bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Supraceliac and Infrarenal Aortic Conduits in Liver Transplantation: Is There a Difference in Patency and Postoperative Renal Dysfunction?
Authors: Livingston David , Lee David D. , Croome Sarah , Burcin Taner C. , Croome Kristopher P.
Published: October 2019

Background.

Aorto-hepatic conduits can provide arterial inflow for liver transplants in cases where the native hepatic artery is unsuitable for use.

Methods.

Clinical outcomes of all patients undergoing liver transplantation (LT) with an aorto-hepatic conduit between 2000 and 2016 were included. Recipients were divided into 2 groups: those with a supraceliac (SC) aortic conduit (N = 22) and those with an infrarenal (IR) aortic conduit (N = 82).

Results.

There was no difference in calculated model for end-stage liver disease score between the 2 groups. The SC group received grafts with a higher mean donor risk index (1.69 versus 1.48; P = 0.02). Early allograft dysfunction was 18.2% in the SC group and 29.3% in the IR group (P = 0.30). In the SC group, 10.5% of patients required initiation of postoperative continuous renal replacement therapy compared to 12.1% of patients in the IR group (P = 0.69). No difference in the rate of postoperative acute kidney injury was seen between the 2 groups (P = 0.54). No significant difference in median creatinine at 1 year was seen between the SC (1.2 mg/dL; IQR 1–1.3) and IR (1.2 mg/dL; IQR 0.9–1.5) groups (P = 0.85). At a median follow-up of 5.3 years, thrombosis of the aortic conduit occurred in 0% of patients in the SC group and 6.1% of patients in the IR group (P = 0.24). Graft survival was not significantly different between the 2 groups (P = 0.47).

Conclusions.

No difference in renal dysfunction as demonstrated by need for post-LT continuous renal replacement therapy, acute kidney injury, or creatinine at 1 year post-LT was seen between SC and IR aortic conduits. A slight trend of higher conduit thrombosis rate was seen with IR compared to SC aortic conduits; however, this did not reach statistical significance. Both SC and IR aortic conduits represent reasonable options when the native hepatic artery is unsuitable for use.
Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii
Authors: Hamidian Mohammad , Nigro Steven J.
Published: October 2019

Acinetobacter baumannii

is a nosocomial pathogen that has emerged as a global threat because of high levels of resistance to many antibiotics, particularly those considered to be last-resort antibiotics, such as carbapenems. Although alterations in the efflux pump and outer membrane proteins can cause carbapenem resistance, the main mechanism is the acquisition of carbapenem-hydrolyzing oxacillinase-encoding genes. Of these, oxa23 is by far the most widespread in most countries, while oxa24 and oxa58 appear to be dominant in specific regions. Historically, much of the global spread of carbapenem resistance has been due to the dissemination of two major clones, known as global clones 1 and 2, although new lineages are now common in some parts of the world. The analysis of all publicly available genome sequences performed here indicates that ST2, ST1, ST79 and ST25 account for over 71 % of all genomes sequenced to date, with ST2 by far the most dominant type and oxa23 the most widespread carbapenem resistance determinant globally, regardless of clonal type. Whilst this highlights the global spread of ST1 and ST2, and the dominance of oxa23 in both clones, it could also be a result of preferential selection of carbapenem-resistant strains, which mainly belong to the two major clones. Furthermore, ~70 % of the sequenced strains have been isolated from five countries, namely the USA, PR China, Australia, Thailand and Pakistan, with only a limited number from other countries. These genomes are a vital resource, but it is currently difficult to draw an accurate global picture of this important superbug, highlighting the need for more comprehensive genome sequence data and genomic analysis.
Microbe Profile: Pseudomonas aeruginosa: opportunistic pathogen and lab rat
Authors: Diggle Stephen P. , Whiteley Marvin
Published: October 2019

Pseudomonas aeruginosa

is a Gram-negative opportunistic pathogen and a model bacterium for studying virulence and bacterial social traits. While it can be isolated in low numbers from a wide variety of environments including soil and water, it can readily be found in almost any human/animal-impacted environment. It is a major cause of illness and death in humans with immunosuppressive and chronic conditions, and infections in these patients are difficult to treat due to a number of antibiotic resistance mechanisms and the organism’s propensity to form multicellular biofilms.
Molecular point-of-care testing for influenza A/B and respiratory syncytial virus: comparison of workflow parameters for the ID Now and cobas Liat systems
Authors: Young Stephen , Phillips Jamie , Griego-Fullbright Christen , Wagner Aaron , Jim Patricia , Chaudhuri Sheena , Tang Shaowu , Sickler Joanna
Published: October 2019

Aims

Point-of-care (POC) tests for influenza and respiratory syncytial virus (RSV) offer the potential to improve patient management and antimicrobial stewardship. Studies have focused on performance; however, no workflow assessments have been published comparing POC molecular tests. This study compared the Liat and ID Now systems workflow, to assist end-users in selecting an influenza and/or RSV POC test.

Methods

Staffing, walk-away, and turnaround time (TAT) of the Liat and ID Now systems were determined using 40 nasopharyngeal samples, positive for influenza or RSV. The ID Now system requires separate tests for influenza and RSV, so parallel (two instruments) and sequential (one instrument) workflows were evaluated.

Results

The ID Now ranged 4.1–6.2 minutes for staffing, 1.9–10.9 minutes for walk-away and 6.4–15.8 minutes for TAT per result. The Liat ranged 1.1–1.8 minutes for staffing, 20.0–20.5 minutes for walk-away and 21.3–22.0 minutes for TAT. Mean walk-away time comprised 38.0% (influenza positive) and 68.1% (influenza negative) of TAT for ID Now and 93.7% (influenza/RSV) for Liat. The ID Now parallel workflow resulted in medians of 5.9 minutes for staffing, 9.7 minutes for walk-away, and 15.6 minutes for TAT. Assuming prevalence of 20% influenza and 20% RSV, the ID Now sequential workflow resulted in medians of 9.4 minutes for staffing, 17.4 minutes for walk-away, and 27.1 minutes for TAT.

Conclusions

The ID Now and Liat systems offer different workflow characteristics. Key considerations for implementation include value of both influenza and RSV results, clinical setting, staffing capacity, and instrument(s) placement.
A Multiomics Approach to Heterogeneity in Alzheimer’s Disease: Focused Review and Roadmap
Authors: Badhwar AmanPreet , McFall G. Peggy , Sapkota Shraddha , Black Sandra E. , Chertkow Howard , Duchesne Simon , Masellis Mario , Li Liang , Dixon Roger A. , Bellec Pierre
Published: October 2019

Etiological and clinical heterogeneity is increasingly recognized as a common characteristic of Alzheimer’s disease and related dementias. This heterogeneity complicates diagnosis, treatment, and the design and testing of new drugs. An important line of research is discovery of multimodal biomarkers that will facilitate the targeting of subpopulations with homogeneous pathophysiological signatures. High-throughput ‘omics’ are unbiased data driven techniques that probe the complex etiology of Alzheimer’s disease from multiple levels (e.g. network, cellular, and molecular) and thereby account for pathophysiological heterogeneity in clinical populations. This review focuses on data reduction analyses that identify complementary disease-relevant perturbations for three omics techniques: neuroimaging-based subtypes, metabolomics-derived metabolite panels, and genomics-related polygenic risk scores. Neuroimaging can track accrued neurodegeneration and other sources of network impairments, metabolomics provides a global small-molecule snapshot that is sensitive to ongoing pathological processes, and genomics characterizes relatively invariant genetic risk factors representing key pathways associated with Alzheimer’s disease. Following this focused review, we present a roadmap for assembling these multiomics measurements into a diagnostic tool highly predictive of individual clinical trajectories, to further the goal of personalized medicine in Alzheimer’s disease.
Depletion of erythropoietic miR-486-5p and miR-451a improves detectability of rare microRNAs in peripheral blood-derived small RNA sequencing libraries
Authors: Juzenas Simonas , Lindqvist Carl Mårten , Ito Go , Dolshanskaya Yewgenia , Halfvarson Jonas , Franke Andre , Hemmrich-Stanisak Georg
Published: October 2019

Erythroid-specific miR-451a and miR-486-5p are two of the most dominant microRNAs (miRNAs) in human peripheral blood. In small RNA sequencing libraries, their overabundance reduces diversity as well as complexity and consequently causes negative effects such as missing detectability and inaccurate quantification of low abundant miRNAs. Here we present a simple, cost-effective and easy to implement hybridization-based method to deplete these two erythropoietic miRNAs from blood-derived RNA samples. By utilization of blocking oligonucleotides, this method provides a highly efficient and specific depletion of miR-486-5p and miR-451a, which leads to a considerable increase of measured expression as well as detectability of low abundant miRNA species. The blocking oligos are compatible with common 5’ ligation-dependent small RNA library preparation protocols, including commercially available kits, such as Illumina TruSeq and Perkin Elmer NEXTflex. Furthermore, the here described method and oligo design principle can be easily adapted to target many other miRNA molecules, depending on context and research question.
The diversity and distribution of endophytes across biomes, plant phylogeny, and host tissues—how far have we come and where do we go from here?
Authors: Harrison Joshua G. , Griffin Eric A.
Published: October 2019

The interiors of plants are colonized by diverse microorganisms that are referred to as endophytes. Endophytes have received much attention over the past few decades, yet many questions remain unanswered regarding patterns in their biodiversity at local to global scales. To characterize research effort to date, we synthesized results from ∼600 published studies. Our survey revealed a global research interest and highlighted several gaps in knowledge. For instance, of the seventeen biomes encompassed by our survey, seven were understudied and together composed only 7% of the studies that we considered. We found that fungal endophyte diversity has been characterized in at least one host from 30% of embryophyte families, while bacterial endophytes have been surveyed in hosts from only 10.5% of families. We complimented our survey with a vote counting procedure to determine endophyte richness patterns among plant tissue types. We found that variation in endophyte assemblages in above-ground tissues varied with host growth habit. Stems were the richest tissue in woody plants, whereas roots were the richest tissue in graminoids. For forbs, we found no consistent differences in relative tissue richness among studies. We propose future directions to fill the gaps in knowledge we uncovered and inspire further research.

Originality-Significance Statement

Much remains to be learned regarding the biodiversity and distribution of the microbes that colonize the interiors of plants. Here, we surveyed approximately 600 publications to characterize gaps in knowledge and provide a roadmap for future research. We compared biomes, plant families, and geographical regions in terms of the research interest that they have garnered. Additionally, we synthesized published results and report that variation in endophyte richness among plant tissue types is a function of host growth habit. Stems were the richest tissue in woody plants, whereas roots were the richest tissue in graminoids. We hope to inspire research to fill the gaps in knowledge that we uncovered.
HSP110 dependent HSP70 disaggregation machinery mediates prion-like propagation of amyloidogenic proteins in metazoa
Authors: Tittelmeier Jessica , Sandhof Carl Alexander , Ries Heidrun Maja , Druffel-Augustin Silke , Mogk Axel , Bukau Bernd , Nussbaum-Krammer Carmen
Published: October 2019

The gradual accumulation and prion-like propagation of α-synuclein and other amyloidogenic proteins is associated with devastating neurodegenerative diseases. The metazoan disaggregation machinery, a specific combination of HSP70 and its co-chaperones, is able to disassemble α-synuclein fibrils in vitro, but the physiological consequence in vivo is unknown. To explore this, we used Caenorhabditis elegans models that exhibit pathological features of α-synuclein, such as misfolding, intercellular spreading and toxicity. We inhibited the HSP70 disaggregase by depleting the crucial component HSP-110 and monitored the effect on α-synuclein related phenotypes. The knockdown of HSP-110 not only impaired HSP70 disaggregation activity and prevented the resolubilization of amorphous heat shock induced firefly luciferase aggregates, but also compromised the cellular folding capacity. In stark contrast, HSP-110 depletion reduced α-synuclein foci formation, cell-to-cell transmission and toxicity. Similar effects were observed for a polyQ model substrate, confirming that inhibition of HSP70 disaggregation function mitigates amyloid toxicity. These data demonstrate that the metazoan HSP70 disaggregation complex plays a critical role in the prion-like propagation of amyloid-type conformers. Therefore, the HSP70 disaggregation activity is a double-edged sword as it is essential for the maintenance of cellular proteostasis while being involved in the generation of toxic amyloid-type protein species.
SalmonellaEnhances Osteogenic Differentiation in Adipose-Derived Mesenchymal Stem Cells
Authors: Foutouhi Soraya H. , Mohamad-Fauzi Nuradilla , Storey Dylan Bobby , Foutouhi Azarene A. , Kong Nguyet , Kol Amir , Borjesson Dori , Desai Prerak , Shah Jigna , Murray James D. , Weimer Bart C.
Published: October 2019

The potential of mesenchymal stem cells (MSCs) for tissue repair and regeneration has garnered great attention. While MSC interaction with microbes at sites of tissue damage and inflammation is likely, especially in the gut, the consequences of bacterial association have yet to be elucidated. This study investigated the effect ofSalmonella entericasspentericaserotype Typhimurium on MSC trilineage differentiation path and mechanism. Through examination of key markers of differentiation, immunomodulatory regulators, and inflammatory cytokines, we demonstrated thatSalmonellaaltered osteogenic and chondrogenic differentiation pathways in human and goat adipose-derived MSCs. Gene expression profiles defined signaling pathway alterations in response toSalmonellaassociation not observed in epithelial cells. We uncovered significant differential expression (P< 0.05) of genes associated with anti-apoptotic and pro-proliferative responses in MSCs duringSalmonellachallenge. These observations led us to conclude that bacteria, specificallySalmonella,induce pathways that influence functional differentiation trajectories in MSCs, thus implicating substantial microbial influence on MSC physiology and immune activity.
Recurrent neural network models of multi-area computation underlying decision-making
Authors: Kleinman Michael , Chandrasekaran Chandramouli , Kao Jonathan C.
Published: October 2019

Cognition emerges from coordinated computations across multiple brain areas. However, elucidating these computations within and across brain regions is challenging because intra- and inter-area connectivity are typically unknown. To study coordinated computation, we trained multi-area recurrent neural networks (RNNs) to discriminate the dominant color of a checker-board and output decision variables reflecting a direction decision, a task previously used to investigate decision-related dynamics in dorsal premotor cortex (PMd) of monkeys. We found that multi-area RNNs, trained with neurophysiological connectivity constraints and Dale’s law, recapitulated decision-related dynamics observed in PMd. The RNN solved this task by a dynamical mechanism where the direction decision was computed and outputted, via precisely oriented dynamics, on an axis that was nearly orthogonal to checkerboard color inputs. This orthogonal direction information was preferentially propagated through alignment with inter-area connections; in contrast, color information was filtered. These results suggest that cortex uses modular computation to generate minimal sufficient representations of task information. Finally, we used multi-area RNNs to produce experimentally testable hypotheses for computations that occur within and across multiple brain areas, enabling new insights into distributed computation in neural systems.
Phenotypic differences in reversible attachment behavior reveal distinctP. aeruginosasurface colonization strategies
Authors: Lee Calvin K. , Vachier Jérémy , Anda Jaime de , Zhao Kun , Baker Amy E. , Bennett Rachel R. , Armbruster Catherine R. , Lewis Kimberley A. , Tarnopol Rebecca L. , Lomba Charles J. , Hogan Deborah A. , Parsek Matthew R. , O’Toole George A. , Golestanian Ramin , Wong Gerard C. L.
Published: October 2019

Despite possessing the machinery to sense, adhere to, and proliferate on surfaces, it is commonly observed that bacteria initially have a difficult time attaching to a surface. Before forming a bacterial biofilm, planktonic bacteria exhibit a random period of transient surface attachment known as “reversible attachment” which is poorly understood. Using community tracking methods at single-cell resolution, we examine how reversible attachment progresses during initial stages of surface sensing.Pseudomonas aeruginosastrains PAO1 and PA14, which exhibit similar exponential trends of surface cell population increase, show unanticipated differences when the behavior of each cell was considered at the full lineage level and interpreted using the unifying quantitative framework of an exactly solvable stochastic model. Reversible attachment comprises two regimes of behavior, processive and nonprocessive, corresponding to whether cells of the lineage stay on the surface long enough to divide, or not, before detaching. Stark differences between PAO1 and PA14 in the processive regime of reversible attachment suggest the existence of two complementary surface colonization strategies, which are roughly analogous to “immediate-” vs “deferred-gratification” in a prototypical cognitive-affective processing system. PAO1 lineages commit relatively quickly to a surface compared to PA14 lineages. PA14 lineages allow detaching cells to retain memory of the surface so that they are primed for improved subsequent surface attachment. In fact, it is possible to identify motility suppression events in PA14 lineages in the process of surface commitment. We hypothesize that these contrasting strategies are rooted in downstream differences between Wsp-based and Pil-Chp-based surface sensing systems.
Smoothened receptor Signaling regulates the developmental shift of GABA polarity in rat somatosensory cortex
Authors: Delmotte Quentin , Medina Igor , Hamze Mira , Buhler Emmanuelle , Zhang Jinwei , Belgacem Yesser H. , Porcher Christophe
Published: October 2019

Sonic Hedgehog (Shh) and its patched-smoothened receptor complex control a variety of functions in the developing central nervous system (CNS) such as neural cell proliferation and differentiation. Recently, Shh signaling components have been found to be expressed at the synaptic level in the postnatal brain, suggesting a potential role in the regulation of synaptic transmission. Usingin uteroelectroporation of constitutively active and dominant-negative forms of the Shh co-receptor smoothened (Smo), we studied the role of Smo signaling in the development and maturation of GABAergic transmission in the somatosensory cortex. Our results show that enhancing Smo activity during development accelerates the shift from depolarizing to hyperpolarizing GABA in dependence on functional expression of potassium-chloride cotransporter type 2 (KCC2). On the other hand, blocking Smo activity maintains GABA response in a depolarizing state in mature cortical neurons resulting in altered chloride homeostasis and increased seizure susceptibility. This study reveals an unexpected function of Smo signaling on the regulation of chloride homeostasis through the control of KCC2 cell surface stability and on the timing of the GABA inhibitory/excitatory shift in brain maturation.

Summary statement

The smoothened receptor controls the time course of inhibitory transmission through the stability of the potassium-chloride cotransporter type 2 at the plasma membrane.
Asymmetric Gait Patterns Alter the Reactive Control of Intersegmental Coordination Patterns during Walking
Authors: Liu Chang , Finley James M.
Published: October 2019

Recovery from perturbations during walking is primarily mediated by reactive control strategies that coordinate multiple body segments to maintain balance. Balance control is often impaired in clinical populations who walk with spatiotemporally asymmetric gait, and, as a result, rehabilitation efforts often seek to reduce asymmetries in these populations. Previous work has demonstrated that the presence of spatiotemporal asymmetries during walking does not impair the control of whole-body dynamics during perturbation recovery. However, it remains to be seen how the neuromotor system adjusts intersegmental coordination patterns to maintain invariant whole-body dynamics. Here, we determined if the neuromotor system generates stereotypical coordination patterns irrespective of the level of asymmetry or if the neuromotor system allows for variance in intersegmental coordination patterns to stabilize whole-body dynamics. Nineteen healthy participants walked on a dual-belt treadmill at a range of step length asymmetries, and they responded to unpredictable, slip-like perturbations. We used principal component analysis of segmental angular momenta to characterize intersegmental coordination patterns before, during, and after imposed perturbations. We found that two principal components were sufficient to explain ~ 95% of the variance in segmental angular momentum during both steading walking and responses to perturbations. Our results also revealed that walking with asymmetric step lengths led to changes in intersegmental coordination patterns during the perturbation and during subsequent recovery steps without affecting whole-body angular momentum. These results suggest that the nervous system allows for variance in segment-level coordination patterns to maintain invariant control of whole-body angular momentum during walking. Future studies exploring how these segmental coordination patterns change in individuals with asymmetries that result from neuromotor impairments can provide further insight into how the healthy and impaired nervous system regulates dynamic balance during walking.
Fetal liver hepcidin secures iron stores in utero
Authors: Kämmerer Lara , Mohammad Goran , Wolna Magda , Robbins Peter A. , Lakhal-Littleton Samira
Published: October 2019

In the adult, the liver-derived hormone hepcidin (HAMP) controls systemic iron levels by blocking the iron-exporting protein ferroportin (FPN) in the gut and spleen, the sites of iron absorption and recycling respectively. Impaired HAMP expression or FPN responsiveness to HAMP result in iron overload. HAMP is also expressed in the fetal liver but its role in controlling fetal iron stores is not understood. To address this question in a manner that safeguards against the confounding effects of altered maternal iron homeostasis, we generated fetuses harbouring a paternally-inherited ubiquitous knock-in of the HAMP-resistantfpnC326Y. Additionally, to safeguard against any confounding effects of altered placental iron homeostasis, we generated fetuses with a liver-specific knock-in offpnC326Y or knockout of thehampgene. These fetuses had reduced liver iron stores, and markedly increased FPN in the liver, but not in the placenta. Thus, in contrast to the adult, fetal liver HAMP operates cell-autonomously to increase fetal liver iron stores. Our findings also suggest that FPN in the placenta is permissive rather than regulatory of iron transport.
High-resolution micro-epidemiology of parasite spatial and temporal dynamics in a high malaria transmission setting in Kenya
Authors: Nelson Cody S. , Sumner Kelsey M. , Freedman Elizabeth , Saelens Joseph W. , Obala Andrew A. , Mangeni Judith N. , Taylor Steve M. , O’Meara Wendy P.
Published: October 2019

Novel interventions that leverage the heterogeneity of parasite transmission are needed to push malaria further towards elimination. To better understand spatial and temporal dynamics of transmission, we applied amplicon NGS of two polymorphic gene regions (csp and ama1) to a cohort identified via reactive case detection in a high-transmission setting in western Kenya. From 4/2013–6/2014, we enrolled 442 symptomatic children with malaria, 442 matched controls, and all household members of both groups. We evaluated genetic similarity between infected individuals using three novel indices: sharing of parasite haplotypes on binary and proportional scales and the L1 norm. Symptomatic children more commonly shared haplotypes with their own household members. Furthermore, we identified robust temporal structuring of parasite genetic similarity that we exploited to identify the molecular signature of an outbreak. These findings of both micro- and macro-scale organization of parasite populations might be harnessed to inform next-generation malaria control measures.
Transcriptomics at maize embryo/endosperm interfaces identify a novel transcriptionally distinct endosperm sub-domain adjacent to the embryo scutellum (EAS)
Authors: Doll Nicolas M. , Just Jeremy , Brunaud Véronique , Caïus José , Grimault Aurélie , Depège-Fargeix Nathalie , Esteban Eddi , Pasha Asher , Provart Nicholas J. , Ingram Gwyneth C. , Rogowsky Peter M. , Widiez Thomas
Published: October 2019

Seeds are complex biological systems comprising three genetically distinct tissues nested one inside another (embryo, endosperm and maternal tissues). However, the complexity of the kernel makes it difficult to understand inter compartment interactions without access to spatially accurate information. Here we took advantage of the large size of the maize kernel to characterize genome-wide expression profiles of tissues at embryo/endosperm interfaces. Our analysis identifies specific transcriptomic signatures in two interface tissues compared to whole seed compartments: The scutellar aleurone layer (SAL), and the newly named endosperm adjacent to scutellum (EAS). The EAS, which appears around 9 days after pollination and persists for around 11 days, is confined to one to three endosperm cell layers adjacent to the embryonic scutellum. Its transcriptome is enriched in genes encoding transporters. The absence of the embryo in anembryo specific(emb) mutant can alter the expression pattern of EAS marker genes. The detection of cell death in some EAS cells together with an accumulation of crushed cell walls suggests that the EAS is a dynamic zone from which cell layers in contact with the embryo are regularly eliminated, and to which additional endosperm cells are recruited as the embryo grows.
Specialization of the Chromatin Remodeler RSC to Mobilize Partially-Unwrapped Nucleosomes
Authors: Schlichter Alisha , Kasten Margaret M. , Parnell Timothy J. , Cairns Bradley R.
Published: October 2019

SWI/SNF-family chromatin remodeling complexes, such as S. cerevisiae RSC, slide and eject nucleosomes to regulate transcription. Within nucleosomes, stiff DNA sequences confer spontaneous partial unwrapping, prompting whether and how SWI/SNF-family remodelers are specialized to remodel partially-unwrapped nucleosomes. RSC1 and RSC2 are orthologs of mammalian PBRM1 (polybromo) which define two separate RSC sub-complexes. Remarkably, in vitro the Rsc1-containing complex remodels partially-unwrapped nucleosomes much better than does the Rsc2-containing complex. Moreover, a rsc1Δ mutation, but not rsc2Δ, is lethal with histone mutations that confer partial unwrapping. Rsc1/2 isoforms both cooperate with the DNA-binding proteins Rsc3/30 and the HMG protein, Hmo1, to remodel partially-unwrapped nucleosomes, but show differential reliance on these factors. Notably, genetic impairment of these factors strongly reduces the expression of genes with wide nucleosome-deficient regions (e.g. ribosomal protein genes), known to harbor partially-unwrapped nucleosomes. Taken together, Rsc1/2 isoforms are specialized through composition and interactions to manage and remodel partially-unwrapped nucleosomes.
Shigella sonneiO-antigen inhibits internalisation, vacuole escape and inflammasome activation
Authors: Watson Jayne L , Sanchez-Garrido Julia , Goddard Philippa J , Torraca Vincenzo , Mostowy Serge , Shenoy Avinash R , Clements Abigail
Published: October 2019

TwoShigellaspecies,flexneriandsonnei, cause approximately 90% of bacterial dysentery worldwide. WhileS. flexneriis the dominant species in low-income countries,S. sonneicauses the majority of infections in middle and high-income countries.S. flexneriis a prototypic cytosolic bacterium; once intracellular it rapidly escapes the phagocytic vacuole and causes pyroptosis of macrophages, which is important for pathogenesis and bacterial spread. By contrast little is known about the invasion, vacuole escape and induction of pyroptosis duringS. sonneiinfection of macrophages. We demonstrate thatS. sonneicauses substantially less pyroptosis in human primary monocyte-derived macrophages and THP1 cells. This is due to reduced bacterial uptake and lower relative vacuole escape, which results in fewer cytosolicS. sonneiand hence reduced activation of caspase-1 inflammasomes. Mechanistically, the O-antigen, which inS. sonneiis contained in both the lipopolysaccharide and the capsule, was responsible for reduced uptake and the T3SS was required for vacuole escape. Our findings suggest thatS. sonneihas adapted to an extracellular lifestyle by incorporating additional O-antigen into its surface structures compared to otherShigellaspecies.
Relaxed constraint and functional divergence of the progesterone receptor (PGR) in the human stem-lineage
Authors: Marinić Mirna , Lynch Vincent J.
Published: October 2019

The steroid hormone progesterone, acting through the progesterone receptor (PR), a ligand-activated DNA-binding transcription factor, plays an essential role in regulating nearly every aspect of female reproductive biology. While many reproductive traits regulated by PR are conserved in mammals, Catarrhine primates evolved several derived traits including spontaneous decidualization, menstruation, and a divergent (and unknown) parturition signal, suggesting that PR may also have evolved divergent functions in Catarrhines. There is conflicting evidence, however, whether the progesterone receptor gene (PGR) was positively selected in the human lineage. Here we show thatPGRevolved rapidly in the human stem-lineage (as well as other Catarrhine primates), which likely reflects an episode of relaxed selection intensity rather than positive selection. Coincident with the episode of relaxed selection intensity, ancestral sequence resurrection and functional tests indicate that the major human PR isoforms (PR-A and PR-B) evolved divergent functions in the human stem-lineage. These results suggest that the regulation of progesterone signaling by PR-A and PR-B may also have diverged in the human lineage and that non-human animal models of progesterone signaling may not faithfully recapitulate human biology.
Fatty acid oxidation impairs macrophage effector functions that controlMycobacterium tuberculosis
Authors: Chandra Pallavi , He Li , Zimmerman Matthew , Yang Guozhe , Köster Stefan , Ouimet Mireille , Wang Han , Moore Kathyrn J. , Dartois Véronique , Schilling Joel D. , Philips Jennifer A.
Published: October 2019

Macrophage activation involves metabolic reprogramming to support antimicrobial cellular functions. How these metabolic shifts influence the outcome of infection by intracellular pathogens remains incompletely understood.M. tuberculosis(Mtb) modulates host metabolic pathways and utilizes host nutrients, including cholesterol and fatty acids, to survive within macrophages. We found that intracellular growth of Mtb depends on host fatty acid catabolism: when host fatty acid β-oxidation (FAO) was blocked chemically with trimetazidine, a compound in clinical use, or genetically by deletion of the mitochondrial fatty acid transporter carnitine palmitoyltransferase 2 (CPT2), Mtb failed to grow in macrophages and its growth was attenuated in mice. Global metabolic profiling and mechanistic studies support a model in which inhibition of FAO generates mitochondrial reactive oxygen species, which enhance macrophage NADPH oxidase and xenophagy activity to better control Mtb infection. Thus, FAO inhibition promotes key antimicrobial functions of macrophages and overcomes immune evasion mechanisms of Mtb.
Site Frequency Spectrum of the Bolthausen-Sznitman Coalescent
Authors: Kersting Götz , Siri-Jégousse Arno , Wences Alejandro H.
Published: October 2019

We derive explicit formulas for the two first moments of he site frequency spectrum (SFSn,b)1≤b≤n−1 of the Bolthausen-Sznitman coalescent along with some precise and efficient approximations, even for small sample sizes n. These results provide new L2-asymptotics for some values of b = o(n). We also study the length of internal branches carrying b > n/2 individuals. In this case we obtain the distribution function and a convergence in law. Our results rely on the random recursive tree construction of the Bolthausen-Sznitman coalescent.
Somatic mutations and genome stability maintenance in clonal coral colonies
Authors: López Elora H. , Palumbi Stephen R.
Published: October 2019

One challenge for multicellular organisms is maintaining genome stability in the face of mutagens across long life spans. Imperfect genome maintenance leads to mutation accumulation in somatic cells, which is associated with tumors and senescence in vertebrates. Colonial reef-building corals are often large, can live for hundreds of years, rarely develop recognizable tumors, and are thought to convert somatic cells into gamete producers, so they are a pivotal group in which to understand long-term genome maintenance. To measure rates and patterns of somatic mutations, we analyzed transcriptomes from 17-22 branches from each of fourAcropora hyacinthuscolonies, determined putative single nucleotide variants, and verified them with Sanger resequencing. Unlike for human skin carcinomas, there is no signature of mutations caused by UV damage, indicating either higher efficiency of repair than in vertebrates, or strong sunscreen protection in these shallow water tropical animals. The somatic mutation frequency per nucleotide inA. hyacinthusis on the same order of magnitude (10−7) as noncancerous human somatic cells, and accumulation of mutations with age is similar. Unlike mammals, loss of heterozygosity variants outnumber gain of heterozygosity mutations about 2:1. Although the mutation frequency is similar in mammals and corals, the preponderance of loss of heterozygosity changes and potential selection may reduce the frequency of deleterious mutations in colonial animals like corals. This may limit the deleterious effects of somatic mutations on the coral organism as well as potential offspring.
Early Polycomb-target deregulations in Hutchinson-Gilford Progeria Syndrome revealed by heterochromatin analysis
Authors: Sebestyén Endre , Marullo Fabrizia , Lucini Federica , Bianchi Andrea , Petrini Cristiano , Valsoni Sara , Olivieri Ilaria , Antonelli Laura , Gregoretti Francesco , Oliva Gennaro , Ferrari Francesco , Lanzuolo Chiara
Published: October 2019

Hutchinson-Gilford progeria syndrome (HGPS) is characterized by the progressive accumulation of progerin, an aberrant form of Lamin A. This leads to chromatin structure disruption, in particular by interfering with Lamina Associated Domains. Although several cellular and molecular alterations have been characterized, it is still unclear how chromatin structural changes translate into premature senescence in HGPS. Moreover, early events in chromatin remodeling have not been detected so far. We developed a new high-throughput sequencing-based method, named SAMMY-seq, for genome-wide characterization of heterochromatin accessibility changes. Using SAMMY-seq, we detected early stage alterations of chromatin structure in HGPS primary fibroblasts. Of note, these structural changes do not disrupt the distribution of H3K9me3 but are associated with site-specific H3K27me3 variations and transcriptional dysregulation of Polycomb target genes. Our results show that SAMMY-seq represents a novel and sensitive tool to characterize heterochromatin alterations. Moreover, we found that the assembly of lamin associated domains is strictly connected to the correct Polycomb repression, rapidly lost in early HGPS pathogenesis.
Temporal analyses of CRISPR-directed gene editing on NRF2, a clinically relevant human gene involved in chemoresistance
Authors: Banas Kelly , Rivera-Torres Natalia , Bialk Pawel , Yoo Byung-Chun , Kmiec Eric B.
Published: October 2019

Recent data suggest that a time lag exists between nuclear penetration and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-directed gene editing activity in human cells. As CRISPR/Cas approaches clinical implementation, it is critical to establish a biological time frame in which the complex enters the cell and nucleus and executes its gene editing function. We are developing CRISPR-directed gene editing for the treatment of non-small cell lung carcinoma focusing Nuclear Factor Erythroid 2-Related Factor-Like (NRF2), a transcription factor which regulates chemoresistance. In this report, we define cellular events that surround the initialization of CRISPR-directed gene editing as a function of time. We analyze the efficiency of cellular transfection of both components of the RNP particle and assess the emergence of indels. For the first time, we image the nuclear positioning of the tracrRNA and Cas9 as a complex and as individual gene editing components. Our results indicate that while the nuclear localization of the CRISPR/Cas complex is efficient and rapid, disruption of the NRF2 gene appears four to eight hours later. We reveal an initial snapshot of the schedule and processing of CRISPR/Cas in a lung cancer cell; information that will be useful as cell-based protocols are designed and advanced.
Response of neuroglia to hypoxia-induced oxidative stress using enzymatically crosslinked hydrogels
Authors: Zambuto Samantha G. , Serrano Julio F. , Vilbert Avery C. , Lu Yi , Harley Brendan A.C. , Pedron Sara
Published: October 2019

Three-dimensional cultures have exciting potential to mimic aspects of healthy and diseased brain tissue to examine the role of physiological conditions on neural biomarkers as well as disease onset and progression. Hypoxia is associated with oxidative stress, mitochondrial damage, and inflammation, key processes potentially involved in Alzheimer’s and multiple sclerosis. We describe the use of an enzymatically-crosslinkable gelatin hydrogel system within a microfluidic device to explore the effects of hypoxia-induced oxidative stress on neuroglia, astrocyte reactivity, and myelin production. This versatile platform offers new possibilities for drug discovery and modeling disease progression.
Palmitate induces apoptotic cell death and inflammasome activation in human placental macrophages
Authors: Rogers Lisa M. , Serezani Carlos H. , Eastman Alison J. , Hasty Alyssa H. , Englund-Ögge Linda , Jacobsson Bo , Vickers Kasey C. , Aronoff David M.
Published: October 2019

Introduction

There is an increasing prevalence of non-communicable diseases worldwide. Metabolic diseases such as obesity and gestational diabetes mellitus (GDM) increasingly affect women during pregnancy, which can harm pregnancy outcomes and the long-term health and wellbeing of exposed offspring. Both obesity and GDM have been associated with proinflammatory effects within the placenta, the critical organ governing fetal development.

Methods

The purpose of these studies was to model, in vitro, the effects of metabolic stress (high levels of glucose, insulin and saturated lipids) on placental macrophage biology, since these cells are the primary innate immune phagocyte within the placenta with roles in governing maternofetal immune tolerance and antimicrobial host defense. Macrophages were isolated from the villous core of term, human placentae delivered through nonlaboring, elective Cesarean sections and exposed to combinations of elevated glucose (30 mM), insulin (10 nM) and the saturated lipid palmitic acid (palmitate, 0.4 mM).

Results

We found that palmitate alone induced the activation of the nucleotide-binding oligomerization domain-like receptor (NLR) Family Pyrin Domain Containing 3 (NLRP3) inflammasome in placental macrophages, which was associated with increased interleukin 1 beta release and an increase in apoptotic cell death. Glucose and insulin neither provoked these effects nor augmented the impact of palmitate itself.

Discussion

Our findings confirm an impact of saturated fat on placental macrophage immune activation and could be relevant to the impact of metabolic stress in vivo.
Differential effects of commensal bacteria on progenitor cell adhesion, division symmetry and tumorigenesis in the Drosophila intestine
Authors: Ferguson Meghan , Petkau Kristina , Shin Minjeong , Galenza Anthony , Fast David , Foley Edan
Published: October 2019

Microbial factors influence homeostatic and oncogenic growth in the intestinal epithelium. However, we know little about immediate effects of commensal bacteria on stem cell division programs. In this study, we examined effects of commensal Lactobacillus species on homeostatic, and tumorigenic stem cell growth in the Drosophila intestine. We identified Lactobacillus brevis as a potent stimulator of stem cell growth. In a wildtype midgut, Lactobacillus brevis activates growth regulatory pathways that drive stem cell divisions. In a Notch-deficient background, Lactobacillus brevis-mediated growth causes rapid expansion of mutant progenitors, leading to accumulation of large, multi-layered tumors throughout the midgut. Mechanistically, we showed that Lactobacillus brevis disrupts expression and subcellular distribution of progenitor cell integrins, supporting symmetric divisions that expand intestinal stem cell populations. Collectively, our data emphasize the impact of commensal microbes on growth and maintenance of the intestinal progenitor compartment.
Litmus-Body: a Molecularly Targeted Sensor for Cell-Surface pH Measurements
Authors: Goudge Marc C. , Kuo Joe Chin-Hun , Metzloff Ann E. , Huang Ling-Ting , Colville Marshall J. , Zipfel Warren R. , Paszek Matthew J.
Published: October 2019

Precise pH measurements in the immediate environment of receptors is essential for elucidating the mechanisms through which local pH changes associated with diseased phenotypes manifest into aberrant receptor function. However, current pH sensors lack the molecular specificity required to make these measurements. Herein we present the Litmus-body, our recombinant protein-based pH sensor, which through fusion to an anti-mouse IgG nanobody is capable of molecular targeting to specific proteins on the cell surface. By normalizing a pH-dependent green fluorescent protein to a long-Stokes shift red fluorophore or fluorescent protein, we readily report pH independent of sensor concentration using a single 488-nm excitation. Our Litmus-body showed excellent responsiveness in solution, with a greater than 50-fold change across the physiological regime of pH. The sensor was further validated for use on live cells, shown to be specific to the protein of interest, and was able to successfully recapitulate the numerous pH changes along the endocytic pathway.
From institutionalized othering to disruptive collaboration
Authors: Holck Lotte , Muhr Sara Louise
Published: October 2019

Purpose

The purpose of this paper is to investigate how the construction and everyday maintenance of racialized psychological borders in the Greenlandic Police Force reproduce a postcolonial hierarchy of knowledge, where Danish knowledge and perceptions of professionalism are constructed as superior to Greenlandic knowledge and perceptions of professionalism.

Design/methodology/approach

The paper is based on an ethnographic study comprising 5 days of observation of a training course for Danish police officers going to Greenland on summer assistance, 13 days of observation of police work in Greenland, 2 days of participatory observation of a leadership development seminar in Greenland, 26 interviews conducted in Denmark and Greenland with both Danish and Greenlandic officers and interventions in Denmark and Greenland.

Findings

The racialized borders create strong perceptions of “us” and “them”, which are maintained and reinforced through everyday work practices. The borders have damaging effects on the way police officers collaborate in Greenland and as the borders are maintained through (often implicit) everyday micro-processes, management has difficulty dealing with it. However, the way the racialized borders became visible through this research project created an awareness of – and sparked conversation about – the colonial stereotypes that have constructed and reinforce the borders. This awareness opens up possibilities of collaborative disruption of those borders.

Research limitations/implications

The paper shows how racialized borders limit the way professionalism is understood in the Greenlandic Police Force. But it also shows that, because these borders are socially constructed, they can be contested. Making the implicit everyday discrimination explicit through vignettes, for example, offers the chance to contest and disrupt the colonial hierarchy otherwise deeply embedded in the work practices of the police force.

Originality/value

Thanks to unique access to Greenland’s police force, this paper offers exclusive in-depth insights into current processes of racialization and colonialization in a contemporary colonial relationship.
Workplace spirituality, psychological well-being and mediating role of subjective stress
Authors: Mahipalan Manju , S. Sheena
Published: October 2019

Purpose

The purpose of this study is to assess the impact of spirituality on subjective stress and psychological well-being (PWB). Additionally, the study also examines the mediating role of stress in the spirituality – well-being relationship.

Design/methodology/approach

The study is quantitative in nature. Data were collected from 322 secondary school teachers using a structured questionnaire. Partial least squares based structural equation modelling was used to analyse the data.

Findings

Results indicated a positive relationship between spirituality and PWB but an inverse relationship between job stresses. Also, subjective stress was found to be a significant mediator in the relationship between spirituality and well-being.

Social implications

The inner resource of spirituality among teachers can be tapped to cope with perceived stress levels thereby augmenting a sense of well-being. Psychologically clear and receptive minds are indispensable in the process of teaching.

Originality/value

The present study combines the evolving construct of workplace spirituality with PWB and subjective stress, which are under explored in the social sector.