bluuebunny/crossref_metadata_2025 huggingface dataset:
The genetic makeup of the electrocardiogram
Authors: Verweij Niek , Benjamins Jan-Walter , Morley Michael P. , van de Vegte Yordi , Teumer Alexander , Trenkwalder Teresa , Reinhard Wibke , Cappola Thomas P. , van der Harst Pim
Published: May 2019

Since its original description in 1893 by Willem van Einthoven, the electrocardiogram (ECG) has been instrumental in the recognition of a wide array of cardiac disorders1,2. Although many electrocardiographic patterns have been well described, the underlying biology is incompletely understood. Genetic associations of particular features of the ECG have been identified by genome wide studies. This snapshot approach only provides fragmented information of the underlying genetic makeup of the ECG. Here, we follow the effecs of individual genetic variants through the complete cardiac cycle the ECG represents. We found that genetic variants have unique morphological signatures not identfied by previous analyses. By exploiting identified abberations of these morphological signatures, we show that novel genetic loci can be identified for cardiac disorders. Our results demonstrate how an integrated approach to analyse high-dimensional data can further our understanding of the ECG, adding to the earlier undertaken snapshot analyses of individual ECG components. We anticipate that our comprehensive resource will fuelin silicoexplorations of the biological mechanisms underlying cardiac traits and disorders represented on the ECG. For example, known disease causing variants can be used to identify novel morphological ECG signatures, which in turn can be utilized to prioritize genetic variants or genes for functional validation. Furthermore, the ECG plays a major role in the development of drugs, a genetic assessment of the entire ECG can drive such developments.
EGR1 transcriptional control of human cytomegalovirus latency
Authors: Buehler Jason , Carpenter Ethan , Zeltzer Sebastian , Igarashi Suzu , Rak Michael , Mikell Iliyana , Nelson Jay A. , Goodrum Felicia
Published: May 2019

Sustained phosphotinositide3-kinase (PI3K) signaling is critical to the maintenance of herpesvirus latency. We have previously shown that the beta-herpesvirus, human cytomegalovirus (CMV), regulates epidermal growth factor receptor (EGFR), upstream of PI3K, to control states of latency and reactivation. Inhibition of EGFR signaling enhances CMV reactivation from latency and increases viral replication, but the mechanisms by which EGFR impacts replication and latency is not known. We demonstrate that HCMV downregulates MEK/ERK and AKT phosphorylation, but not STAT3 or PLCγ for productive replication. Similarly, inhibition of either MEK/ERK or PI3K/AKT, but not STAT or PLCγ, pathways increases viral reactivation from latently infected CD34+hematopoietic progenitor cells (HPCs), defining a role for these pathways in latency. We hypothesized that CMV modulation of EGFR signaling might impact viral transcription. Indeed, EGF-stimulation increased expression of theUL138latency gene, but not immediate early or early viral genes, suggesting that EGFR signaling promotes latent gene expression. The early growth response-1 (EGR1) transcription factor is induced downstream of EGFR signaling through both PI3K/AKT and MEK/ERK pathways. EGR1 expression is important for the maintenance of HPC stemness and its downregulation drives HPC differentiation and mobilization. We demonstrate that EGR1 binds upstream ofUL138and is sufficient to promoteUL138expression. Further, disruption of EGR1 binding upstream ofUL138prevented CMV from establishing a latent infection in CD34+HPCs. Our results indicate a model whereby UL138 modulation of EGFR signaling feeds back to promote UL138 expression and suppression of replication to establish or maintain viral quiescence.

AUTHOR SUMMARY

CMV regulates EGFR signaling to balance states of viral latency and replication. CMV blocks downstream PI3K/AKT and MEK/ERK signaling pathways through down-regulation of EGFR at the plasma membrane. PI3K/AKT and MEK/ERK signaling increases expression of the EGR1 transcription factor that is necessary for the maintenance of stem cell stemness. A decrease in EGR1 expression promotes HPC mobilization to the periphery and differentiation, a known stimulus for CMV reactivation. We identified functional EGR1 binding sites upstream of theUL138gene and EGR-1 binding stimulatesUL138expression. Additionally, down-regulation of EGR1 by CMV miR-US22 decreasesUL138expression emphasizing the importance of this transcription factor in expression of this latency gene. Lastly, we demonstrate that a CMV mutant virus lacking an upstream EGR1 binding site is unable to establish latency in CD34+HPCs. This study defines one mechanism by which EGFR signaling impacts viral gene expression to promote CMV latency.
A cell-free DNA metagenomic sequencing assay that integrates the damage response to infection
Authors: Cheng Alexandre Pellan , Burnham Philip , Lee John Richard , Cheng Matthew Pellan , Suthanthiran Manikkam , Dadhania Darshana , De Vlaminck Iwijn
Published: May 2019

High-throughput metagenomic sequencing offers an unbiased approach to identify pathogens in clinical samples. Conventional metagenomic sequencing however does not integrate information about the host, which is often critical to distinguish infection from infectious disease, and to assess the severity of disease. Here, we explore the utility of high-throughput sequencing of cell-free DNA after bisulfite conversion to map the tissue and cell types of origin of host-derived cell-free DNA, and to profile the bacterial and viral metagenome. We applied this assay to 51 urinary cfDNA isolates collected from a cohort of kidney transplant recipients with and without bacterial and viral infection of the urinary tract. We find that the cell and tissue types of origin of urinary cell-free DNA can be derived from its genome-wide profile of methylation marks, and strongly depend on infection status. We find evidence of kidney and bladder tissue damage due to viral and bacterial infection, respectively, and of the recruitment of neutrophils to the urinary tract during infection. Through direct comparison to conventional metagenomic sequencing as well as clinical tests of infection, we find this assay accurately captures the bacterial and viral composition of the sample. The assay presented here is straightforward to implement, offers a systems view into bacterial and viral infections of the urinary tract, and can find future use as a tool for the differential diagnosis of infections.
The parallel auditory brainstem response
Authors: Polonenko Melissa J , Maddox Ross K
Published: May 2019

The frequency-specific tone-evoked auditory brainstem response (ABR) is an indispensable tool in both the audiology clinic and research laboratory. Most frequently the toneburst ABR is used to estimate hearing thresholds in infants, toddlers and other patients for whom behavioral testing is not feasible. Therefore, results of the ABR exam form the basis for decisions regarding interventions and hearing habilitation with implications extending far into the child’s future. Currently, responses are elicited by periodic sequences of toneburst stimuli presented serially to one ear at a time, which take a long time to measure multiple frequencies and intensities, and provide incomplete information if the infant wakes up early. Here we describe a new method, the parallel ABR (pABR), which uses randomly timed toneburst stimuli to simultaneously acquire ABR waveforms to 5 frequencies in both ears. Here we describe the pABR and quantify its effectiveness in addressing the greatest drawback of current methods: test duration. We show that in adults with normal hearing the pABR yields high-quality waveforms over a range of intensities, with similar morphology to the standard ABR in a fraction of the recording time. Furthermore, longer latencies and smaller amplitudes for low frequencies at a high intensity evoked by the pABR versus serial ABR suggest that responses may have better place specificity due to the masking provided by the other simultaneous toneburst sequences. Thus, the pABR has substantial potential for facilitating faster accumulation of more diagnostic information that is important for timely identification and treatment of hearing loss.
Intentions of Canadian health professionals towards recommending exercise to people living with ALS
Authors: Jones Kelvin E , Berry Tanya R , Bello-Haas Vanina Dal
Published: May 2019

Background

To provide a nationwide overview of the attitudes, social pressure, perceived ability and intentions of health professionals toward exercise prescription for people living with ALS (pALS).

Methods

An online survey of physician and other health professionals (HPs) working in academic ALS clinics across Canada.

Results

The response rate was 48% (84/176) with 30% of respondents identifying as physicians, 63% as other HPs and the remainder as administrative or research personnel. Respondents were sharply divided in their intentions to provide exercise counsel: 24% unlikely and 45% likely. Respondents with low intentions were HPs that considered this activity outside their scope of practice. Measures of intention and attitude were more positive for flexibility compared to strength and aerobic exercise. Perceptions of social pressure and ability to provide exercise counsel were significantly correlated with intention across the three exercise modes in all respondents. Qualitative themes identified as barriers to exercise prescription were lack of confidence or competence (31% physicians, 32% HP), patient tolerance (30% HP), lack of evidence (22% physicians) and lack of infrastructure (22% physicians).

Conclusions

While “lack of evidence” for the benefit of exercise was a deterrent for physicians, the larger issue for all respondents was building competence and confidence in exercise prescription for pALS.
Toward Broad Spectrum DHFR inhibitors Targeting Trimethoprim Resistant Enzymes Identified in Clinical Isolates of Methicillin-Resistant Staphylococcus aureus
Authors: Reeve Stephanie M. , Si Debjani , Krucinska Jolanta , Yan Yongzhao , Viswanathan Kishore , Wang Siyu , Holt Graham T. , Frenkel Marcel S. , Ojewole Adegoke A. , Estrada Alexavier , Agabiti Sherry S. , Alverson Jeremy B. , Gibson Nathan D. , Priestly Nigel D. , Wiemer Andrew J. , Donald Bruce R. , Wright Dennis L.
Published: May 2019

The spread of plasmid borne resistance enzymes in clinical Staphylococcus aureus isolates is rendering trimethoprim and iclaprim, both inhibitors of dihydrofolate reductase (DHFR), ineffective. Continued exploitation of these targets will require compounds that can broadly inhibit these resistance-confering isoforms. Using a structure-based approach, we have developed a novel class of ionized non-classical antifolates (INCAs) that capture the molecular interactions that have been exclusive to classical antifolates. These modifications allow for a greatly expanded spectrum of activity across these pathogenic DHFR isoforms, while maintaining the ability to penetrate the bacterial cell wall. Using biochemical, structural and computational methods, we are able to optimize these inhibitors to the conserved active sites of the endogenous and trimethoprim resistant DHFR enzymes. Here, we report a series of INCA compounds that exhibit low nanomolar enzymatic activity and potent cellular activity with human selectivity against a panel of clinically relevant TMPR MRSA isolates.
Type 2 Diabetes: One Disease, Many Pathways
Authors: Ha Joon , Sherman Arthur
Published: May 2019

Diabetes is a chronic, progressive disease that calls for longitudinal data and analysis. We introduce a longitudinal mathematical model that is capable of representing the metabolic state of an individual at any point in time during their progression from normal glucose tolerance to type 2 diabetes (T2D) over a period of years. As an application of the model, we account for the diversity of pathways typically followed, focusing on two extreme alternatives, one that goes through impaired fasting glucose (IFG) first, and one that goes through impaired glucose tolerance (IGT) first. These two pathways are widely recognized to stem from distinct metabolic abnormalities in hepatic glucose production and peripheral glucose uptake, respectively. We confirm this but go beyond to show that IFG and IGT lie on a continuum ranging from high hepatic insulin resistance and low peripheral insulin resistance to low hepatic resistance and high peripheral resistance. We show that IFG generally incurs IGT, and IGT generally incurs IFG on the way to T2D, highlighting the difference between innate and acquired defects and the need to assess patients early to determine their underlying primary impairment and appropriately target therapy. We also consider other mechanisms, showing that IFG can result from impaired insulin secretion, that non-insulin dependent glucose uptake can also mediate or interact with these pathways, and that impaired incretin signaling can accelerate T2D progression. We consider whether hyperinsulinemia can cause insulin resistance in addition to being a response to it and suggest that this is a minor effect.
Metabolic reprogramming and elevation of glutathione in chromophobe renal cell carcinomas
Authors: Xiao Yi , Clima Rosanna , Busch Jonas Felix , Rabien Anja , Kilic Ergin , Villegas Sonia , Türkmen Seval , Timmermann Bernd , Attimonelli Marcella , Jung Klaus , Meierhofer David
Published: May 2019

Chromophobe renal cell carcinomas (chRCC) are derived from intercalated cells of the collecting duct system, and are thought to be the malignant counterpart of benign renal oncocytomas. Here, we report the characterization of nine chRCC with adjacent healthy kidney tissues by applying proteome-, transcriptome (TCGA)-, and metabolome profiling. Most strikingly, the reactive oxygen species scavenger glutathione was significantly elevated in chRCC, caused by down-regulated enzymes involved in glutathione degradation. Metabolic reprogramming including stalled gluconeogenesis, down-regulated fatty acid- and amino acid metabolism was identified, even though, the abundance of amino acids and “energy carrier” molecules were unchanged. A striking anti-correlation of the mitochondrial respiratory chain between the transcriptome and the proteome was discovered, the transcripts coding for the respiratory chain were up-, while corresponding proteins and enzymatic activities were down-regulated. Similar to renal oncocytomas, chRCC exhibited a significant increase in glutathione, but are distinguishable by distinct regulation of the respiratory chain.
Exercise does not induce browning of WAT at thermoneutrality and induces an oxidative, myogenic signature in BAT
Authors: Aldiss Peter , Lewis Jo E , Lupini Irene , Boocock David J , Miles Amanda K , Ebling Francis J P , Budge Helen , Symonds Michael E
Published: May 2019

Background and aim

Exercise training elicits diverse effects on brown (BAT) and white adipose tissue (WAT) physiology in rodents. However, these animals are typically housed below their thermoneutral zone (i.e. 28-32°C). In these conditions, BAT is chronically hyperactive and, unlike human residence, closer to thermoneutrality. Therefore, we set out to determine the effects of exercise training in obese animals at 28°C (i.e. thermoneutrality) on BAT and WAT in its basal (i.e. inactive) state.

Methods

Sprague-Dawley rats (n=12) were housed at thermoneutrality from 3 weeks of age and fed a high-fat diet (HFD). At 12 weeks of age half these animals were randomised to 4-weeks of exercise exercise training, i.e. swim-training (1 hour/day, 5 days per week). Metabolic assessment was undertaken during the final 48h and was followed by interscapular and perivascular BAT and inguinal (I)WAT sampling for the analysis of thermogenic genes and the proteome.

Results

Exercise attenuated weight gain but did not affect fat mass or general metabolic parameters (i.e. fasting insulin and glucose). Interestingly, although BAT mass was increased, there was no change in thermogenic gene expression. Differentially regulated proteins in BAT enriched gene ontology (GO) terms including 2-oxoglutarate metabolic process, cytochrome-c activity and mitochondrial respiratory chain complex IV. This was accompanied by an upregulation of multiple proteins and GO terms involved in skeletal muscle physiology suggesting an adipocyte to myocyte switch in BAT. UCP1 mRNA was undetectable in IWAT despite an increase in classical ‘browning’ markers (i.e. PGC1a and ADRB3) with exercise. Enriched GO terms in IWAT included DNA binding and positive regulation of apoptosis. Impact analysis highlighted carbon metabolism and OXPHOS pathways were regulated by exercise in BAT whilst HIF-1 signalling and cytokine-cytokine receptor interaction were among those modified in IWAT.

Conclusion

Exercise training reduces weight gain in obese animals at thermoneutrality and is accompanied by an oxidative, myogenic signature in BAT, rather than induction of thermogenic genes. This may represent a new, UCP1-independent pathway through which BAT regulates body weight at thermoneutrality.
Identifying gene function and module connections by the integration of multi-species expression compendia
Authors: Li Hao , Rukina Daria , David Fabrice P. A. , Li Terytty Yang , Oh Chang-Myung , Gao Arwen W. , Katsyuba Elena , Sleiman Maroun Bou , Komljenovic Andrea , Huang Qingyao , Williams Robert W. , Robinson-Rechavi Marc , Schoonjans Kristina , Morgenthaler Stephan , Auwerx Johan
Published: May 2019

The functions of many eukaryotic genes are still poorly understood. We developed and validated a new method, termed GeneBridge, which is based on two linked approaches to impute gene function and bridge genes with biological processes. First,Gene-ModuleAssociationDetermination (G-MAD) allows the annotation of gene function. Second,Module-ModuleAssociationDetermination (M-MAD) allows predicting connectivity among modules. We applied the GeneBridge tools to large-scale multi-species expression compendia—1,700 datasets with over 300,000 samples from human, mouse, rat, fly, worm, and yeast—collected in this study. Unlike most existing bioinformatics tools, GeneBridge exploits both positive and negative gene/module-module associations. We constructed association networks, such as those bridging mitochondria and proteasome, mitochondria and histone demethylation, as well as ribosomes and lipid biosynthesis. The GeneBridge tools together with the expression compendia are available atsystems-genetics.org, to facilitate the identification of connections linking genes, modules, phenotypes, and diseases.
A Human Liver Cell Atlas: Revealing Cell Type Heterogeneity and Adult Liver Progenitors by Single-Cell RNA-sequencing
Authors: Aizarani Nadim , Saviano Antonio , Sagar  , Mailly Laurent , Durand Sarah , Pessaux Patrick , Baumert Thomas F. , Grün Dominic
Published: May 2019

The human liver is an essential multifunctional organ, and liver diseases are rising with limited treatment options. However, the cellular complexity and heterogeneity of the liver remain poorly understood. Here, we performed single-cell RNA-sequencing of ~5,000 cells from normal liver tissue of 6 human donors to construct the first human liver cell atlas. Our analysis revealed previously unknown sub-types among endothelial cells, Kupffer cells, and hepatocytes with transcriptome-wide zonation of these populations. We show that the EPCAM+ population is highly heterogeneous and consists of hepatocyte progenitors, cholangiocytes and a MUC6+ stem cell population with a specific potential to form liver organoids. As proof-of-principle, we applied our atlas to unravel phenotypic changes in cells from hepatocellular carcinoma tissue and to investigate cellular phenotypes of human hepatocytes and liver endothelial cells engrafted into a humanized FAH-/- mouse liver. Our human liver cell atlas provides a powerful and innovative resource enabling the discovery of previously unknown cell types in the normal and diseased liver.
Distinct properties of layer 3 pyramidal neurons from prefrontal and parietal areas of the monkey neocortex
Authors: Gonzalez-Burgos Guillermo , Miyamae Takeaki , Krimer Yosef , Gulchina Yelena , Pafundo Diego , Krimer Olga , Bazmi Holly , Arion Dominique , Enwright John F , Fish Kenneth , Lewis David A
Published: May 2019

In primates, working memory function depends on activity in a distributed network of cortical areas that display different patterns of delay task-related activity. These differences are correlated with, and might depend on, distinctive properties of the neurons located in each area. For example, layer 3 pyramidal neurons (L3PNs) differ significantly between primary visual and dorsolateral prefrontal (DLPFC) cortices. However, to what extent L3PNs differ between DLPFC and other association cortical areas is less clear. Hence, we compared the properties of L3PNs in monkey DLPFC versus posterior parietal cortex (PPC), a key node in the cortical working memory network. Using patch clamp recordings and biocytin cell filling in acute brain slices, we assessed the physiology and morphology of L3PNs from monkey DLPFC and PPC. The L3PN transcriptome was studied using laser microdissection combined with DNA microarray or quantitative PCR. We found that in both DLPFC and PPC, L3PNs were divided into regular spiking (RS-L3PNs) and bursting (B-L3PNs) physiological subtypes. Whereas regional differences in single-cell excitability were modest, B-L3PNs were rare in PPC (RS-L3PN:B-L3PN, 94:6), but were abundant in DLPFC (50:50), showing greater physiological diversity. Moreover, DLPFC L3PNs display larger and more complex basal dendrites with higher dendritic spine density. Additionally, we found differential expression of hundreds of genes, suggesting a transcriptional basis for the differences in L3PN phenotype between DLPFC and PPC. These data show that the previously observed differences between DLPFC and PPC neuron activity during working memory tasks are associated with diversity in the cellular/molecular properties of L3PNs.

Significance statement

In the human and non-human primate neocortex, layer 3 pyramidal neurons (L3PNs) differ significantly between dorsolateral prefrontal (DLPFC) and sensory areas. Hence, L3PN properties reflect, and may contribute to, a greater complexity of computations performed in DLPFC. However, across association cortical areas, L3PN properties are largely unexplored. We studied the physiology, dendrite morphology and transcriptome of L3PNs from macaque monkey DLPFC and posterior parietal cortex (PPC), two key nodes in the cortical working memory network. L3PNs from DLPFC had greater diversity of physiological properties and larger basal dendrites with higher spine density. Moreover, transcriptome analysis suggested a molecular basis for the differences in the physiological and morphological phenotypes of L3PNs from DLPFC and PPC.
Can processing of face trustworthiness bypass early visual cortex? A transcranial magnetic stimulation masking study
Authors: Janssens Shanice E. W. , Sack Alexander T. , Jessen Sarah , de Graaf Tom A.
Published: May 2019

As a highly social species, we constantly evaluate human faces to decide whether we can trust someone. Previous studies suggest that face trustworthiness can be processed unconsciously, but the underlying neural pathways remain unclear. Specifically, the question remains whether processing of face trustworthiness relies on early visual cortex (EVC), required for conscious perception. If processing of trustworthiness can bypass EVC, then disrupting EVC should impair conscious trustworthiness perception while leaving forced-choice trustworthiness judgment intact. We applied double-pulse transcranial magnetic stimulation (TMS) to right EVC, at different stimulus onset asynchronies (SOAs) from presentation of a face in either the left or right hemifield. Faces were slightly rotated clockwise or counterclockwise, and were either trustworthy or untrustworthy. On each trial, participants discriminated 1) trustworthiness, 2) stimulus rotation, and 3) subjective visibility of trustworthiness. At early SOAs and specifically in the left hemifield, orientation processing (captured by the rotation task) was impaired by TMS. Crucially, though TMS also impaired subjective visibility of trustworthiness, no effects on trustworthiness discrimination were obtained. Conscious perception of face trustworthiness (captured by visibility ratings) relies on intact EVC, while forced-choice trustworthiness judgments may not. These results are consistent with the hypothesis that trustworthiness processing can bypass EVC. For basic visual features, extrastriate pathways are well-established; but face trustworthiness depends on a complex configuration of features. Its processing without EVC and outside of awareness is therefore of particular interest, further highlighting its ecological relevance.
Exautomate: A user-friendly tool for region-based rare variant association analysis (RVAA)
Authors: Davis Brent D. , Dron Jacqueline S. , Robinson John F. , Hegele Robert A. , Lizotte Dan J.
Published: May 2019

Region-based rare variant association analysis (RVAA) is a popular method to study rare genetic variation in large datasets, especially in the context of complex traits and diseases. Although this method shows great promise in increasing our understanding of the genetic architecture of complex phenotypes, performing a region-based RVAA can be challenging. The sequence kernel association test (SKAT) can be used to perform this analysis, but its inputs and modifiable parameters can be extremely overwhelming and may lead to results that are difficult to reproduce. We have developed a software package called “Exautomate” that contains the tools necessary to run a region-based RVAA using SKAT and is easy-to-use for any researcher, regardless of their previous bioinformatic experiences. In this report, we discuss the utilities of Exautomate and provide detailed examples of implementing our package. Importantly, we demonstrate a proof-of-principle analysis using a previously studied cohort of 313 familial hypercholesterolemia (FH) patients. Our results show an increased burden of rare variants in genes known to cause FH, thereby demonstrating a successful region-based RVAA using Exautomate. With our easy-to-use package, we hope researchers will be able to perform reproducible region-based RVAA to further our collective understanding behind the genetics of complex traits and diseases.
Dynamic colonization of microbes and their functions after fecal microbiota transplantation for inflammatory bowel disease
Authors: Chu Nathaniel D. , Crothers Jessica W. , Nguyen Le T.T. , Kearney Sean M. , Smith Mark B. , Kassam Zain , Collins Cheryl , Xavier Ramnik , Moses Peter L. , Alm Eric J.
Published: May 2019

For fecal microbiota transplantation (FMT) to be successful in complex immune diseases like inflammatory bowel disease (IBD), it is assumed that therapeutic microbes and their beneficial functions and immune interactions must colonize the recipient and persist in sufficient quantity and for a long enough period of time to result in a clinical benefit. But few studies have comprehensively profiled the colonization and persistence of transferred microbes along with the transfer of their microbial and immune functions. Using 16S, metagenomic, and immunoglobulin A (IgA) sequencing, we analyzed hundreds of longitudinal microbiome samples from a randomized controlled trial of 12 patients with ulcerative colitis who received fecal transplant or placebo for 12 weeks. We uncovered a range of competitive dynamics among donor and patient strains, showing that persistence of transferred microbes is far from static. Indeed, one patient experienced dramatic loss of donor bacteria 10 weeks into the trial, coinciding with a bloom of pathogenic bacteria and worsening clinical symptoms. We similarly evaluated transfer of microbial functions, including desired ones like butyrate production and unintended ones like antibiotic resistance. By profiling bacteria coated with IgA, we identified IgA-coated bacteria associated with inflammation, and we found that microbial interactions with the host immune system can be transferred across people. This transfer of immune function is likely critical for gut microbiome therapeutics for immune-related diseases. Our findings elucidate the colonization dynamics of gut microbes as well as their functions in the context of FMT to treat a complex disease—information that may provide a critical foundation for the development of more-targeted therapeutics.
2dSS: a web server for protein secondary structure visualization
Authors: Lotun Diksha Priya , Cochard Charlotte , Vieira Fabio R.J , Bernardes Juliana Silva
Published: May 2019

2dSS is a web-server for visualising and comparing secondary structure predictions. It provides two main functionalities: 2D-alignment and compare predictions. The “2D-alignment” has been designed to visualise conserved secondary structure elements in a multiple sequence alignment (MSA). From this we can study the secondary structure content of homologous proteins (a protein family) and highlight its structural patterns. The “compare predictions” has been designed to compare the output of several secondary structure prediction tools, and check their accuracy when compared with real secondary structure elements extracted from 3D-structure. 2dSS provides a comprehensive representation of protein secondary structure elements, and it can be used to visualise and compare secondary structures of any prediction tool.

Availability

http://genome.lcqb.upmc.fr/2dss/
Malpighamoebainfection compromises fluid secretion and P-glycoprotein detoxification in Malpighian tubules
Authors: Rossi Marta , Ott Swidbert R. , Niven Jeremy E.
Published: May 2019

Malpighian tubules, analogous to vertebrate nephrons, play a key role in insect osmoregulation and detoxification. Tubules can become infected with a protozoan,Malpighamoeba,which damages their epithelial cells, potentially compromising their function. Here we used a modified Ramsay assay to quantify the impact ofMalpighamoebainfection on fluid secretion and P-glycoprotein-dependent detoxification by desert locust Malpighian tubules. Infected tubules have a greater surface area and a higher fluid secretion rate than uninfected tubules. Infection also impairs P-glycoprotein-dependent detoxification by reducing the net rhodamine extrusion per surface area. However, due to the increased surface area and fluid secretion rate, infected tubules have similar total net extrusion per tubule to uninfected tubules. Increased fluid secretion rate of infected tubules likely exposes locusts to greater water stress and increased energy costs. Coupled with reduced efficiency of P-glycoprotein detoxification per surface area,Malpighamoebainfection is likely to reduce insect survival in natural environments.
Does variation in glucocorticoid regulation predict fitness? A phylogenetic meta-analysis
Authors: Schoenle Laura A. , Zimmer Cedric , Miller Eliot T. , Vitousek Maren N.
Published: May 2019

Glucocorticoid hormones (GCs) are central mediators of metabolism and the response to challenges. Because circulating levels of GCs increase in response to challenges, within-population variation in GCs could reflect individual variation in condition or experience. At the same time, individual variation in the degree to which GCs increase in response to challenges (which is relatively consistent within individuals over time) could have causal effects on stress coping capacity, and the ability to survive and reproduce. Although a number of studies in vertebrates have tested whether within-population variation in GCs predicts components of fitness, it is not clear whether there are consistent patterns across taxa. Here we present the first phylogenetic meta-analysis testing whether within-population variation in GCs is associated with components of fitness across vertebrates. At the same time, we introduce and test predictions about an overlooked but potentially important mediator of GC-fitness relationships: life history context. We suggest that strong context-dependence in the fitness benefit of maintaining elevated GCs could obscure consistent patterns between GCs and fitness across taxa. Meta-analyses revealed that across vertebrates, baseline and stress-induced GCs were consistently negatively correlated with reproductive success. This relationship did not differ depending on life history context. In contrast, the relationships between GCs and survival were highly context dependent, differing according to life history strategy. Both baseline and stress-induced GCs were more strongly negatively associated with survival in longer-lived populations and species. Stress-induced GCs were also more negatively associated with survival in organisms that engage in relatively more valuable reproductive attempts. Fecal GCs did not predict survival or reproductive success. We also used a meta-analytic approach to test whether experimental increases in GCs had consistent causal effects on fitness. Experimental increases in GCs reduced both survival and reproductive success, although the latter relationship was not significant when accounting for phylogeny. Overall, these results support the prediction that GC-fitness relationships can be strongly context dependent, and suggest that incorporating life history may be particularly important for understanding GC-survival relationships. Future studies that explore the role of other aspects of context (e.g., the nature and frequency of stressors, environmental variation) within and across species could provide important insights how and when variation in GC regulation predicts fitness.
Novel mouse model of encephalocele: post-neurulation origin and relationship to open neural tube defects
Authors: Rolo Ana , Galea Gabriel L. , Savery Dawn , Greene Nicholas D. E. , Copp Andrew J.
Published: May 2019

Encephalocele is a clinically important birth defect that can lead to severe disability in childhood and beyond. The embryonic pathogenesis of encephalocele is poorly understood and, while usually classified as a ‘neural tube defect’, there is conflicting evidence on whether encephalocele results from defective neural tube closure, or is a post-neurulation defect. It is also unclear whether encephalocele can result from the same causative factors as anencephaly and open spina bifida, or whether it is aetiologically distinct. This lack of information results largely from the scarce availability of animal models of encephalocele, particularly ones that resemble the commonest, non-syndromic human defects. Here we report a novel mouse model of occipito-parietal encephalocele, in which the small GTPase Rac1 is conditionally ablated in the (non-neural) surface ectoderm. Most mutant fetuses have open spina bifida, and some also exhibit exencephaly/anencephaly. However, a large proportion of mutant fetuses exhibit encephalocele affecting the occipito-parietal region. The encephalocele phenotype does not result from a defect in neural tube closure, but rather from a later disruption of the surface ectoderm covering the already closed neural tube, allowing the brain to herniate. The neuroepithelium itself shows no down-regulation of Rac1 and appears morphologically normal until late gestation. A large skull defect develops overlying the region of brain herniation. Our work provides a new genetic model of occipito-parietal encephalocele, particularly resembling non-syndromic human cases. While encephalocele has a different, later-arising pathogenesis than open neural tube defects, both can share the same genetic causation.

SUMMARY STATEMENT

Encephalocele - a severe brain defect - arises after neural tube closure, but can share a common genetic cause with anencephaly, a defect of neural tube closure.
Leishmaniatargets the macrophage epigenome and dampens the NF-κB/NLRP3-mediated inflammatory response
Authors: Lecoeur Hervé , Prina Eric , Rosazza Thibault , Kokou Kossiwa , N’Diaye Paya , Aulner Nathalie , Varet Hugo , Bussotti Giovanni , Xing Yue , Weil Robert , Meng Guangxun , Späth Gerald F.
Published: May 2019

Aberrant macrophage activation during intracellular infection generates important immunopathologies that can cause severe human morbidity. A better understanding of microbial immune subversion strategies and macrophage phenotypic and functional responses is a prerequisite for the design of novel, host-directed intervention strategies. Here, we uncover a fine-tuned transcriptional response induced in primary macrophages infected by the human parasiteLeishmania amazonensisthat prevents NF-κB and NLRP3 inflammasome activation. This unusual subversion is characterized by respectively suppression and induction of activating and de-activating components of the NF-κB and NLRP3 pathways. This dichotomic modulation was associated with histone H3 hypoacetylation at promoters of NF-κB-related, pro-inflammatory genes. Our results reveal a novelLeishmaniaimmune subversion strategy targeting host cell epigenetic regulation to modulate the macrophage phenotype. Modulation of the macrophage epigenetic landscape establishes conditions beneficial for intracellular parasite survival, and opens interesting new venues for host-directed, anti-microbial drug discovery.
Prenatal alcohol exposure disrupts Shh pathway and primary cilia genes in the mouse neural tube
Authors: Boschen Karen E. , Fish Eric W. , Parnell Scott E.
Published: May 2019

Neurulation-stage alcohol exposure (NAE; embryonic day [E] 8-10) is associated with midline craniofacial and CNS defects that likely arise from disruption of morphogen pathways, such as Sonic hedgehog (Shh). Notably, midline anomalies are also a hallmark of genetic ciliopathies such as Joubert syndrome. We tested whether NAE alters Shh pathway signaling and the number and function of primary cilia, organelles critical for Shh pathway transduction. Female C57BL/6J mice were administered two doses of alcohol (2.9 g/kg/dose) or vehicle on E9. Embryos were collected 6, 12, or 24 hr later, and changes to Shh, cell cycle genes, and primary cilia were measured in the rostroventral neural tube (RVNT). Within the first 24 hours post-NAE, reductions in Shh pathway and cell cycle gene expression and the ratio of Gli3 forms in the full-length activator state were observed. RVNT volume and cell layer width were reduced at 12 hr. In addition, expression of multiple cilia-related genes were observed at 6 hr post-NAE. As a further test of cilia gene-ethanol interaction, mice heterozygous forKif3aexhibited perturbed behavior during adolescence following NAE compared to vehicle-treated mice, andKif3aheterozygosity exacerbated the hyperactive effects of NAE on exploratory activity. These data demonstrate that NAE downregulates the Shh pathway in a region of the neural tube that gives rise to alcohol-sensitive brain structures and identifies disruption of primary cilia function, or a “transient ciliopathy”, as a possible cellular mechanism of prenatal alcohol pathogenesis.
Overexpression of a non-muscle RBFOX2 isoform triggers cardiac conduction defects in myotonic dystrophy
Authors: Misra Chaitali , Bangru Sushant , Lin Feikai , Lam Kin , Koenig Sara N. , Lubbers Ellen R. , Hedhli Jamila , Murphy Nathaniel P. , Parker Darren J. , Dobrucki Lawrence W. , Cooper Thomas A. , Tajkhorshid Emad , Mohler Peter J. , Kalsotra Auinash
Published: May 2019

Myotonic dystrophy type 1 (DM1) is a multisystemic genetic disorder caused by a CTG trinucleotide repeat expansion in the 3′ untranslated region ofDMPKgene. Heart dysfunctions occur in nearly 80% of DM1 patients and are the second leading cause of DM1-related deaths. Despite these figures, the mechanisms underlying cardiac-based DM1 phenotypes are unknown. Herein, we report that upregulation of a non-muscle splice isoform of RNA binding protein RBFOX2 in DM1 heart tissue—due to altered splicing factor and microRNA activities—induces cardiac conduction defects in DM1 individuals. Mice engineered to express the non-muscle RBFOX2 isoform in heart via tetracycline-inducible transgenesis, or CRISPR/Cas9-mediated genome editing, reproduced DM1-related cardiac-conduction delay and spontaneous episodes of arrhythmia. Further, by integrating RNA binding with cardiac transcriptome datasets from both DM1 patients and mice expressing the non-muscle RBFOX2 isoform, we identified RBFOX2-driven splicing defects in the voltage-gated sodium and potassium channels, which can alter their electrophysiological properties. Thus, our results uncover atrans-dominant role for an aberrantly expressed RBFOX2 isoform in DM1 cardiac pathogenesis.
Fast sequence-based microsatellite genotyping development workflow
Authors: Lepais Olivier , Chancerel Emilie , Boury Christophe , Salin Franck , Manicki Aurélie , Taillebois Laura , Dutech Cyril , Aissi Abdeldjalil , Bacles Cecile F. E. , Daverat Françoise , Launey Sophie , Guichoux Erwan
Published: May 2019

Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast,de novo ad hocprimer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20 to 40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence, quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.
Temporal learning of bottom-up connections via spatially nonspecific top-down inputs
Authors: Lee Jung Hoon , Kim Mean-Hwan , Vijayan Sujith
Published: May 2019

In the brain, high-order and low-order areas are connected via bottom-up connections (from low-order to high-order areas) and top-down connections (from high-order to low-order areas). While bottom-up signals are thought to be critical in generating perception, functions of top-down signals have not been clearly delineated. One popular theory is that top-down inputs modify the activity of specific cell assemblies to modulate responses to bottom-up inputs. However, a different line of studies proposes that not all top-down inputs are specifically delivered. As the leading theories cannot account for nonspecific top-down inputs, we seek potential functions of nonspecific top-down signals using network models in our study. Our simulation results suggest that top-down inputs can regulate low-order area responses by providing temporal information even without spatial specificity. Specifically, the temporal information in nonspecific top-down inputs can weaken the undesired bottom-up connections, contributing to bottom-up connections’ learning. Further, we found that cortical rhythms (synchronous oscillatory neural responses) are critical in the proposed learning process of bottom-up connections in our model.
Functional analysis of the UVR8 photoreceptor from the monocot Zea mays
Authors: Belén Fernández María , Lorenzo Lamattina , Raúl Cassia
Published: May 2019

Low UV-B fluence is a signaling stimulus that regulates various physiological processes and induces photomorphogenic responses in plants. The specific UV-B receptor UVR8 is a key component in these processes. Although UVR8 sequence is conserved, few homologs have been cloned and reported to be functional. Here we show the cloning and functional analysis of Zea mays UVR8 (ZmUVR8). ZmUVR8 presents 73% of identity with AtUVR8, maintaining the key tryptophan responsible of UV-B perception. ZmUVR8 also contains the VP domain, involved in the interaction with the proteins CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and REPRESSOR OF UV-B PHOTOMOPHOGENESIS 1 (RUP1). Whereas UVR8 was expressed in non-irradiated Arabidopsis and maize leaves, after 2h of UV-B irradiation, its expression was reduced. The expression of chalcone synthase (CHS), involved in flavonoid biosynthesis and regulated by UVR8, was increased in irradiated Arabidopsis and maize leaves. Arabidopsis uvr8-1 null mutant was complemented with ZmUVR8 driven by the CaMV-35S promoter and fused to eGFP. ZmUVR8-eGFP fusion was mainly localized in nuclei of transgenic lines, irrespective of UV-B treatments. UV-B suppressed hypocotyl elongation in WT Arabidopsis plants, whereas in uvr8-1 hypocotyl growth was observed. However, hypocotyl elongation was reduced in UV-B irradiated transgenic lines complemented with ZmUVR8. Moreover, CHS and transcription factor HY5 (ELONGATED HYPOCOTYL 5) expression were also restored in these plants. These results confirm that ZmUVR8 is similar enough to AtUVR8 to restore UV-B perception and signaling in Arabidopsis mutant uvr8-1, thus being a functional UV-B photoreceptor.
Altered protein expression of galactose and N-acetylgalactosamine transferases in schizophrenia superior temporal gyrus
Authors: Mueller Toni M. , Mallepalli Nikita R. , Meador-Woodruff James H.
Published: May 2019

Abnormal glycosylation in schizophrenia brain has been previously implicated in disruptions to protein trafficking, localization, and function. Glycosylation is an enzyme-mediated posttranslational modification and, along with reports of altered glycan biosynthesis and abnormal glycan levels in peripheral fluids, growing evidence for altered glycosylation pathway activity in schizophrenia prompted investigation of specific enzymes which may be responsible for these abnormalities. Glycosylation is a highly variable yet tightly controlled cellular process and, depending on the molecule(s) affected, altered glycan modifications can influence the trajectory of many key functional pathways. In a preliminary gene array study, abnormal transcript expression of 36 glycosylation-associated enzymes was identified in schizophrenia brain. Subsequently, protein expression abnormalities of enzymes which act on glucose (UGGT2), mannose (EDEM2), fucose (FUT8, POFUT2), and N-acetylglucosamine (MGAT4A, B3GNT8) have been reported in this illness. The current study investigates protein expression levels by western blot analysis of the galactose and N-acetylgalactosamine (GalNAc) transferases B3GALTL1, B4GALT1, C1GALT1, GALNT2, GALNT7, GALNT16, and GALNTL5, as well as a related chaperone protein, COSMC, in superior temporal gyrus of age- and sex-matched pairs of schizophrenia and non-psychiatrically ill comparison subjects (N = 16 pairs). In schizophrenia, reduced β-1,4-galactosyltransferase 1 (B4GALT1) and polypeptide GalNAc-transferase 16 (GALNT16) were identified. These findings add support to the hypothesis that dysregulated glycosylation-associated enzyme expression contributes to altered protein glycosylation and downstream substrate-specific defects in schizophrenia.