bluuebunny/crossref_metadata_2025 huggingface dataset:
Bilateral Quadriceps Muscle Strength and Pain Correlate With Gait Speed and Gait Endurance Early After Unilateral Total Knee Arthroplasty
Authors: Suh Min Ji , Kim Bo Ryun , Kim Sang Rim , Han Eun Young , Nam Kwang Woo , Lee So Young , Park Yong Geun , Kim Won Bin
Published: May 2019

Objective

The aim of this study was to determine the correlations between objective performance-based physical function, self-reported physical function, quality of life, and gait function at 1 mo after unilateral total knee arthroplasty.

Design

Cross-sectional data from 195 patients who underwent unilateral primary total knee arthroplasty were analyzed. The isometric knee extensor and flexor strength of both knees, gait parameters, 6-min walk test, timed up-and-go test, timed stair-climbing test, knee flexion and extension range of motion of surgical knee, Western Ontario McMaster Universities Osteoarthritis Index pain, stiffness, and functional levels, EuroQol five-dimensions questionnaire, and visual analog scale for knee pain were assessed.

Results

In bivariate analyses, both postoperative gait speed and gait endurance had significant positive correlations with postoperative peak torque of the extensor and flexor of both knees, cadence, stride length, and significant negative correlation with timed up-and-go, stair-climbing test ascent, stair-climbing test descent, visual analog scale, Western Ontario McMaster Universities Osteoarthritis Index pain, stiffness, and function levels. In the linear regression analyses, postoperative peak torque of the extensors of both knees and VAS for knee pain were factors correlated with postoperative gait speed and gait endurance.

Conclusions

Quadriceps muscle strength of both knees and knee pain were important factors correlated with gait function early after total knee arthroplasty.
S1PR1-Associated Molecular Signature Predicts Survival in Patients with Sepsis
Authors: Feng Anlin , Rice Amanda D. , Zhang Yao , Kelly Gabriel T. , Zhou Tong , Wang Ting
Published: May 2019

Background:

Sepsis is a potentially life-threatening complication of an underlying infection that quickly triggers tissue damage in multiple organ systems. To date, there are no established useful prognostic biomarkers for sepsis survival prediction. Sphingosine-1-phosphate (S1P) and its receptor S1P receptor 1 (S1PR1) are potential therapeutic targets and biomarkers for sepsis, as both are active regulators of sepsis-relevant signaling events. However, the identification of an S1PR1-related gene signature for prediction of survival in sepsis patients has yet to be identified. This study aims to find S1PR1-associated biomarkers which could predict the survival of patients with sepsis using gene expression profiles of peripheral blood to be used as potential prognostic and diagnostic tools.

Methods:

Gene expression analysis from sepsis patients enrolled in published datasets from Gene Expression Omnibus was utilized to identify both S1PR1-related genes (co-expression genes or functional-related genes) and sepsis survival-related genes.

Results:

We identified 62-gene and 16-gene S1PR1-related molecular signatures (SMS) associated with survival of patients with sepsis in discovery cohort. Both SMS genes are significantly enriched in multiple key immunity-related pathways that are known to play critical roles in sepsis development. Meanwhile, the SMS performs well in a validation cohort containing sepsis patients. We further confirmed our SMSs, as newly developed gene signatures, perform significantly better than random gene signatures with the same gene size, in sepsis survival prognosis.

Conclusions:

Our results have confirmed the significant involvement of S1PR1-dependent genes in the development of sepsis and provided new gene signatures for predicting survival of sepsis patients.
Cardiogenic Shock Following Acute Myocardial Infarction: What's New?
Authors: Pepe Martino , Bortone Alessandro Santo , Giordano Arturo , Cecere Annagrazia , Burattini Osvaldo , Nestola Palma Luisa , Patti Giuseppe , Di Cillo Ottavio , Signore Nicola , Forleo Cinzia , Favale Stefano
Published: May 2019

Cardiogenic shock (CS) is a state of critical end-organ hypoperfusion primarily due to cardiac dysfunction. This condition is the most common cause of death in patients affected by acute myocardial infarction (AMI). Despite early revascularization, prompt optimal medical therapy, and up-to-date mechanical circulatory supports, mortality of patients with CS remains high.

The objective of this review is to summarize epidemiology, pathophysiology, and treatment options of CS in light of the new European Society of Cardiology (ESC) recommendations. The latest European guidelines on myocardial revascularization have reviewed the previous guidelines with respect to early multivessel revascularization and routine use of intra-aortic balloon pump (IABP) in patients with AMI-related CS.

Most of the current evidences come partly from randomized trials, but mostly from observational registries because of the difficulty to test different treatments in this life-threatening clinical setting.

Some of the latest studies highlight the potential crucial benefit of newly introduced mechanical circulatory support devices, although evidences are not sufficient to definitely assess the benefit/risk ratio of the different systems.

Many questions remain unanswered in this field, and further trials are advocated to better elucidate the best medical, reperfusion, and circulatory support approaches aimed to improve the poor prognosis of patients with CS after AMI.
Simultaneous regulation of cytokinetic furrow and nucleus positions by cortical tension contributes to proper DNA segregation during late mitosis
Authors: Pacquelet Anne , Jousseaume Matthieu , Etienne Jocelyn , Michaux Grégoire
Published: May 2019

Coordinating mitotic spindle and cytokinetic furrow positioning is essential to ensure proper DNA segregation. Here we present a novel mechanism, which corrects DNA segregation defects due to cytokinetic furrow mispositioning. We show that DNA segregation defects following the abnormal displacement of the cytokinetic furrow towards the anterior side of C. elegans one-cell embryos are unexpectedly corrected at the end of cytokinesis. This correction relies on the concomitant displacement of the furrow and of the anterior nucleus towards the posterior and anterior poles, respectively. It also coincides with cortical blebbing and an anteriorly directed flow of cytoplasmic particles. While microtubules contribute to nuclear displacement, relaxation of an excessive tension at the anterior cortex plays a central role in the correction process and simultaneously regulates cytoplasmic flow as well as nuclear and furrow displacements. This work thus reveals the existence of a so far uncharacterized correction mechanism, which is critical to correct DNA segregation defects due to cytokinetic furrow mispositioning.
Entecavir resistance mutations rtL180M/T184L/M204V combined with rtA200V lead to tenofovir resistance
Authors: Jiang Dong , Wang Jianghua , Zhao Xuesen , Li Yuxin , Zhang Qun , Song Chuan , Zeng Hui , Wang Xianbo
Published: May 2019

Background & Aims

Tenofovir disoproxil fumarate (TDF) imposes a high genetic barrier to drug resistance and potently inhibits replication of multidrug-resistant hepatitis B virus (MDR HBV) and few clinical cases with confirmed TDF-resistance have been reported to date. We reported a quadruple mutant which showed moderate resistant to TDF.

Methods and results

Viral rebound was reported in a patient with chronic hepatitis B who underwent TDF monotherapy and harbored a quadruple mutant consisting of classic ETV-resistance mutations (rtL180M/T184L/M204V) together with an rtA200V mutation in the reverse transcriptase gene. Sequencing analysis revealed that this quadruple mutant emerged as a major viral population. In vitro phenotyping demonstrated that the rtL180M/T184L/A200V/M204V mutant had moderate resistance to TDF treatment, with a 4.52-fold higher half maximal effective concentration than that of wild-type virus. Importantly, this patient with TDF resistance achieved virological suppression after TDF/ETV combination rescue therapy.

Conclusion

An rtL180M/T184L/A200V/M204V mutant with moderate resistance to TDF monotherapy was selected during sequential NA treatment in a stepwise manner. ETV/TDF combination therapy effectively suppressed replication of this TDF resistant mutant. Our studies provide novel insights into the treatment of NA-naïve patients as well as patients with TDF resistance.
The effect of tongue-tie application on stress responses in resting horses
Authors: Marsh Laura , McGreevy Paul , Hazel Susan , Santos Luiz , Hebart Michelle , Franklin Samantha
Published: May 2019

Tongue-ties (TT) are commonly applied to both Standardbred and Thoroughbred racehorses to increase control, by preventing them from getting their tongue over the bit, and as a conservative treatment for equine respiratory conditions, principally dorsal displacement of the soft palate. This study investigated responses to TT application in horses, at rest, using both behavioural (head-tossing, ear position, gaping and lip licking) and physiological (salivary cortisol concentrations, eye surface temperature and heart rate) indices. Twelve Standardbred horses (six of which were naïve to TT) were used in a randomised crossover design. The study comprised 3 phases; Phase 1 (Baseline), Phase 2 (Treatment), and Phase 3 (Recovery). At phase 2, tongue tie application (TTA) was performed using a rubber band that was looped around the tongue and secured to the mandible for 20 minutes. The control treatment (C) incorporated 30 secs of tongue manipulation, at the start of the 20 min, however no TT was applied. Behaviours (head-tossing, ear position, mouth gaping and lip-licking) and heart rate (HR) were recorded for the duration of the study and analysed in ten minute intervals. Salivary samples were taken at the end of each phase for subsequent cortisol assays and infrared thermography images were taken of each eye at 5-minute intervals. Statistical analyses were performed in SPSS using linear mixed effects models and repeated measures general linear models, to determine differences between treatments and within treatments, over time. Compared to control, there was more head-tossing/shaking (p<0.001), gaping (p<0.001) and backwards ear position (p<0.001) and less forward ear position (p<0.001) during TTA, in Phase 2. Horses with previous experience of TT showed more head-tossing (p=0.040) and gaping (p=0.030) than naïve horses. Lip-licking was more frequent after TTA treatment than control, during Phase 3 (p<0.001). Salivary cortisol concentrations increased after TTA (1846.1pg/mL ± 478.3pg/mL vs 1253.6pg/mL ± 491.6pg/mL, p=0.047). Mean HR, and mean right and left eye temperature did not differ significantly between treatments in any phase (all p> 0.05). The findings of this study suggest the application of a tongue-tie causes changes to both behavioural and physiological parameters suggestive of a stress-related response. Further research is needed that will enable racing and sport horse regulatory bodies to make informed decisions about the appropriate use of tongue-ties in horses.
When 90% of the variance is not enough: residual EMG from muscle synergy extraction influences task performance
Authors: Barradas Victor R. , Kutch Jason J. , Kawase Toshihiro , Koike Yasuharu , Schweighofer Nicolas
Published: May 2019

Muscle synergies are usually identified via dimensionality reduction techniques, such that the identified synergies reconstruct the muscle activity to a level of accuracy defined heuristically, such as 90% of the variance explained. Here, we question the assumption that the residual muscle activity not explained by the synergies is due to noise. We hypothesize instead that the residual activity is structured and can therefore influence the execution of a motor task. Young healthy subjects performed an isometric reaching task in which surface electromyography of 10 arm muscles was mapped onto estimated two-dimensional forces used to control a cursor. Three to five synergies were extracted to account for 90% of the variance explained. We then altered the muscle-force mapping via “hard” and “easy” virtual surgeries. Whereas in both surgeries the forces associated with synergies spanned the same single dimension of the virtual environment, the muscle-force mapping was as close as possible to the initial mapping in the easy surgery and as far as possible in the hard surgery. This design therefore maximized potential differences in reaching errors attributable to the residual muscle activity. Results show that the easy surgery produced much smaller directional errors than the hard task. In addition, systematic estimations of the errors for easy and hard surgeries constructed with 1 to 10 synergies show that the errors differ significantly for up to 8 synergies, which account for 98% of the variance on average. Our study therefore indicates the need for cautious interpretations of results derived from synergy extraction techniques based on heuristics with lenient levels of accuracy.

Author summary

The muscle synergy hypothesis states that the central nervous system simplifies motor control by grouping muscles that share common functions into modules called muscle synergies. Current techniques use unsupervised dimensionality reduction algorithms to identify these synergies. However, these techniques rely on arbitrary criteria to determine the number of synergies, which is actually unknown. An example of such criteria is that the identified synergies must be able to reconstruct the measured muscle activity to at least a 90% level of accuracy. Thus, the residual muscle activity, the remaining 10% of the muscle activity, is often disregarded as noise. We show that residual muscle activity following muscle synergy identification has a large systematic effect on movements even when the number of synergies approaches the number of muscles. This suggests that current synergy extraction techniques may discard a component of muscle activity that is important for motor control. Therefore, current synergy extraction techniques must be updated to identify true physiological synergies.
Fatty acid starvation activates RelA by depleting lysine precursor pyruvate
Authors: Sinha Anurag Kumar , Winther Kristoffer Skovbo , Roghanian Mohammad , Gerdes Kenn
Published: May 2019

Bacteria experiencing nutrient starvation induce the ubiquitous stringent response, a profound physiological change that reprograms cell physiology from fast to slow growth and stress survival. The stringent response is mediated by the secondary messengers pppGpp and ppGpp collectively referred to as (p)ppGpp or “alarmone”. InEscherichia coli, two paralogs, RelA and SpoT, synthesize (p)ppGpp. RelA is activated by amino acid starvation whereas SpoT, which can also degrade (p)ppGpp, responds to fatty acid (FA), carbon and phosphate starvation. Here, we discover that FA starvation leads to rapid activation of RelA and reveal the underlying mechanism. We show that fatty acid starvation leads to depletion of lysine that, in turn, leads to the accumulation of uncharged tRNAlysand activation of RelA. SpoT was also activated by fatty acid starvation but to a lower level and with a delayed kinetics. Next, we discovered that pyruvate, a precursor of lysine, is depleted by FA starvation. We also propose a mechanism that explains how FA starvation leads to pyruvate depletion. Together our results indicate that many responses to nutrient depletion may ultimately result indirectly from depletion of amino acids and thereby activating RelA. Interestingly, FA starvation provoked a ~100-fold increase inrelAdependent ampicillin tolerance.
Climate adaptation shaped by subtle to moderate allele frequency shifts in loblolly pine
Authors: De La Torre Amanda R. , Neale David B
Published: May 2019

Understanding the genomic basis of local adaptation is crucial to determine the potential of long-lived woody species to withstand changes in their natural environment. In the past, efforts to dissect the genomic architecture in gymnosperms species have been limited due to the absence of reference genomes. Recently, the genomes of some commercially important conifers, such as loblolly pine, have become available, allowing whole-genome studies of these species. In this study, we test for associations between 87k SNPs, obtained from whole-genome re-sequencing of loblolly pine individuals, and 270 environmental variables and combinations of them. We determine the geographic location of significant alleles and identify their genomic location using our newly constructed ultra-dense 26k SNP linkage map. We found that water availability is the main climatic variable shaping local adaptation of the species, and found 492 SNPs showing significant associations with climatic variables or combinations of them. Our results suggest that adaptation to climate in the species might have occurred by many changes in the allele frequency of alleles with moderate to small effect sizes, and by the smaller contribution of large effect alleles in genes related to moisture deficit, temperature and precipitation. Genomic regions of low recombination and high population differentiation harbored SNPs associated with principal components but not with individual climatic variables, suggesting climate adaptation might have evolved as a result of different selection pressures acting on groups of genes associated with an aspect of climate rather than on individual climatic variables.
Cell generation dynamics underlying naïve T cell homeostasis in adult humans
Authors: Mold Jeff E. , Réu Pedro , Olin Axel , Bernard Samuel , Michaëlsson Jakob , Rane Sanket , Yates Andrew , Khosravi Azadeh , Salehpour Mehran , Possnert Göran , Brodin Petter , Frisén Jonas
Published: May 2019

Thymic involution and proliferation of naive T cells both contribute to shaping the naive T cell repertoire as humans age, but a clear understanding of the roles of each throughout a human lifespan has been difficult to determine. By measuring nuclear bomb test-derived14C in genomic DNA we determined the turnover rates of CD4+and CD8+naïve T cell populations and defined their dynamics in healthy individuals ranging from 20-65 years of age. We demonstrate that naïve T cell generation decreases with age, and that this could be explained by a combination of declining cell loss, peripheral division and thymic production during adulthood. We investigated putative mechanisms underlying age-related changes in homeostatic regulation of naïve T cell turnover using mass cytometry to profile candidate signaling pathways involved in T cell activation and proliferation in CD4+naive T cells relative to CD31 expression, a marker of thymic proximity. We show that basal NF-κB phosphorylation inversely correlated with CD31 expression and thus is decreased in peripherally expanded naive T cell clones. Functionally we found that NF-κB signaling was essential for naive T cell proliferation to the homeostatic growth factor IL-7, and reduced NF-κB phosphorylation in CD4+CD31−naive T cells is linked to reduced homeostatic proliferation potential. Our results reveal an age-related decline in naïve T cell turnover as a putative regulator of naïve T cell diversity and identify a molecular pathway that restricts proliferation of peripherally expanded naive T cell clones that accumulate with age.
Drug-resistant epimutants exhibit organ-specific stability and induction during murine infections caused by the human fungal pathogenMucor circinelloides
Authors: Chang Zanetta , Heitman Joseph
Published: May 2019

The environmentally ubiquitous fungusMucor circinelloidesis a primary cause of the emerging disease mucormycosis.Mucorinfection is notable for causing high morbidity and mortality, especially in immunosuppressed patients, while being inherently resistant to the majority of clinically available antifungal drugs. A new, RNAi-dependent, and reversible epigenetic mechanism of antifungal resistance – epimutation - was recently discovered inM. circinelloides. However, the effects of epimutation in a host-pathogen setting were unknown. We employed a systemic, intravenous murine model ofMucorinfection to elucidate the potential impact of epimutationin vivo. Infection with an epimutant strain resistant to the antifungal agents FK506 and rapamycin revealed that the epimutant-induced drug resistance was stablein vivoin a variety of different organs and tissues. Reversion of the epimutant-induced drug resistance was observed to be more rapid in isolates from the brain, as compared to those recovered from the liver, spleen, kidney, or lungs. Importantly, infection with a wild-type strain ofMucorled to increased rates of epimutation after strains were recovered from organs and exposed to FK506 stressin vitro.Once again, this effect was more pronounced in strains recovered from the brain than from other organs. In summary, we report the rapid induction and reversion of RNAi-dependent drug resistance afterin vivopassage through a murine model, with pronounced impact in strains recovered from brain. Defining the role played by epimutation in drug resistance and infection advances our understanding ofMucorand other fungal pathogens, and may have implications for antifungal therapy.

IMPORTANCE

The emerging fungal pathogenMucor circinelloidescauses a severe infection, mucormycosis, which leads to considerable morbidity and mortality. Treatment ofMucorinfection is challenging becauseMucoris inherently resistant to nearly all clinical antifungal agents. An RNAi-dependent and reversible mechanism of antifungal resistance, epimutation, was recently described inMucor. Epimutation has not been studiedin vivoand it was unclear whether it would contribute to antifungal resistance observed clinically. We demonstrate that epimutation can be both induced and reverted afterin vivopassage through a mouse model; rates of both induction and reversion are higher after brain infection than after infection of other organs (liver, spleen, kidneys, or lungs). Elucidating the roles played by epimutation in drug resistance and infection will improve our understanding ofMucorand other fungal pathogens, and may have implications for antifungal treatment.
Dynamics of transcription-dependent H3K36me3 marking by the SETD2:IWS1:SPT6 ternary complex
Authors: Cermakova Katerina , Smith Eric A. , Veverka Vaclav , Hodges H. Courtney
Published: May 2019

SETD2 contributes to gene expression by marking gene bodies with H3K36me3, which is thought to assist in the concentration of transcription machinery at the small portion of the coding genome. Despite extensive genome-wide data revealing the precise localization of H3K36me3 over gene bodies, the physical basis for the accumulation, maintenance, and sharp borders of H3K36me3 over these sites remains rudimentary. Here we propose a model of H3K36me3 marking based on stochastic transcription-dependent placement and transcription-independent spreading. Our analysis of the spatial distributions and dynamic features of these marks indicates that transcription-dependent placement dominates the establishment of H3K36me3 domains compared to transcription-independent spreading processes, and that turnover of H3K36me3 limits its capacity for epigenetic memory. By adding additional terms for asymmetric histone turnover occurring at transcription start sites, our model provides a remarkably accurate representation of H3K36me3 levels and dynamics over gene bodies. Furthermore, we validate our findings by revealing that loss of SPT6 impairs the transcription-coupled activity of the SETD2:IWS1:SPT6 ternary complex, thereby reducing the tight correlation between transcription and H3K36me3 levels at gene bodies.
Metastatic breast cancer cells induce altered microglial morphology and electrical excitabilityin vivo
Authors: Simon Anna , Yang Ming , Marrison Joanne L. , James Andrew D. , O’Toole Peter J. , Kaye Paul M. , Whittington Miles A. , Chawla Sangeeta , Brackenbury William J.
Published: May 2019

Background

An emerging problem in the treatment of breast cancer is the increasing incidence of metastases to the brain. Metastatic brain tumours are incurable and can cause epileptic seizures and cognitive impairment, so better understanding of this niche, and the cellular mechanisms, is urgently required. Microglia are the resident brain macrophage population, becoming “activated” by neuronal injury, eliciting an inflammatory response. Microglia promote proliferation, angiogenesis and invasion in brain tumours and metastases. However, the mechanisms underlying microglial involvement appear complex and better models are required to improve understanding of function.

Methods

Here, we sought to address this need by developing a model to study metastatic breast cancer cell-microglial interactions using intravital imaging combined withex vivoelectrophysiology. We implanted an optical window on the parietal bone to facilitate observation of cellular behaviourin situin the outer cortex of heterozygousCx3cr1GFP/+mice. Results: We detected GFP-expressing microglia inCx3cr1GFP/+mice up to 350 µm below the window without significant loss of resolution. When DsRed-expressing metastatic MDA-MB-231 breast cancer cells were implanted in Matrigel under the optical window, significant accumulation of activated microglia around invading tumour cells could be observed. This inflammatory response resulted in significant cortical disorganisation and aberrant spontaneously-occurring local field potential spike events around the metastatic site.

Conclusions

These data suggest that peritumoral microglial activation and accumulation may play a critical role in local tissue changes underpinning aberrant cortical activity, which offers a possible mechanism for the disrupted cognitive performance and seizures seen in patients with metastatic breast cancer.
Electron cryomicroscopy observation of acyl carrier protein translocation in type I fungal fatty acid synthase
Authors: Lou Jennifer W. , Iyer Kali R. , Naimul Hasan S. M. , Cowen Leah E. , Mazhab-Jafari Mohammad T.
Published: May 2019

During fatty acid biosynthesis, acyl carrier proteins (ACPs) from type I fungal fatty acid synthase (FAS) shuttle substrates and intermediates within a reaction chamber that hosts multiple spatially-fixed catalytic centers. A major challenge in understanding the mechanism of ACP-mediated substrate shuttling is experimental observation of its transient interaction landscape within the reaction chamber. Here, we have shown that ACP spatial distribution is sensitive to the presence of substrates in a catalytically inhibited state, which enables high-resolution investigation of the ACP-dependent conformational transitions within the enoyl reductase (ER) reaction site. In two fungal FASs with distinct ACP localization, the shuttling domain is targeted to the ketoacyl-synthase (KS) domain and away from other catalytic centers, such as acetyl-transferase (AT) and ER domains by steric blockage of the KS active site followed by addition of substrates. These studies strongly suggest that acylation of phosphopantetheine arm of ACP may be an integral part of the substrate shuttling mechanism in type I fungal FAS.
Age and mortality associated DNA methylation patterns on the X-chromosome in male and female samples
Authors: Li Shuxia , Lund Jesper B. , Baumbach Jan , Christensen Kaare , Mengel-From Jonas , Li Weilong , Mohammadnejad Afsaneh , Pattie Alison , Marioni Riccardo E. , Deary Ian J. , Tan Qihua
Published: May 2019

Background

Multiple epigenetic association studies on human aging have been performed reporting large numbers of sites differentially methylated across ages on the autosomal chromosomes. The X-chromosome has been studied little, due to analytical difficulties in dealing with sex differences in X-chromosome content and X-inactivation in females. Based on large collections of genome-wide DNA methylation data on two Danish cohorts of identical twins (mean ages, 66 and 79 years) and the Lothian Birth Cohort 1921 (mean age 79 years), we conducted a chromosome-wide association analysis on male and female samples separately with equal sample sizes to discover age-dependent X-linked DNA methylation patterns using chromosome 20 with about same number of CpGs analysed as an autosomal reference, and compare the age-related changes in DNA methylation between the two sexes. In addition, age-related methylation sites were assessed for their associations with mortality.

Results

We identified more age-related DNA methylation sites (FDR<0.05) in females than in males. Among them, predominantly more sites were hypermethylated in the older as compared with the younger cohorts, a pattern similar to that observed on chromosome 20. Among the age-related sites, 13 CpGs in males and 24 CpGs in females were found significant (FDR<0.05) in all cohorts. Survival analysis showed that there are more age-methylated CpGs that contribute to reduce mortality than those that increase mortality in male but not in female samples.

Conclusion

The X-chromosome displays significant age-and sex-dependent methylation patterns which might be differentially associated with mortality in the two sexes.
Detection and quantification of house mouse Eimeria at the species level – challenges and solutions for the assessment of Coccidia in wildlife
Authors: Jarquín-Díaz Víctor Hugo , Balard Alice , Jost Jenny , Kraft Julia , Dikmen Mert Naci , Kvičerová Jana , Heitlinger Emanuel
Published: May 2019

Detection and quantification of coccidia in studies of wildlife can be challenging. Therefore, the prevalence of coccidia is often not assessed at the parasite species level in non-livestock animals. Parasite species-specific prevalences are especially important when studying evolutionary questions in wild populations. We tested whether increased host population density increases the prevalence of individual Eimeria species at the farm level, as predicted by epidemiological theory. We studied free-living commensal populations of the house mouse (Mus musculus) in Germany and established a strategy to detect and quantify Eimeria infections. We show that a novel diagnostic primer targeting the apicoplast genome (Ap5) and coprological assessment after flotation provide complementary detection results increasing sensitivity. Genotyping PCRs confirm detection in a subset of samples and cross-validation of different PCR markers does not indicate a bias towards a particular parasite species in genotyping. We were able to detect double infections and to determine the preferred niche of each parasite species along the distal-proximal axis of the intestine. Parasite genotyping from tissue samples provides an additional indication for the absence of species bias in genotyping amplifications. Three Eimeria species were found infecting house mice at different prevalences: Eimeria ferrisi (16.7%; 95% CI 13.2 – 20.7), E. falciformis (4.2%; 95% CI 2.6 – 6.8) and E. vermiformis (1.9%; 95% CI 0.9 – 3.8). We also find that mice in dense populations are more likely to be infected with E. falciformis and E. ferrisi.

We provide methods for the assessment of prevalences of coccidia at the species level in rodent systems. We show and discuss how such data can help to test hypotheses in ecology, evolution and epidemiology on a species level.
LIR-dependent LMX1A/LMX1B autophagy crosstalk shapes human midbrain dopaminergic neuronal resilience
Authors: Jiménez-Moreno Natalia , Stathakos Petros , Antón Zuriñe , Shoemark Deborah K. , Sessions Richard B. , Witzgall Ralph , Caldwell Maeve , Lane Jon D.
Published: May 2019

The LIM homeodomain transcription factors LMX1A and LMX1B are essential mediators of midbrain dopaminergic neuronal (mDAN) differentiation and survival. Here we show that LMX1A and LMX1B are autophagy transcription factors in iPSC-derived human mDANs, each contributing to the expression of important autophagy genes including ULK1, ATG7, ATG16L1 and TFEB. Suppression of LMX1A and LMX1B in mDANs reduces basal autophagy, lowers mitochondrial respiration, and elevates mitochondrial ROS levels; meanwhile overexpression protects against rotenone poisoning in mDANs in vitro. Significantly, we show that LMX1A and LMX1B bind to multiple ATG8 proteins via LIR-type interactions, in a manner dependent on subcellular localisation and nutrient status: LMX1B interacts with LC3B in the nucleus under basal conditions via a C-terminal LIR, but binds to cytosolic LC3B and is degraded by autophagy during nutrient starvation, and LIR mutant LMX1B is unable to protect mDANs against rotenone. This establishes an LMX1A/LMX1B-autophagy regulatory nexus that helps explain the protective roles of these transcription factors in the adult midbrain, thus having implications for our understanding of mDAN decline in PD.
A gene expression program activated by neuronal inactivity
Authors: Zhu Zhonghua , Lennon Jennifer , Barry Timothy M. , Ortiz Tamara Sanchez , Lymer Seana , Mezan Shaul , Kadener Sebastian , Blau Justin
Published: May 2019

Long term synaptic plasticity requires transcriptional changes in response to neuronal activity. While neuronal activity rapidly increases transcription of activity-regulated genes, it is less clear how neurons respond to neuronal inactivity. The plasticity genePuraencodes a Rho1 GEF whose rhythmic expression drives 24 hour rhythms in the retraction of the projections ofDrosophilaLNvcircadian pacemaker neurons. We found thatPuratranscription in LNvs is repressed by neuronal activity and induced by neuronal inactivity – the opposite of canonical activity-regulated genes. We identified the Pax6 transcription factor Toy as the relevant activator ofPuratranscription, and found thattoytranscription itself is induced by neuronal inactivity and by reducing intracellular calcium. Thus we propose that neurons contain complementary gene expression programs that are activated by either increased or decreased neuronal activity.
Developmental changes in connectivity between the amygdala subnuclei and occipitotemporal cortex
Authors: Hansen Heather A. , Saygin Zeynep M.
Published: May 2019

The amygdala, a subcortical structure known for social and emotional processing, can be subdivided into multiple nuclei with unique functions and connectivity patterns. Tracer studies in adult macaques have shown that the lateral and basal amygdala subnuclei decrease in connectivity to visual cortical areas moving from anterior to posterior, and that infants have similar adult-like projections plus additional connections that are refined with development. Can we delineate the connectivity between the amygdala subnuclei and occipitotemporal cortex in humans, and will it show similar developmental differences as macaques? If so, what functional regions may be contributing to this pattern of connectivity? To address these questions, we anatomically defined the lateral and basal amygdala subnuclei in 20 adult subjects, 27 kids (aged 7-8), and 15 neonates. We then defined the occipitotemporal region in each individual’s native anatomy, and split this entire region into five equal sections from anterior to posterior. We also defined visual functional parcellations in the occipitotemporal cortex (e.g. FFA, PPA) and anatomically defined primary visual cortex (i.e., V1). Using Diffusion Weighted Imaging data, we ran probabilistic tractography with FSL between the amygdala subnuclei as seeds and the occipitotemporal cortical parcellations as targets. Results showed that like macaques, the mean connectivity across subjects to the occipitotemporal cortex significantly decreased on a gradient from anterior to posterior, and that connectivity in kids and neonates was adult-like but became more refined across development. Further, refinement of connectivity to mid and posterior occipitotemporal cortex was largely driven by anterior PPA, LO, and V1, with connectivity to higher order visual areas increasing with age. The functional maturation of these regions may contribute to the continued refinement of these connections, in line with Interactive Specialization hypotheses of brain development.
Visual self-motion feedback affects the sense of self in virtual reality
Authors: Schettler Aubrieann , Holstead Ian , Turri John , Barnett-Cowan Michael
Published: May 2019

We assessed how self-motion affects the visual representation of the self. We constructed a novel virtual reality experiment that systematically varied an avatar’s motion and also biological sex. Participants were presented with pairs of avatars that visually represented the participant (“self avatar”), or another person (“opposite avatar”). Avatar motion either corresponded with the participant’s motion, or was decoupled from the participant’s motion. The results show that participants identified with i) “self avatars” over “opposite avatars”, ii) avatars moving congruently with self-motion over incongruent motion, and importantly iii) identification with the “opposite avatar” over the “self avatar” when the opposite avatar’s motion was congruent with self-motion. Our results suggest that both self-motion and biological sex are relevant to the body schema and body image and that congruent bottom-up visual feedback of self-motion is particularly important for the sense of self and capable of overriding top-down self-identification factors such as biological sex.
The Salt-Inducible Kinase inhibitor YKL-05-099 suppresses MEF2C function and acute myeloid leukemia progressionin vivo
Authors: Tarumoto Yusuke , Lin Shan , Wang Jinhua , Milazzo Joseph P. , Xu Yali , Gray Nathanael S. , Stegmaier Kimberly , Vakoc Christopher R.
Published: May 2019

Lineage-defining transcription factors (TFs) are compelling targets for leukemia therapy, yet they are among the most challenging proteins to modulate directly with small molecules. We previously used CRISPR screening to identify a Salt-Inducible Kinase 3 (SIK3) requirement for the growth of acute myeloid leukemia (AML) cell lines that overexpress the lineage TF MEF2C. In this context, SIK3 maintains MEF2C function by directly phosphorylating histone deacetylase 4 (HDAC4), a repressive cofactor of MEF2C. Here, we evaluated whether inhibition of SIK3 with the tool compound YKL-05-099 can suppress MEF2C function and attenuate disease progression in animal models of AML. Genetic targeting of SIK3 or MEF2C selectively suppressed the growth of transformed hematopoietic cells underin vitroandin vivoconditions. Similar phenotypes were obtained when exposing cells to YKL-05-099, which caused cell cycle arrest and apoptosis in MEF2C-expressing AML cell lines. An epigenomic analysis revealed that YKL-05-099 rapidly suppressed MEF2C function by altering the phosphorylation state and nuclear localization of HDAC4. Using a gatekeeper allele ofSIK3, we found that the anti-proliferative effects of YKL-05-099 occurred through on-target inhibition of SIK3 kinase activity. Based on these findings, we treated two different mouse models of MLL-AF9 AML with YKL-05-099, which attenuated disease progressionin vivoand extended animal survival at well-tolerated doses. These findings validate SIK3 as a therapeutic target in MEF2C-positive AML and provide a rationale for developing drug-like inhibitors of SIK3 for definitive pre-clinical investigation and for studies in human patients with leukemia.

Key Points

AML cells are uniquely sensitive to genetic or chemical inhibition of Salt-Inducible Kinase 3in vitroandin vivo.

A SIK inhibitor YKL-05-099 suppresses MEF2C function and AMLin vivo.
Functional analysis of OCTN2 and ATB0,+ in normal human airway epithelial cells
Authors: Rotoli Bianca Maria , Visigalli Rossana , Barilli Amelia , Ferrari Francesca , Bianchi Massimiliano G. , Di Lascia Maria , Riccardi Benedetta , Puccini Paola , Dall’Asta Valeria
Published: May 2019

In human, OCTN2 (SLC22A5) and ATB0,+ (SLC6A14) transporters mediate the uptake of L-carnitine, essential for the transport of fatty acids into mitochondria and the subsequent degradation by β-oxidation. Aim of the present study is to characterize L-carnitine transport in EpiAirway™, a 3D organotypic in vitro model of primary human tracheal-bronchial epithelial cells that form a fully differentiated, pseudostratified columnar epithelium at air-liquid interface (ALI) condition. In parallel, Calu-3 monolayers grown at ALI were used as comparison. In EpiAirway™, ATB0,+ was highly expressed and functional on the apical side while OCTN2 transporter was active on the basolateral side. Calu-3 cells showed a different pattern of expression and activity for ATB0,+: indeed, L-carnitine uptake on apical side was evident in Calu-3 at 8 days of culture but not in fully differentiated 21d ALI culture. As both ATB0,+ and OCTN2, beyond transporting L-carnitine, have a significant potential as delivery systems for drugs, the identification of these transporters in EpiAirway™ can open new fields of investigation in the studies of drug inhalation and pulmonary delivery.
Adult neurogenesis promotes efficient, nonspecific search strategies in a spatial alternation water maze task
Authors: Yu Ru Qi , Cooke Matthew , Zhao Jiaying , Snyder Jason S.
Published: May 2019

Goal-directed navigation requires learning strategies that are efficient and minimize costs. In some cases it may be desirable to flexibly adjust behavioral responses depending on the cues that vary from one episode to the next. In others, successful navigation might be achieved with inflexible, habit-like responses that reduce cognitive load. Adult neurogenesis is believed to contribute to the spatial processing functions of the hippocampus, particularly when behavioral flexibility is required. However, little is known about the role of neurogenesis in spatial navigation when goals are unpredictable or change according to certain rules. We hypothesized that neurogenesis is necessary in a spatial navigation task that involves different patterns of reinforcement. Intact and neurogenesis-deficient rats were trained to escape to one of two possible platform locations in a spatial water maze. The platform either repeated in the same location for all trials in a day, alternated between two locations across trials, or randomly moved between the two locations. Neurogenesis selectively enhanced escape performance in the alternating condition, but not by improving platform choice accuracy. Instead, neurogenesis-intact rats made fewer search errors and developed an efficient habit-like strategy where they consistently swam to a preferred location. If the platform was not present, they proceeded to the other possible location. In contrast, neurogenesis-deficient rats were indecisive and navigationally less-efficient. Thus, in conditions where goals follow a predictable spatiotemporal pattern, adult neurogenesis promotes the adoption of navigation strategies that are spatially nonspecific but, nonetheless, accurate and efficient.
The Paraventricular Thalamus is a Critical Mediator of Top-down Control of Cue-motivated Behavior in Rats
Authors: Campus Paolo , Covelo Ignacio R. , Kim Youngsoo , Parsegian Aram , Kuhn Brittany N. , Lopez Sofia A. , Neumaier John F. , Ferguson Susan M. , Woods Leah C. Solberg , Sarter Martin , Flagel Shelly B.
Published: May 2019

Cues in the environment can elicit complex emotional states, and thereby maladaptive behavior, as a function of their ascribed value. Here we capture individual variation in the propensity to attribute motivational value to reward-cues using the sign-tracker/goal-tracker animal model. Goal-trackers attribute predictive value to reward-cues, and sign-trackers attribute both predictive and incentive value. Using chemogenetics and microdialysis, we show that, in sign-trackers, stimulation of the neuronal pathway from the prelimbic cortex (PrL) to the paraventricular nucleus of the thalamus (PVT) decreases the incentive value of a reward-cue. In contrast, in goal-trackers, inhibition of the PrL-PVT pathway increases both the incentive value and dopamine levels in the nucleus accumbens shell. The PrL-PVT pathway, therefore, exerts top-down control over the dopamine-dependent process of incentive salience attribution. These results highlight PrL-PVT pathway as a potential target for treating psychopathologies associated with the attribution of excessive incentive value to reward-cues, including addiction.
Retinal outputs depend on behavioural state
Authors: Schröder Sylvia , Steinmetz Nicholas A. , Krumin Michael , Pachitariu Marius , Rizzi Matteo , Lagnado Leon , Harris Kenneth D , Carandini Matteo
Published: May 2019

The operating mode of the visual system depends on behavioural states such as arousal1,2. This dependence is seen both in primary visual cortex3–7 (V1) and in subcortical brain structures receiving direct retinal input4,8. Here we show that this effect arises as early as in the output of the retina. We first measured activity in a region that receives retinal projections9, the superficial superior colliculus (sSC), and found that this activity strongly depended on behavioural state. This modulation was not mediated by feedback inputs from V1 as it was immune to V1 inactivation. We then used Neuropixels probes10 to record activity in the optic tract, and we found some retinal axons whose activity significantly varied with arousal, even in darkness. To characterize these effects on a larger sample of retinal outputs, we imaged the activity of retinal boutons11,12 in sSC during behaviour using a calcium indicator. The activity of these boutons correlated with arousal as strongly as that of sSC neurons, and this correlation persisted also during darkness. These results reveal a novel property of retinal function in mice, which could be observed only during behaviour: retinal outputs are modulated by behavioural state before they reach the rest of the brain.
Isolation and Diversity of Sediment Bacteria in the Hypersaline Aiding Lake, China
Authors: Guan Tong-Wei , Lin Yi-Jin , Ou Meng-Ying , Chen Ke-Bao
Published: May 2019

A total of 343 bacteria from sediment samples of Aiding Lake, China, were isolated using nine different media with 5% or 15% (w/v) NaCl. The number of species and genera of bacteria recovered from the different media significantly varied, indicating the need to optimize the isolation conditions. The results showed an unexpected level of bacterial diversity, with four phyla (Firmicutes, Actinobacteria, Proteobacteria, and Rhodothermaeota), fourteen orders (Actinopolysporales, Alteromonadales, Bacillales, Balneolales, Chromatiales, Glycomycetales, Jiangellales, Micrococcales, Micromonosporales, Oceanospirillales, Pseudonocardiales, Rhizobiales, Streptomycetales, and Streptosporangiales), including 17 families, 41 genera, and 71 species. In this study, the predominant phyla included Firmicutes and Actinobacteria and the predominant genus includedHalomonas,Gracilibacillus,Streptomyces, andActinopolyspora. To our knowledge, this is the first time that members of phylum Rhodothermaeota were identified in sediment samples from a salt lake. This study has identified at least four novel isolates.