couplings of insular, cingulate, and parietal cortices. Our findings suggest that the brain state transition underlying the loss of consciousness is predominantly driven by the uncoupling of specific brain regions from the rest of the network.
Phencyclidine-induced psychosis causes hypersynchronization and disruption of connectivity within prefrontal-hippocampal circuits that is rescued by antipsychotic drugs
Authors: Delgado-Sallent Cristina , Nebot Pau , Gener Thomas , Timplalexi Melina , Fath Amanda B , Puig M Victoria
Published: February 2021

Neural synchrony and functional connectivity are disrupted in neuropsychiatric disorders such as schizophrenia. However, these alterations and how they are affected by commonly prescribed neuropsychiatric medication have not been characterized in depth. Here, we investigated changes in neural dynamics of circuits involving the prefrontal cortex and the hippocampus during psychosis induced by the NMDAR antagonist phencyclidine and subsequent recovery by three different antipsychotic drugs (APDs), the classical APD haloperidol and two atypical APDs, clozapine and risperidone, in freely moving mice. We found that the psychotomimetic effects of phencyclidine were associated with hypersynchronization and disrupted communication of prefrontal-hippocampal pathways. Major alterations occurred in the prefrontal cortex, where phencyclidine increased oscillatory power at delta, high gamma and high frequencies (<100 Hz) and generated aberrant cross-frequency coupling, suggesting the presence of hypersynchronous cortical microcircuits. Cross-regional coupling and phase coherence were also enhanced, further reflecting that the circuit’s functional connectivity was increased. Phencyclidine also redirected the intrinsic flow of information at theta frequencies that traveled from the hippocampus to the prefrontal cortex into delta rhythms that traveled in the opposite direction. The three APDs rescued most phencyclidine-induced changes in power, coupling, phase coherence, and directionality, suggesting common cellular mechanisms of antipsychotic action. However, some differential effects were identified, likely resulting from the distinct affinity the three APDs have for dopamine and serotonin receptors. We therefore investigated how serotonin 1A (5-HT1AR) and 2A receptors (5-HT2AR) compare to the actions of the APDs. 5-HT2AR antagonism by M100907 and 5-HT1AR agonism by 8-OH-DPAT rescued phencyclidine-induced increased power, coupling and phase coherence but were unable to normalize the circuit’s theta directionality. This suggests that other targets of the AAPDs working in tandem with 5-HT1ARs and 5-HT2ARs are required to ameliorate this key feature of the circuit.
Connection Failure: Differences in White Matter Microstructure are associated with5-HTTLPRbut not with Risk-Seeking for Losses
Authors: Neukam Philipp T. , Müller Dirk K. , Deza-Araujo Yacila I. , Pooseh Shakoor , Witt Stephanie H. , Rietschel Marcella , Smolka Michael N.
Published: February 2021

In a previous study (Neukam, Kroemer et al. 2018), we found for the5-HTTLPRgenotype higher risk-seeking for losses in S/S vs. L/L carrier, which could not be explained by acutely changed central serotonin levels. This finding alternatively may be the result of reduced top-down control from the frontal cortex due to altered signal pathways involving the amygdala and ventral striatum. The serotonergic system is known to be involved in neurodevelopment and neuroplasticity. Therefore, the aim of this study was to investigate whether structural differences in white matter can explain the differences in risk-seeking behaviour that we observed in our previous study and whether5-HTTLPRgroups differ in their white matter microstructure. These differences can be detected using diffusion-weighted imaging (DWI). We assumed lower structural connectivity in S/S compared to L/L carrier, and a negative relationship between risk-seeking for losses and connectivity. We used DWI to compute diffusion parameters for the frontostriatal and uncinate tract in 175 individuals (39 S/S, 80 S/L, 56 L/L). Results showed no significant relationship between diffusion parameters and risk-seeking for losses. Furthermore, we did not find significant differences in diffusion parameters of the S/S vs. L/L group. There were only group differences in the frontostriatal tract showing stronger structural connectivity in the S/L group, which is also reflected in the whole brain approach. Therefore, the data do not support our hypothesis that the association between5- HTTLPRand risk-seeking for losses is related to differences in white matter pathways implicated in decision-making.
CRISPR-Cas9 gene editing and rapid detection of gene-edited mutants using high-resolution melting in the apple scab fungus,Venturia inaequalis
Authors: Rocafort Mercedes , Arshed Saadiah , Hudson Debbie , Singh Jaspreet , Bowen Joanna K. , Plummer Kim M. , Bradshaw Rosie E. , Johnson Richard D. , Johnson Linda J. , Mesarich Carl H.
Published: February 2021

Background

Scab, or black spot, caused by the filamentous fungal pathogenVenturia inaequalis, is the most economically important disease of apple (Malusxdomestica) worldwide. To develop durable control strategies against this disease, a better understanding of the genetic mechanisms underlying the growth, reproduction, virulence and pathogenicity ofV. inaequalisis required. A major bottleneck for the genetic characterization ofV. inaequalisis the inability to easily delete or disrupt genes of interest using homologous recombination. Indeed, no gene deletions or disruptions inV. inaequalishave yet been published. Recently, CRISPR-Cas9 has emerged as an efficient tool for gene editing in filamentous fungi. With this in mind, we set out to establish CRISPR-Cas9 as a gene editing tool inV. inaequalis.

Results

We showed that CRISPR-Cas9 can be used for gene inactivation in the apple scab fungus. As a proof of concept, we targeted the melanin biosynthesis pathway genetrihydroxynaphthalene reductase(THN), which has previously been shown to result in a light-brown colony phenotype when transcriptionally silenced using RNA interference. Using one of two CRISPR-Cas9 single guide RNAs (sgRNAs) targeted to theTHNgene, delivered by a single autonomously replicating Golden Gate-compatible plasmid, we were able to identify six of 36 stable transformants with a light-brown phenotype, indicating an~16.7% gene inactivation efficiency. Notably, of these sixTHNmutants, five had an independent mutation. As part of our pipeline, we also report a high-resolution melting (HRM) curve protocol for the rapid detection of CRISPR-Cas9 gene-edited mutants ofV. inaequalis. This protocol identified a single base pair deletion mutation in a sample containing only 5% mutant genomic DNA, indicating high sensitivity for mutant screening.

Conclusions

In establishing CRISPR-Cas9 as a tool for gene editing inV. inaequalis, we have provided a strong starting point for studies aiming to decipher the function of genes associated with the growth, reproduction, virulence and pathogenicity of this fungus. The associated HRM curve protocol will enable CRISPR-Cas9 transformants to be screened for gene inactivation in a high-throughput and low-cost manner, which will be particularly powerful in cases where the CRISPR-Cas9-mediated gene inactivation efficiency is low.
Evolution and connectivity influence the persistence and recovery of coral reefs under climate change in the Caribbean, Southwest Pacific, and Coral Triangle
Authors: McManus Lisa C. , Forrest Daniel L. , Tekwa Edward W. , Schindler Daniel E. , Colton Madhavi A. , Webster Michael M. , Essington Timothy E. , Palumbi Stephen R. , Mumby Peter J. , Pinsky Malin L.
Published: February 2021

Corals are experiencing unprecedented decline from climate change-induced mass bleaching events. Dispersal not only contributes to coral reef persistence through demographic rescue but can also hinder or facilitate evolutionary adaptation. Locations of reefs that are likely to survive future warming therefore remain largely unknown, particularly within the context of both ecological and evolutionary processes across complex seascapes that differ in temperature range, strength of connectivity, network size, and other characteristics. Here, we used eco-evolutionary simulations to examine coral adaptation to warming across reef networks in the Caribbean, the Southwest Pacific, and the Coral Triangle. We assessed the factors associated with coral persistence in multiple reef systems to understand which results are general and which are sensitive to particular geographic contexts. We found that evolution can be critical in preventing extinction and facilitating the long-term recovery of coral communities in all regions. Furthermore, the strength of immigration to a reef (destination strength) and current sea surface temperature robustly predicted reef persistence across all reef networks and across temperature projections. However, we found higher initial coral cover, slower recovery, and more evolutionary lag in the Coral Triangle, which has a greater number of reefs and more larval settlement than the other regions. We also found the lowest projected future coral cover in the Caribbean. These findings suggest that coral reef persistence depends on ecology, evolution, and habitat network characteristics, and that, under an emissions stabilization scenario (RCP 4.5), recovery may be possible over multiple centuries.
Sublingual allergen immunotherapy with recombinant dog allergens prevents airway hyperresponsiveness in a model of asthma marked by vigorous TH2 and TH17 cell responses
Authors: Stark Julian M. , Liu Jielu , Tibbitt Christopher A. , Christian Murray , Ma Junjie , Wintersand Anna , Murrell Ben , Adner Mikael , Grönlund Hans , Gafvelin Guro , Coquet Jonathan M.
Published: February 2021

Allergy to dogs affects around ten percent of the population in developed countries. Immune therapy of allergic patients with dog allergen extracts has shown limited therapeutic benefit. Herein, we established a mouse model of dog allergy and tested the efficacy of a recombinant protein containing Can f 1, f 2, f 4 and f 6 as a sublingual immune therapy (SLIT). Repeated inhalation of dog extracts induced infiltration of the airways by TH2 cells, eosinophils and goblet cells, reminiscent of the house dust mite (HDM) model of asthma. However, dog allergen extracts also induced robust TH17 cell responses, which was associated with a high neutrophilic infiltration of the airways and promoted airway hyperresponsiveness more potently than HDM allergens. scRNA-Seq analysis of T helper cells responding to dog allergens identified several unique clusters with TH17 cells being hallmarked by the expression of several receptors including IL-17RE. Analysis of T cell receptors also depicted a high frequency of clones that were shared between TH17, TH2 and suppressive Treg cells, indicative of the plasticity of T helper cells in this model. Importantly, prophylactic SLIT reduced airway hyperresponsiveness and type 2-mediated inflammation in this model supporting the use of recombinant allergens in immune therapy.
Phylogenetic reconstruction of ancestral ecological networks through time for pierid butterflies and their host plants
Authors: Braga Mariana P , Janz Niklas , Nylin Sören , Ronquist Fredrik , Landis Michael J
Published: February 2021

The study of herbivorous insects underpins much of the theory that concerns the evolution of species interactions. In particular, Pieridae butterflies and their host plants have served as a model system for studying evolutionary arms-races. To learn more about the coevolution of these two clades, we reconstructed ancestral ecological networks using stochastic mappings that were generated by a phylogenetic model of host-repertoire evolution. We then measured if, when, and how two ecologically important structural features of the ancestral networks (modularity and nestedness) evolved over time. Our study shows that as pierids gained new hosts and formed new modules, a subset of them retained or recolonized the ancestral host(s), preserving connectivity to the original modules. Together, host-range expansions and recolonizations promoted a phase transition in network structure. Our results demonstrate the power of combining network analysis with Bayesian inference of host-repertoire evolution to understand changes in complex species interactions over time.
GRAFIMO: variant and haplotype aware motif scanning on pangenome graphs
Authors: Tognon Manuel , Bonnici Vincenzo , Garrison Erik , Giugno Rosalba , Pinello Luca
Published: February 2021

Transcription factors (TFs) are proteins that promote or reduce the expression of genes by binding short genomic DNA sequences known as transcription factor binding sites (TFBS). While several tools have been developed to scan for potential occurrences of TFBS in linear DNA sequences or reference genomes, no tool exists to find them in pangenome variation graphs (VGs). VGs are sequence-labelled graphs that can efficiently encode collections of genomes and their variants in a single, compact data structure. Because VGs can losslessly compress large pangenomes, TFBS scanning in VGs can efficiently capture how genomic variation affects the potential binding landscape of TFs in a population of individuals. Here we present GRAFIMO (GRAph-based Finding of Individual Motif Occurrences), a command-line tool for the scanning of known TF DNA motifs represented as Position Weight Matrices (PWMs) in VGs. GRAFIMO extends the standard PWM scanning procedure by considering variations and alternative haplotypes encoded in a VG. Using GRAFIMO on a VG based on individuals from the 1000 Genomes project we recover several potential binding sites that are enhanced, weakened or missed when scanning only the reference genome, and which could constitute individual-specific binding events. GRAFIMO is available as an open-source tool, under the MIT license, athttps://github.com/pinellolab/GRAFIMOandhttps://github.com/InfOmics/GRAFIMO.

Author summary

Transcription factors (TFs) are key regulatory proteins and mutations occurring in their binding sites can alter the normal transcriptional landscape of a cell and lead to disease states. Pangenome variation graphs (VGs) efficiently encode genomes from a population of individuals and their genetic variations. GRAFIMO is an open-source tool that extends the traditional PWM scanning procedure to VGs. By scanning for potential TBFS in VGs, GRAFIMO can simultaneously search thousands of genomes while accounting for SNPs, indels, and structural variants. GRAFIMO reports motif occurrences, their statistical significance, frequency, and location within the reference or alternative haplotypes in a given VG. GRAFIMO makes it possible to study how genetic variation affects the binding landscape of known TFs within a population of individuals.
Machine learning for single cell genomics data analysis
Authors: Raimundo Félix , Papaxanthos Laetitia , Vallot Céline , Vert Jean-Philippe
Published: February 2021

Single-cell omics technologies produce large quantities of data describing the genomic, transcriptomic or epigenomic profiles of many individual cells in parallel. In order to infer biological knowledge and develop predictive models from these data, machine learning (ML)-based model are increasingly used due to their flexibility, scalability, and impressive success in other fields. In recent years, we have seen a surge of new ML-based method development for low-dimensional representations of single-cell omics data, batch normalization, cell type classification, trajectory inference, gene regulatory network inference or multimodal data integration. To help readers navigate this fast-moving literature, we survey in this review recent advances in ML approaches developed to analyze single-cell omics data, focusing mainly on peer-reviewed publications published in the last two years (2019-2020).
Bone Marrow-Derived AXL Tyrosine Kinase Promotes Mitogenic Crosstalk and Cardiac Allograft Vasculopathy
Authors: Glinton Kristofor , DeBerge Matthew , Fisher Emily , Schroth Samantha , Sinha Arjun , Wang Jiao-Jing , Wasserstrom J. Andrew , Ansari Mohammed Javeed , Zhang Zheng Jenny , Feinstein Matthew , Leventhal Joseph R. , Forbess Joseph M. , Lomasney Jon , Luo Xunrong , Thorp Edward B.
Published: February 2021

Cardiac Allograft Vasculopathy (CAV) is a leading contributor to late transplant rejection. Although implicated, the mechanisms by which bone marrow-derived cells promote CAV remain unclear. Emerging evidence implicates the cell surface receptor tyrosine kinase AXL to be elevated in rejecting human allografts. AXL protein is found on multiple cell types, including bone marrow-derived myeloid cells. The causal role of AXL from this compartment and during transplant is largely unknown. This is important because AXL is a key regulator of myeloid inflammation. Utilizing experimental chimeras deficient in the bone marrow-derivedAxl gene, we report thatAxlantagonizes cardiac allograft survival and promotes CAV. Flow cytometric and histologic analyses ofAxl-deficient transplant recipients revealed reductions in both allograft immune cell accumulation and vascular intimal thickness. Co-culture experiments designed to identify cell-intrinsic functions ofAxluncovered complementary cell-proliferative pathways by whichAxlpromotes CAV-associated inflammation. Specifically,Axl-deficient myeloid cells were less efficient at increasing the replication of both antigen-specific T cells and vascular smooth muscle cells (VSMCs), the latter a key hallmark of CAV. For the latter, we discovered thatAxl-was required to amass the VSMC mitogen Platelet-Derived Growth Factor. Taken together, our studies reveal a new role for myeloidAxlin the progression of CAV and mitogenic crosstalk. Inhibition of AXL-protein, in combination with current standards of care, is a candidate strategy to prolong cardiac allograft survival.
High similarity among ChEC-seq datasets
Authors: Mittal Chitvan , Rossi Matthew J. , Pugh B. Franklin
Published: February 2021

ChEC-seq is a method used to identify protein-DNA interactions across a genome. It involves fusing micrococcal nuclease (MNase) to a protein of interest. In principle, specific genome-wide interactions of the fusion protein with chromatin result in local DNA cleavages that can be mapped by DNA sequencing. ChEC-seq has been used to draw conclusions about broad gene-specificities of certain protein-DNA interactions. In particular, the transcriptional regulators SAGA, TFIID, and Mediator are reported to generally occupy the promoter/UAS of genes transcribed by RNA polymerase II in yeast. Here we compare published yeast ChEC-seq data performed with a variety of protein fusions across essentially all genes, and find high similarities with negative controls. We conclude that ChEC-seq patterning for SAGA, TFIID, and Mediator differ little from background at most promoter regions, and thus cannot be used to draw conclusions about broad gene specificity of these factors.
Focused X-ray Luminescence Computed Tomography using a Continuous Scanning Scheme
Authors: Lun Michael C. , Fang Yile , Li Changqing
Published: February 2021

X-ray luminescence computed tomography (XLCT) imaging is a hybrid molecular imaging modality combining the merits of both conventional x-ray imaging (high spatial resolution) and optical imaging (high measurement sensitivity). The narrow x-ray beam based XLCT imaging has been shown to be promising. However due to the selective excitation scheme, the imaging speed is slow thus limiting its practical applications forin vivoimaging. In this work, we have introduced a continuous scanning scheme to acquire data for each angular projection in one motion, eliminating the previous stepping scheme and reducing the data acquisition time, which makes it feasible for multiple transverse scans for three-dimensional (3D) imaging. We have introduced a high accuracy vertical stage to our focused x-ray beam based XLCT imaging system to perform high-resolution and 3D XLCT imaging. We have also included a scintillator crystal coupled to a PMT to act as a single-pixel detector for boundary detection purposes to replace our previous flat panel x-ray detector. We have verified the feasibility of our proposed scanning scheme and imaging system by performing phantom experimental studies. A phantom was embedded with a set of cylindrical targets with 200 µm edge-to-edge distance and was scanned in our imaging system with the proposed method. To test the feasibility for 3D scanning, we took measurements from 4 transverse slices with a vertical step size of 1 mm. The results of the experiments verified the feasibility of our proposed method to perform 3D XLCT imaging using a narrow x-ray beam in a reasonable time.
Practical selection of representative sets of RNA-seq samples using a hierarchical approach
Authors: Tung Laura H. , Kingsford Carl
Published: February 2021

Despite numerous RNA-seq samples available at large databases, most RNA-seq analysis tools are evaluated on a limited number of RNA-seq samples. This drives a need for methods to select a representative subset from all available RNA-seq samples to facilitate comprehensive, unbiased evaluation of bioinformatics tools. In sequence-based approaches for representative set selection (e.g. a k-mer counting approach that selects a subset based on k-mer similarities between RNA-seq samples), because of the huge number of available RNA-seq samples and the large number of k-mers/sequences in each sample, computing the full similarity matrix between all samples using k-mers/sequences for the entire set of RNA-seq samples in a large database (e.g. the SRA) has memory and runtime challenges, making direct representative set selection infeasible with limited computing resources. Therefore, we developed a novel computational method called “hierarchical representative set selection” to handle this challenge. Hierarchical representative set selection is a divide-and-conquer-like algorithm that breaks the representative set selection into sub-selections and hierarchically selects representative samples through multiple levels. We demonstrate that hierarchical representative set selection can achieve performance close to that of direct representative set selection, while largely reducing the runtime and memory requirements of computing the full similarity matrix (up to 8.4X runtime reduction and 4.7X memory reduction for 10000 samples that could be practically run with direct subset selection). We show that hierarchical representative set selection substantially outperforms random sampling on the entire SRA set of RNA-seq samples, making it a practical solution to representative set selection on large databases such as the SRA.
On the robustness of inference of association with the gut microbiota in stool, swab and mucosal tissue samples
Authors: Sun Shan , Zhu Xiangzhu , Huang Xiang , Murff Harvey J. , Ness Reid M. , Seidner Douglas L. , Sorgen Alicia , Blakley Ivory , Yu Chang , Dai Qi , Azcarate-Peril M. Andrea , Shrubsole Martha J. , Fodor Anthony A.
Published: February 2021

The gut microbiota plays an important role in human health and disease. Stool, swab and mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. We previously reported differences in microbial community composition with 16S rRNA amplicon sequencing between stool, swab and mucosal tissue samples. Here, we extended the previous study to a larger cohort and performed shotgun metagenome sequencing of 1,397 stool, swab and mucosal tissue samples from 240 participants. Consistent with previous results, taxonomic composition of stool and swab samples was distinct, but still more similar to each other than mucosal tissue samples, which had a substantially different community composition, characterized by a high relative abundance of the mucus metabolizersBacteroidesandSubdoligranulum,as well as bacteria with higher tolerance for oxidative stress such asEscherichia. As has been previously reported, functional profiles were more uniform across sample types than taxonomic profiles with differences between stool and swab samples smaller, but mucosal tissue samples remained distinct from the other two types. When the taxonomic and functional profiles of different sample types were used for inference in association with host phenotypes of age, sex, body mass index (BMI), antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs) use, hypothesis testing using either stool or swab gave broadly similar results, but inference performed on mucosal tissue samples gave results that were generally less consistent with either stool or swab. Our study represents an important resource for the experimental design of studies aimed to understand microbiota perturbations specific to defined micro niches within the human intestinal tract.
SARS-CoV-2 ORF7b: is a bat virus protein homologue a major cause of COVID-19 symptoms?
Authors: Fogeron Marie-Laure , Montserret Roland , Zehnder Johannes , Nguyen Minh-Ha , Dujardin Marie , Brigandat Louis , Cole Laura , Ninot-Pedrosa Marti , Lecoq Lauriane , Meier Beat H , Böckmann Anja
Published: February 2021

ORF7b is an accessory protein of SARS-CoV-2, the virus behind the COVID-19 pandemic. Using cell-free synthesized ORF7b, we experimentally show that ORF7b assembles into stable multimers. The ORF7b sequence shows a transmembrane segment, which multimerizes through a leucine zipper. We hypothesize that ORF7b has the potential to interfere with important cellular processes that involve leucine-zipper formation, and present two particularly striking examples. First, leucine zippers are central in heart rhythm regulation through multimerization of phospholamban in cardiomyocytes. Second, epithelial cell-cell adhesion relies on E-cadherins, which dimerize using a transmembrane leucine zipper. Most common symptoms of SARS-CoV-2 infection, including heart arrythmias, odor loss, impaired oxygen uptake and intestinal problems, up to multiorgan failure, can be rationalized by a possible interference of ORF7b with the functions of these proteins. We ask whether this is pure coincidence, or whether our observations point to disruption by ORF7b of vital processes in COVID-19.
Caprin-1 binding to the critical stress granule protein G3BP1 is regulated by pH
Authors: Schulte Tim , Panas Marc D. , Williams Lucy , Kedersha Nancy , Fleck Jonas Simon , Tan Timothy J.C. , Olsson Anders , Morro Ainhoa Moliner , Hanke Leo , Nilvebrant Johan , Giang Kim Anh , Nygren Per-Åke , Anderson Paul , Achour Adnane , McInerney Gerald M.
Published: February 2021

G3BP is the central hub within the protein-RNA interaction network of stress-induced bio-molecular condensates known as stress granules (SG). The SG-associated proteins Caprin-1 and USP10 exhibit mutually exclusive binding to the structured NTF2-domain of G3BP1, thereby regulating G3BP1-mediated condensation, but with opposite effects: Caprin-1 promotes but USP10 inhibits SG formation. Herein, we present the crystal structure of G3BP1-NTF2 in complex with a Caprin-1 derived short linear motif (SLiM), which provides a molecular understanding for the mutually exclusive binding of USP10 and Caprin-1 to G3BP1. Caprin-1 but not USP10 contacts two G3BP1-NTF2 histidine residues, which was confirmed using biochemical, biophysical and cellular biological binding assays. G3BP1/Caprin-1 interactions disrupted via point mutations resulted in fewer and smaller SG condensates. In addition, biochemical binding assays demonstrated reduced binding of Caprin-1 to G3BP1 at lower pH values. Finally, ratiometric pH sensitive measurements of SGs revealed a substantial drop in pH compared to the adjacent cytosol, suggesting that reduced pH can fine-tune and regulate the G3BP1-mediated interaction network via a NTF2-mediated pH-sensitive SLiM-selection mechanism.