bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of the φCTX-like Pseudomonas aeruginosa phage Dobby isolated from the kidney stone microbiota
Authors: Johnson Genevieve , Wolfe Alan J. , Putonti Catherine
Published: March 2019

Bacteriophages (phages) are vital members of the human microbiota. They are abundant even within low biomass niches of the human body, including the lower urinary tract. While several prior studies have cultured bacteria from kidney stones, this is the first study to explore phages within the kidney stone microbiota. Here we report Dobby, a temperate phage isolated from a strain of

Pseudomonas aeruginosa

cultured from a kidney stone. Dobby is capable of lysing clinical

P. aeruginosa

strains within our collection from the urinary tract. Sequencing was performed producing a 37 152 bp genome that closely resembles the temperate

P. aeruginosa

phage φCTX, a member of the P2 phage group. Dobby does not, however, encode for the cytotoxin CTX. Dobby’s genome was queried against publicly available bacterial sequences identifying 44 other φCTX-like prophages. These prophages are integrated within the genomes of

P. aeruginosa

strains from a variety of environments, including strains isolated from urine samples and other niches of the human body. Phylogenetic analysis suggests that the temperate φCTX phage species is widespread. With the isolation of Dobby, we now have evidence that phages are members of the kidney stone microbiota. Further investigation, however, is needed to determine their abundance and diversity within these communities.
Compromised longevity due to Mycobacterium abscessus pulmonary disease in lungs scarred by tuberculosis
Authors: Singh Urvashi B. , Das Rojaleen , Shrestha Prajowl , Bala Kiran , Pandey Pooja , Verma Santosh Kumar , Gautam Hitender , Story-Roller Elizabeth , Lamichhane Gyanu , Guleria Randeep
Published: March 2019

Structural lung diseases or scarring related to prior infections such as tuberculosis (TB) are risk factors for the development of invasive nontuberculous mycobacterial (NTM) pulmonary infections, such as

Mycobacterium abscessus
.
M. abscessus

is intrinsically resistant to many antibiotics and in vitro susceptibility correlates poorly with clinical response, especially in pulmonary disease. Treatment is often difﬁcult due to the lack of effective antibiotic regimens. We present a case of a 56-year-old male previously treated for TB, with presumed exacerbation, who was diagnosed after much delay with pulmonary

M. abscessus

disease and subsequently failed initial treatment with an empirical antibiotic regimen. When placed on a synergistic combination regimen that included amikacin, linezolid, clarithromycin, ethambutol and faropenem, the patient showed a favourable response and was culture-negative for over 12 months when the treatment was stopped as per American Thoracic Society (ATS) recommendations. Unfortunately, he developed recurrent symptoms and died 9 months after stopping treatment, following an acute exacerbation of fever and respiratory failure.
Dosing regimen of gentamicin and the effect of antenatal steroids on clearance in preterm infants
Authors: Santos Roberto P. , Chang Yin , Oliveira Carlos R. , Adams-Huet Beverly , Gard John , Sanchez Pablo J.
Published: March 2019

Objective

Determine the gentamicin pharmacokinetic and pharmacodynamic (PK/PD) profiles of once daily dosing (ODD) versus every 18-hour (q18h) regimens and to characterize the effect of antenatal steroid on gentamicin clearance (GentCL).

Study Design

Retrospective cohort of preterm infants (≤34 weeks gestation; ≤7 days) who received gentamicin for >48 hours from January 2005 to June 2007. Serum gentamicin peak and trough concentrations were determined, and PK/PD profiles calculated using standard noncompartmental methods.

Result

122 (63%) infants received ODD and 73 (37%) received q18h regimen. Desired gentamicin peak (5 to 12 mcg/mL) and trough (<2 mcg/mL) concentrations were achieved in 80% (95%CI, 72-86) on ODD vs. 47% (95%CI, 36-58) on q18h (p<0.001). Target drug exposure (AUC >72 mcg/mL/hr) was achieved in 73% (89/122) of infants on ODD vs. 22% (16/73) on q18h (p < 0.001). GentCLwas significantly lower in those who receive antenatal steroid (37+/-8 mL/kg/hr vs. 42+/-13 mL/kg/hr,p=0.04)but not affected by postnatal indomethacin treatment (p>0.86).

Conclusion

PK/PD profile of gentamicin is improved by ODD in preterm infants. GentClwas significantly less in infants exposed to antenatal steroids but not in those treated with indomethacin.
Tracking trends in monarch abundances over the 20thcentury is currently impossible using museum records: a response to Boyle et al. (2019)
Authors: Ries Leslie , Zipkin Elise F. , Guralnick Rob P.
Published: March 2019

The onslaught of opportunistic data offers new opportunities to examine biodiversity patterns at large scales. However, the techniques for tracking abundance trends with such data are new and require careful consideration to ensure that variations in sampling effort do not lead to biased estimates. The analysis by Boyle et al. (2019) showing a mid-century increase in monarch abundance followed by a decrease starting in the 1960s used an inappropriate correction with respect to three dimensions of sampling effort: taxonomy, place, and time. When the data presentenced by Boyle et al. (2019) are corrected to account for biases in the collection process, the results of their analyses do not hold. The paucity of data that remain after accounting for spatial and temporal biases suggests that analyses of monarch trends back to the beginning of the 20thare currently not possible. Continued digitization of museum records is needed to provide a firm data basis to estimate population trends.
Diverse commensal E. coli clones and plasmids disseminate antimicrobial resistance genes in domestic animals and children in a semi-rural community in Ecuador
Authors: Salinas Liseth , Cárdenas Paúl , Johnson Timothy J. , Vasco Karla , Graham Jay , Trueba Gabriel
Published: March 2019

The increased prevalence of antimicrobial resistance (AMR) among Enterobacteriaceae has had major clinical and economic impacts in human medicine. Many of the multi-drug resistant (MDR) Enterobacteriaceae found in humans are community-acquired and linked to food animals (i.e. livestock raised for meat and dairy products). In this study, we examined whether numerically dominant, commensal Escherichia coli strains from humans (n=63 isolates) and domestic animals (n=174 isolates) in the same community and with matching phenotypic AMR patterns, were clonally related or shared the same plasmids. We identified 25 multi-drug resistant isolates (i.e. resistant to 3 or more antimicrobial classes) that shared identical phenotypic resistance patterns. We then investigated the diversity of E. coli clones, AMR genes and plasmids carrying the AMR genes using conjugation, replicon typing and whole genome sequencing. None of the MDR E. coli isolates (from children and domestic animals) analyzed were clonal. While the majority of isolates shared the same antimicrobial resistance genes and replicons, DNA sequencing indicated that these genes and replicons were found on different plasmid structures. Our findings suggest that nonclonal resistance gene dissemination is common in this community and that diverse plasmids carrying AMR genes presents a significant challenge for understanding the movement of AMR in a community.

IMPORTANCE

Even though Escherichia coli strains may share nearly identical AMR profiles, AMR genes, and overlap in space and time, the diversity of clones and plasmids challenges to research that aims to identify sources of AMR. Horizontal gene transfer appears to play a much larger role than clonal expansion in the spread of AMR in the community.
Environmental chemical diethylhexyl phthalate alters intestinal microbiota community structure and metabolite profile in mice
Authors: Lei Ming , Menon Rani , Manteiga Sara , Alden Nicholas , Hunt Carrie , Alaniz Robert C. , Lee Kyongbum , Jayaraman Arul
Published: March 2019

Exposure to environmental chemicals during windows of development is a potentially contributing factor in gut microbiota dysbiosis, and linked to chronic diseases and developmental disorders. We used a community-level model of microbiota metabolism to investigate the effects of diethylhexyl phthalate (DEHP), a ubiquitous plasticizer implicated in neurodevelopmental disorders, on the composition and metabolite outputs of gut microbiota in young mice. Administration of DEHP by oral gavage increased the abundance ofLachnoclostridum, while decreasingAkkermansia, Odoribacter, andClostridium sensu stricto. Addition of DEHP toin vitrocultured cecal microbiota increased the abundance ofAlistipes, Paenibacillus, andLachnoclostridium. Untargeted metabolomics showed that DEHP broadly altered the metabolite profile in the culture. Notably, DEHP enhanced the production ofp-cresol, while inhibiting butyrate synthesis. Metabolic model-guided correlation analysis indicated that the likely sources ofp-cresol areClostridiumspecies. Our results suggest that DEHP can directly modify the microbiota to affect production of bacterial metabolites linked with neurodevelopmental disorders.

Importance

Several previous studies have pointed to environmental chemical exposure during windows of development as a contributing factor in neurodevelopmental disorders, and correlated these disorders with microbiota dysbiosis, little is known about how the chemicals specifically alter the microbiota to interfere with development. The findings reported in this paper unambiguously establish that a pollutant linked with neurodevelopmental disorders can directly modify the microbiota to promote the production of a potentially toxic metabolite (p-cresol) that has also been correlated with neurodevelopmental disorders. Further, we use a novel modeling strategy to identify the responsible enzymes and bacterial sources of this metabolite. To the best of our knowledge, the present study is the first to characterize the functional consequence of phthalate exposure on a developed microbiota. Our results suggest that specific bacterial pathways could be developed as diagnostic and therapeutic targets against health risks posed by ingestion of environmental chemicals.
Coxiella burnetii epitope-specific T-cell responses in chronic Q fever patients
Authors: Scholzen Anja , Richard Guilhem , Moise Leonard , Hartman Eva , Bleeker-Rovers Chantal P. , Reeves Patrick M. , Paul Susan Raju , Martin William D. , Groot Anne S. De , Poznansky Mark C. , Sluder Ann E. , Garritsen Anja
Published: March 2019

Infection with Coxiella burnetii, the causative agent of Q fever, can result in life-threatening persistent infection. Reactogenicity hinders worldwide implementation of the only licensed human Q fever vaccine. We previously demonstrated long-lived immunoreactivity in individuals with past symptomatic and asymptomatic Coxiella infection (convalescents) to promiscuous HLA-class II C. burnetii epitopes, providing the basis for a novel T-cell-targeted subunit vaccine. Here we investigated in a cohort of 22 individuals with persistent infection (chronic Q fever) whether they recognize the same set of epitopes, or distinct epitopes that could be candidates for a therapeutic vaccine or aid in the diagnosis of persistent infection.

Individuals with chronic Q fever showed strong class II epitope-specific cultured ELISpot responses largely overlapping with the peptide repertoire identified previously for convalescents. Five additional peptides were recognized more frequently by chronic subjects, but there was no combination of epitopes uniquely recognized by or non-reactive in chronic Q fever subjects. Consistent with more recent/prolonged exposure, we found, however, stronger direct ex vivo responses to whole-cell C. burnetii and individual peptides in direct ELISpot than in convalescents.

In conclusion, we have validated and expanded a previously published set candidate epitopes for a novel T-cell targeted subunit Q fever vaccine in the context of chronic Q fever patients and demonstrated that they successfully mounted a T-cell response comparable to that of convalescents. Finally, we demonstrate that individuals treated for chronic Q fever mount a broader ex vivo response to class II epitopes than convalescents, which could be explored for diagnostic purposes.
Septate junctions regulate gut homeostasis through regulation of stem cell proliferation and enterocyte behavior inDrosophila
Authors: Izumi Yasushi , Furuse Kyoko , Furuse Mikio
Published: March 2019

Smooth septate junctions (sSJs) contribute to the epithelial barrier, which restricts leakage of solutes through the paracellular route of epithelial cells in theDrosophilamidgut. We previously identified three sSJ-associated membrane proteins, Ssk, Mesh, and Tsp2A, and showed that these proteins were required for sSJ formation and intestinal barrier function in the larval midgut. Here, we investigated the roles of sSJs in theDrosophilaadult midgut. Depletion of any of the sSJ-proteins from enterocytes resulted in remarkably shortened lifespan and intestinal barrier dysfunction in flies. Interestingly, the sSJ protein-deficient flies showed intestinal hypertrophy accompanied by accumulation of morphologically abnormal enterocytes. The phenotype was associated with increased stem cell proliferation and activation of the MAP kinase and Jak-Stat pathways in stem cells. Loss of cytokines Unpaired2 and Unpaired3, which are involved in Jak-Stat pathway activation, suppressed the intestinal hypertrophy, but not the increased stem cell proliferation, in flies lacking Mesh. The present findings suggest that SJs play a crucial role in maintaining tissue homeostasis through regulation of stem cell proliferation and enterocyte behavior in theDrosophilaadult midgut.

Summary statement

Depletion of smooth septate junction-associated proteins from enterocytes in theDrosophilaadult midgut results in intestinal hypertrophy accompanied by accumulation of morphologically aberrant enterocytes and increased stem cell proliferation.
Individual variation in the attribution of incentive salience to social cues
Authors: Fitzpatrick Christopher J. , Morrow Jonathan D.
Published: March 2019

Research on the attribution of incentive salience to drug cues has furthered our understanding of drug self-administration in animals as well as drug relapse and craving in humans. The influence of peers and other social cues on drug-seeking has garnered more attention recently, but few studies have investigated the ability of social cues to gain incentive-motivational value. In the present study, a Pavlovian conditioned approach procedure was used to identify rats that are more (sign-trackers) or less (goal-trackers) prone to attribute incentive salience to food reward cues. A novel procedure then employed social ‘peers’ to compare the tendency of sign-trackers and goal-trackers to attribute incentive salience to social reward cues. Social behavior of sign-trackers and goal-trackers was also compared using social interaction and choice tests. Finally, basal levels of plasma oxytocin were measured in sign-trackers and goal-trackers, because oxytocin is known to modulate the mesolimbic reward system and social behavior. Compared to goal-trackers, sign-trackers attributed more incentive salience to social cues and exhibited more prosocial behaviors. No group differences were observed in baseline plasma oxytocin levels. Taken together, these experiments demonstrate a concordance of individual variation in social behavior, the attribution of incentive salience to social cues following peer interaction, and attribution of incentive salience to food cues. This general tendency to attribute motivational value to reward cues has important implications for the pathophysiology of addiction and other disorders of reward learning.
Comparison of real-time PCR and droplet digital PCR for the detection of Xylella fastidiosa in plants
Authors: Dupas Enora , Legendre Bruno , Olivier Valérie , Poliakoff Françoise , Manceau Charles , Cunty Amandine
Published: March 2019

Xylella fastidiosa (Xf) is a quarantine plant pathogen bacterium originating from the Americas and that has emerged in Europe in 2013. Xf can be detected directly on plant macerate using molecular methods such as real-time PCR, which is a sensitive technique. However, some plants may contain components that can act as PCR reaction inhibitors, which can lead to false negative results or an underestimation of the bacterial concentration present in the analyzed plant sample. Droplet digital PCR (ddPCR) is an innovative tool based on the partitioning of the PCR reagents and the DNA sample into thousands of droplets, allowing the quantification of the absolute number of target DNA molecules present in a reaction mixture, or an increase of the detection sensitivity. In this study, a real-time PCR protocol, already used for Xf detection in the framework of official surveys in the European Union, was transferred and optimized for Xf detection using ddPCR. This new assay was evaluated and compared to the initial real-time PCR on five plant matrices artificially inoculated and on naturally infected plants. In our conditions, this new ddPCR enabled the detection of Xf on all artificially inoculated plant macerates with a similar limit of detection, or a slight benefit for Quercus ilex. Moreover, ddPCR improved diagnostic sensitivity as it enabled detection of Xf in samples of Polygala myrtifolia or Q. ilex that were categorized as negative or close to the limit of detection using the real-time PCR. Here, we report for the first time a ddPCR assay for the detection of the bacterium Xf.
Local cortical desynchronization and pupil-linked arousal differentially shape brain states for optimal sensory performance
Authors: Waschke Leonhard , Tune Sarah , Obleser Jonas
Published: March 2019

Instantaneous brain states have consequences for our sensation, perception, and behaviour. Fluctuations in arousal and neural desynchronization likely pose perceptually relevant states. However, their relationship and their relative impact on perception is unclear. We here show that, at the single-trial level in humans, local desynchronization in sensory cortex (expressed as time-series entropy) versus pupil-linked arousal differentially impact perceptual processing. While we recorded electroencephalography (EEG) and pupillometry data, stimuli of a demanding auditory discrimination task were presented into states of high or low desynchronization of auditory cortex via a real-time closed-loop setup. Desynchronization and arousal distinctly influenced stimulus-evoked activity and shaped behaviour displaying an inverted u-shaped relationship: States of intermediate desynchronization elicited minimal response bias and fastest responses, while states of intermediate arousal gave rise to highest response sensitivity. Our results speak to a model in which independent states of local desynchronization and global arousal jointly optimise sensory processing and performance.
A generic deviance detection principle for cortical On/Off responses, omission response, and mismatch negativity
Authors: Chien Shih-Cheng , Maess Burkhard , Knösche Thomas R.
Published: March 2019

Neural responses to sudden changes can be observed in many parts of the sensory pathways at different organizational levels. For example, deviants that violate regularity at various levels of abstraction can be observed as simple On/Off responses of individual neurons or as cumulative responses of neural populations. The cortical deviance-related responses supporting different functionalities (e.g. gap detection, chunking, etc.) seem unlikely to arise from different function-specific neural circuits, given the relatively uniform and self-similar wiring patterns across cortical areas and spatial scales. Additionally, reciprocal wiring patterns (with heterogeneous combinations of excitatory and inhibitory connections) in the cortex naturally speak in favor of a generic deviance detection principle. Based on this concept, we propose a network model consisting of reciprocally coupled neural masses as a blueprint of a universal change detector. Simulation examples reproduce properties of cortical deviance-related responses including the On/Off responses, the omitted-stimulus response (OSR), and the mismatch negativity (MMN). We propose that the emergence of change detectors relies on the involvement of disinhibition. The analysis on network connection settings further suggests a supportive effect of synaptic adaptation and a destructive effect of N-methyl-D-aspartate receptor (NMDA-r) antagonists on change detection. We conclude that the nature of cortical reciprocal wirings gives rise to a whole range of local change detectors supporting the notion of a generic deviance detection principle. Several testable predictions are provided based on the network model. Notably, we predict that the NMDA-r antagonists would generally dampen the cortical Off response, the cortical OSR, and the MMN.
DOCK2 sets the threshold for entry into the virtual memory CD8+T cell compartment by negatively regulating tonic TCR triggering
Authors: Demissie Ezana , Mahajan Vinay S , Alsufyani Faisal , Kumari Sudha , Yuen Grace J , Viswanadham Vinayak , Tran Johnson Q. , Moon James J. , Irvine Darrell J , Pillai Shiv
Published: March 2019

The control of cytoskeletal dynamics by Dedicator of cytokinesis 2 (DOCK2), a hematopoietic cell-specific actin effector protein, has been implicated in TCR signaling and T cell migration. Biallelic mutations inDock2have been identified in patients with a recessive form of combined immunodeficiency with defects in T, B and NK cell activation. Surprisingly, we show here that certain immune functions of CD8+T cells are enhanced in the absence of DOCK2.Dock2-deficient mice have a pronounced expansion of their memory T cell compartment. Bone marrow chimera and adoptive transfer studies indicate that these memory T cells develop in a cell-intrinsic manner following thymic egress. Transcriptional profiling, TCR repertoire analyses and cell surface marker expression indicate thatDock2-deficient naive CD8+T cells directly convert into virtual memory cells without clonal effector T cell expansion. This direct conversion to memory is associated with a selective increase in TCR sensitivity to selfpeptide MHCin vivoand an enhanced response to weak agonist peptidesex vivo. In contrast, the response to strong agonist peptides remains unaltered inDock2-deficient T cells. Collectively, these findings suggest that the regulation of the actin dynamics by DOCK2 enhances the threshold for entry into the virtual memory compartment by negatively regulating tonic TCR triggering in response to weak agonists.
Training propulsion: Locomotor adaptation to accelerations of the trailing limb
Authors: Farrens Andria J. , Marbaker Rachel , Lilley Maria , Sergi Fabrizio
Published: March 2019

Many stroke survivors suffer from hemiparesis, a condition that results in impaired walking ability. Walking ability is commonly assessed by walking speed, which is dependent on propulsive force both in healthy and stroke populations. Propulsive force is determined by two factors: ankle moment and the posture of the trailing limb during push-off. Recent work has used robotic assistance strategies to modulate propulsive force with some success. However, robotic strategies are limited by their high cost and the technical difficulty of fitting and operating robotic devices with stroke survivors in a clinical setting.

We present a new paradigm for goal-oriented gait training that utilizes a split belt treadmill to train both components of propulsive force generation, achieved by accelerating the treadmill belt of the trailing limb during push off. Belt accelerations require subjects to produce greater propulsive force to maintain their position on the treadmill and increases trailing limb angle through increased velocity of the accelerated limb.

We hypothesized that accelerations would cause locomotor adaptation that would result in measurable after effects in the form of increased propulsive force generation. We tested our protocol on healthy subjects at two levels of belt accelerations. Our results show that 79% of subjects significantly increased propulsive force generation, and that larger accelerations translated to larger, more persistent behavioral gains.
A genetic screen using theDrosophila melanogasterTRiP RNAi collection to identify metabolic enzymes required for eye development
Authors: Pletcher Rose C. , Hardman Sara L. , Intagliata Sydney F. , Lawson Rachael L. , Page Aumunique , Tennessen Jason M.
Published: March 2019

The metabolic enzymes that compose glycolysis, the citric acid cycle, and other pathways within central carbon metabolism have emerged as key regulators of animal development. These enzymes not only generate the energy and biosynthetic precursors required to support cell proliferation and differentiation, but also moonlight as regulators of transcription, translation, and signal transduction. Many of the genes associated with animal metabolism, however, have never been analyzed in a developmental context, thus highlighting how little is known about the intersection of metabolism and development. Here we address this deficiency by using theDrosophilaTRiP RNAi collection to disrupt the expression of over 1,100 metabolism-associated genes within cells of the eye imaginal disc. Our screen not only confirmed previous observations that oxidative phosphorylation serves a critical role in the developing eye, but also implicated a host of other metabolic enzymes in the growth and differentiation of this organ. Notably, our analysis revealed a requirement for glutamine and glutamate metabolic processes in eye development, thereby revealing a role of these amino acids in promotingDrosophilatissue growth. Overall, our analysis highlights how theDrosophilaeye can serve as a powerful tool for dissecting the relationship between development and metabolism.
Combining gene network, metabolic, and leaf-level models show means to future-proof soybean photosynthesis under rising CO2
Authors: Kannan Kavya , Wang Yu , Lang Meagan , Challa Ghana S. , Long Stephen P. , Marshall-Colon Amy
Published: March 2019

Global population increase coupled with rising urbanization underlies the predicted need for 60% more food by 2050, but produced on the same amount of land as today. Improving photosynthetic efficiency is a largely untapped approach to addressing this problem. Here, we scale modeling processes from gene expression through photosynthetic metabolism to predict leaf physiology in evaluating acclimation of photosynthesis to rising [CO2]. Model integration with the yggdrasil interface enabled asynchronous message passing between models. The multiscale model of soybean photosynthesis calibrated to physiological measures at ambient [CO2] successfully predicted the acclimatory changes in the photosynthetic apparatus that were observed at 550 ppm [CO2] in the field. We hypothesized that genetic alteration is necessary to achieve optimal photosynthetic efficiency under global change. Flux control analysis in the metabolic system under elevated [CO2] identified enzymes requiring the greatest change to adapt optimally to the new conditions. This predicted that Rubisco was less limiting under elevated [CO2] and should be down-regulated allowing re-allocation of resource to enzymes controlling the rate of regeneration of ribulose-1:5 bisphosphate (RubP). By linking the GRN through protein concentration to the metabolic model it was possible to identify transcription factors (TF) that matched the up- and down-regulation of genes needed to improve photosynthesis. Most striking was TF GmGATA2, which down-regulated genes for Rubisco synthesis while up-regulating key genes controlling RubP regeneration and starch synthesis. The changes predicted for this TF most closely matched the physiological ideotype that the modeling predicted as optimal for the future elevated [CO2] world.
Population genomics of the facultatively asexual duckweedSpirodela polyrhiza
Authors: Ho Eddie , Bartkowska Magdalena , Wright Stephen I. , Agrawal Aneil
Published: March 2019

Clonal propagation allows some plant species to achieve massive population sizes quickly but also reduces the evolutionary independence of different sites in the genome.

We examine genome-wide genetic diversity inSpirodela polyrhiza, a duckweed that reproduces primarily asexually.

We find that this geographically widespread and numerically abundant species has very low levels of genetic diversity. Diversity at nonsynonymous sites relative to synonymous sites is high, suggesting that purifying selection is weak. A potential explanation for this observation is that a very low frequency of sex renders selection in effective. However, there is a pronounced decay in linkage disequilibrium over 40 kb, suggesting that though sex may be rare at the individual level it is not too infrequent at the population level. In addition, neutral diversity is affected by the physical proximity of selected sites, which would be unexpected if sex was exceedingly rare at the population level.

The amount of genetic mixing as assessed by the decay in linkage disequilibrium is not dissimilar from selfing species such asArabidopsis thaliana, yet selection appears to be much less effective in duckweed. We discuss alternative explanations for the signature of weak purifying selection.
Differential N-end rule degradation of RIN4/NOI fragments generated by the AvrRpt2 effector protease
Authors: Goslin Kevin , Eschen-Lippold Lennart , Naumann Christin , Linster Eric , Sorel Maud , Klecker Maria , Marchi Rémi de , Kind Anne , Wirtz Markus , Lee Justin , Dissmeyer Nico , Graciet Emmanuelle
Published: March 2019

The protein RPM1-INTERACTING PROTEIN4 (RIN4) is a central regulator of both layers of plant immunity systems, the so-called pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). RIN4 is targeted by several effectors, including thePseudomonas syringaeprotease effector AvrRpt2. Cleavage of RIN4 by AvrRpt2 generates unstable RIN4 fragments, whose degradation leads to the activation of the resistance protein RPS2 (RESISTANT TO P. SYRINGAE2). Hence, identifying the determinants of RIN4 degradation is key to understanding RPS2-mediated ETI, as well as virulence functions of AvrRpt2. In addition to RIN4, AvrRpt2 cleaves host proteins from the nitrate-induced (NOI) domain family. Although cleavage of NOI-domain proteins by AvrRpt2 may contribute to PTI regulation, the (in)stability of these proteolytic fragments and the determinants that regulate their stability have not been examined. Notably, a common feature of RIN4 and of many NOI-domain protein fragments generated by AvrRpt2 cleavage is the exposure of a new N-terminal residue that is destabilizing according to the N-end rule. Using antibodies raised against endogenous RIN4, we show that the destabilization of AvrRpt2-cleaved RIN4 fragments is independent of the N-end rule pathway (recently renamed N-degron pathway). By contrast, several NOI-domain protein fragments arebona fidesubstrates of the N-degron pathway. The discovery of this novel set of substrates considerably expands the number of proteins targeted for degradation by this ubiquitin-dependent pathway, for which very few physiological substrates are known in plants. Our results also open new avenues of research to understand the role of AvrRpt2 in promoting bacterial virulence.

One sentence summary

Analysis of RIN4/NOI fragments released after cleavage by the bacterial effector protease AvrRpt2 reveals a novel role of the N-end rule in the degradation of NOI-domain proteins, but not of RIN4.
ITGA2is a target of miR-206 promoting cancer stemness and lung metastasis through enhancedACLYandCCND1expression in triple negative breast cancer
Authors: Adorno-Cruz Valery , Hoffmann Andrew D. , Liu Xia , Wray Brian , Keri Ruth A. , Liu Huiping
Published: March 2019

Accumulating evidence demonstrates that cancer stemness is essential for both tumor development and progression, regulated by multi-layer factors at genetic, epigenetic and micro-environmental levels. However, how to target stemness-driven plasticity and eliminate metastasis remains one of the biggest challenges in the clinic. We aim to identify novel molecular mechanisms underlying stemness of triple negative breast cancer (TNBC) which frequently metastasizes to the visceral organs but lacks targeted therapies. Following our previous discovery of miR-206 as an epigenetic suppressor of tumorigenesis and metastasis, we now report that the integrin receptor CD49b-encodingITGA2is an oncogenic target of miR-206 in TNBC.ITGA2knockdown abolished cancer stemness (mammosphere formation, pluripotency marker expression, and FAK phosphorylation), inhibited cell cycling, compromised migration and invasion, and thereby decreasing lung metastasis of TNBC. RNA sequencing analyses of breast cancer cells revealed thatITGA2knockdown inhibits gene expression essential for both classical integrin-regulated pathways (cell cycle, wounding response, protein kinase, etc) and newly identified pathways such as lipid metabolism. Notably,ACLY-encoded ATP citrate lyase is one of the top targets in CD49b-regulated lipid metabolism andCCND1-encoded Cyclin D1 represents regulation of cell cycle and many other pathways. ACLY, known to catalyze the formation of cytosolic acetyl-CoA for fatty acid biosynthesis, is indispensable for cancer stemness. Overexpression ofCCND1rescues the phenotype ofITGA2knockdown-induced cell cycle arrest. High expression levels of theITGA2/ACLY/CCND1axis are correlated with an unfavorable relapse-free survival of patients with high grade breast cancer, in both basal-like and other subtypes. This study identifiesITGA2as a potential therapeutic target of TNBC stemness and metastasis.
Making plants into cost-effective bioreactors for highly active antimicrobial peptides
Authors: Ghidey Meron R , Islam S M Ashiqul , Pruett Grace , Kearney Christopher Michel
Published: March 2019

As antibiotic-resistant bacterial pathogens become an ever-increasing concern, antimicrobial peptides (AMPs) have grown increasingly attractive as alternatives. Potentially, plants could be used as cost-effective AMP bioreactors; however, reported heterologous AMP expression is much lower in plants compared toE. coliexpression systems and often results in plant cytotoxicity, even for AMPs fused to carrier proteins. We wondered if there were a physical factor that made heterologous AMPs difficult to express in plants. Using a meta-analysis of protein databases, we determined that native plant AMPs were significantly less cationic than AMPs native to other taxa. To apply this finding to plant expression, we tested the transient expression of 10 different heterologous AMPs, ranging in charge from +7 to −5, in the the tobacco,Nicotiana benthamiana. We first tested several carrier proteins and were able to express AMPs only with elastin-like polypeptide (ELP). Conveniently, ELP fusion allows for a simple, cost-effective temperature shift purification. Using the ELP system, all five anionic AMPs expressed well, with two at unusually high levels (375 and 563 µg/gfw). Furthermore, antimicrobial activity againstStaphylococcus epidermidiswas an order of magnitude stronger (average MIC = 0.26 µM) than that typically seen for AMPs expressed inE. coliexpression systems. Unexpectedly, this high level of antimicrobial activity was associated with the uncleaved fusion peptide. In contrast, all previous reports of AMPs expressed in both plant andE. coliexpression systems show cleavage from the fusion partner to be required before activity is seen. In summary, we describe a means of expressing AMP fusions in plants in high yield, purified with a simple temperature-shift protocol, resulting in a fusion peptide with high antimicrobial activity, without the need for a peptide cleavage step.
The Distributed Engram
Authors: Feldesh Ran
Published: March 2019

Neural connectionism is a common theoretical abstraction of biological neural networks (1–3) and a basis for common artificial neural networks (4). Yet, it is clear that connectionism abstracts out much of the biological phenomena significant and necessary for many cognitive-driven behaviors, in particular intra-neuronal and inter-neuronal biochemical processes (5–8). This paper presents a model which adds an abstraction of these processes to a standard connectionism-based model. Specifically, a sub-system determines the synaptic weights. The resulting network has plastic synapses during non-learning-related behavior, in sharp contrast with most common models in which synapses are fixed outside of a learning-phase. Some synapses introduce plasticity that is causally related with behavior, while in others the plasticity randomly fluctuates, in correspondence with recent data (9,10). In this model the memory engram is distributed over the biochemical system, in addition to the synapses. The model yields better performance in memory-related tasks compared to a standard recurrent neural network trained with backpropagation.
Whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants
Authors: Zhang Shijie , He Yukun , Liu Huanhuan , Zhai Haoyu , Huang Dandan , Yi Xianfu , Dong Xiaobao , Wang Zhao , Zhao Ke , Zhou Yao , Wang Jianhua , Yao Hongcheng , Xu Hang , Yang Zhenglu , Sham Pak Chung , Chen Kexin , Li Mulin Jun
Published: March 2019

Predicting the functional or pathogenic regulatory variants in the human non-coding genome facilitates the interpretation of disease causation. While numerous prediction methods are available, their performance is inconsistent or restricted to specific tasks, which raises the demand of developing comprehensive integration for those methods. Here, we compile whole genome base-wise aggregations, regBase, that incorporate largest prediction scores. Building on different assumptions of causality, we train three composite models to score functional, pathogenic and cancer driver non-coding regulatory variants respectively. We demonstrate the superior and stable performance of our models using independent benchmarks and show great success to fine-map causal regulatory variants. We believe that regBase database together with three composite models will be useful in different areas of human genetic studies, such as annotation-based casual variant fine-mapping, pathogenic variant discovery as well as cancer driver mutation identification. regBase is freely available athttps://github.com/mulinlab/regBase.
Reconstructing the evolutionary history of a functionally diverse gene family reveals complexity at the genetic origins of novelty
Authors: Koludarov Ivan , Jackson Timothy NW , Suranse Vivek , Pozzi Andrea , Sunagar Kartik , Mikheyev Alexander S
Published: March 2019

Gene duplication is associated with the evolution of many novel biological functions at the molecular level. The dominant view, often referred to as “neofunctionalization”, states that duplications precede many novel gene functions by creating functionally redundant copies which are less constrained than singletons. However, numerous alternative models have been formulated, including some in which novel functions emerge prior to duplication. Unfortunately, few studies have reconstructed the evolutionary history of a functionally diverse gene family sufficiently well to differentiate between these models. Here we examined the evolution of the g2 family of phospholipase A2 (EC 3.1.1.4) in the genomes of 93 species from all major lineages of Vertebrata. This family is evolutionarily important and has been co-opted for a diverse range of functions, including innate immunity and venom. The genomic region in which this family is located is remarkably syntenic. This allowed us to reconstruct all duplication events over hundreds of millions of years of evolutionary history using manual annotation of gene clusters, which enabled the discovery of a large number of previously un-annotated genes. Intriguingly, we found that the same ancestral gene in the phospholipase gene cluster independently acquired novel molecular functions in birds, mammals and snake, and all subsequent expansion of the cluster originates from this locus. This suggests that the locus has a deep ancestral propensity for multiplication, likely conferred by a structural arrangement of genomic material (i.e. the “genomic context” of the locus) that dates back at least the amniote MRCA. These results highlight the underlying complexity of gene family evolution, as well as the historical- and context-dependence of gene family evolution.

Graphical abstract
Engineering strategy and vector library for the rapid generation of modular light-controlled protein-protein interactions
Authors: Tichy Alexandra-Madelaine , Gerrard Elliot J. , Legrand Julien M.D. , Hobbs Robin M. , Janovjak Harald
Published: March 2019

Optogenetics enables the spatio-temporally precise control of cell and animal behaviour. Many optogenetic tools are driven by light-controlled protein-protein-interactions (PPIs) that are repurposed from natural light-sensitive domains (LSDs). Applying light-controlled PPI to new target proteins is challenging because it is difficult to predict whether one the many available LSDs will yield robust light regulation. As a consequence, fusion protein libraries need to be prepared and tested, but methods and platforms to facilitate this process are currently not available. Here, we developed a genetic engineering strategy and vector library for the rapid generation of light-controlled PPIs. The strategy permits fusing a target protein to LSDs efficiently and in two orientations. The public and expandable library contains 29 vectors with blue, green or red light-responsive LSDs many of which have been previously appliedex vivoandin vivo.We demonstrate the versatility of the approach and the necessity for sampling LSDs by generating light-activated caspase-9 (casp9) enzymes. Collectively, this work provides a new resource for optical regulation of a broad range of target proteins in cell and developmental biology.
Efferocytosis perpetuates substance accumulation inside macrophage populations
Authors: Ford Hugh Z. , Zeboudj Lynda , Purvis Gareth S. D. , ten Bokum Annemieke , Zarebski Alexander E. , Bull Joshua A. , Byrne Helen M. , Myerscough Mary R. , Greaves David R.
Published: March 2019

In both cells and animals, cannibalism can transfer harmful substances from the consumed to the consumer. Macrophages are immune cells that consume their own dead via a process called cannibalistic efferocytosis. Macrophages that contain harmful substances are found at sites of chronic inflammation, yet the role of cannibalism in this context remains unexplored. Here we take mathematical and experimental approaches to study the relationship between cannibalistic efferocytosis and substance accumulation in macrophages. Through mathematical modelling, we deduce that substances which transfer between individuals through cannibalism will concentrate inside the population via a coalescence process. This prediction was confirmed for macrophage populations inside a closed system. We used image analysis of whole slide photomicrographs to measure both latex microbead and neutral lipid accumulation inside murine bone marrow-derived macrophages (104 – 105 cells) following their stimulation into an inflammatory state ex vivo. While the total number of phagocytosed beads remained constant, cell death reduced cell numbers and efferocytosis concentrated the beads among the surviving macrophages. Since lipids are also conserved during efferocytosis, these cells accumulated lipid derived from the membranes of dead and consumed macrophages (becoming macrophage foam cells). Consequently, enhanced macrophage cell death increased the rate and extent foam cell formation. Our results demonstrate that cannibalistic efferocytosis perpetuates exogenous (e.g. beads) and endogenous (e.g. lipids) substance accumulation inside macrophage populations. As such, cannibalism has similar detrimental consequences in both cells and animals.
Interleukin-17 and senescence regulate the foreign body response
Authors: Chung Liam , Maestas David , Lebid Andriana , Mageau Ashlie , Rosson Gedge D. , Wu Xinqun , Wolf Matthew T , Tam Ada , Vanderzee Isabel , Wang Xiaokun , Andorko James I , Narain Radhika , Sadtler Kaitlyn , Fan Hongni , Čiháková Daniela , Le Saux Claude Jourdan , Housseau Franck , Pardoll Drew M , Elisseeff Jennifer H.
Published: March 2019

Synthetic biomaterials and medical devices suffer to varying levels from fibrosis via the foreign body response (FBR). To explore mechanistic connections between the immune response and fibrosis from the FBR, we first analyzed fibrotic capsule surrounding human breast implants and found increased numbers of interleukin (IL)17-producing γδ+T cells and CD4+TH17 cells as well as senescent cells. Further analysis in a murine model demonstrated an early innate IL17 response to synthetic implants, mediated by innate lymphoid cells and γδ+T cells, was followed by a chronic adaptive antigen dependent CD4+TH17 cell response. Mice deficient in IL17 signaling established that IL17 was required for the fibrotic response to materials and the development of p16INK4asenescent cells. Treatment with a senolytic agent reduced IL17 expression and fibrosis. Discovery of a feed-forward loop between the TH17 and senescence response to synthetic materials introduces new targets for therapeutic intervention in the foreign body response.
Acid–ammonium heterodimer and N(ammonium)–H...N(pyridine) synthon preference in three salts of nicotinic acid with (1R,2R)-1,2-diphenylethylenediamine
Authors: Han Yang , Fu Qiang , Zhang Peng , Guan Hongyu , Guo Fang
Published: March 2019

Nicotinic acid (NA), known as vitamin B3, has been widely studied in pharmaceutical science. Herein, three salts derived from NA and (1R,2R)-1,2-diphenylethylenediamine (DPEN), including one solvent-free salt (DPEN)(NA)2 and two solvated salts, (DPEN)(NA)2(EA) and (DPEN)(NA)2(ACN) (EA: ethyl acetate, ACN: acetonitrile), have been obtained and characterized by solid-state techniques. By the investigation of single-crystal structures, the synthons, acid–ammonium heterodimer and Nammonium—H...Npyridine between functional groups of 1,2-diphenylethylenediammonium and NA are revealed and further identified using Hirshfeld surface analysis. The utility of the synthons is further demonstrated by making salts with the NA isomer, isonicotinic acid. Here the synthon occurrences in cocrystals/salts of NA (including NA derivatives) and diamine coformers reported in the Cambridge Structure Database (CSD) are compared. The robustness of acid–ammonium heterodimer and Nammonium—H...Npyridine is investigated by a search of the CSD. The NA salts also show their improved solubility in pH 1.2, 4.5 and 6.8 buffer mediums compared with pure NA material.
Quantum pressure focusing in solids: a reconstruction from experimental electron density
Authors: Tsirelson Vladimir G. , Stash Adam I. , Tokatly Ilya V.
Published: March 2019

Here an approach is presented for reconstructing the distribution of electronic internal quantum pressure in the electronic continuum of solids from the experimental electron density. Using the formalism of the density functional theory, the spatial inner-crystal map of the quantum pressure is obtained. The results are visualized via the indicator of quantum pressure focusing (IQPF) which reveals the regions where the pressure is concentrated or depleted due to quantum effects. IQPF contains all quantum electron-shell structure-forming contributions resulting from kinetic, exchange and correlation effects, and presents a clear picture of the chemical bond features in crystals with different type of bonding mechanisms.