bluuebunny/crossref_metadata_2025 huggingface dataset:
Aging Alters Phenotypic Traits of Thyroid Dysfunction in Male Mice With Divergent Effects on Complex Systems but Preserved Thyroid Hormone Action in Target Organs
Authors: Engels Kathrin , Rakov Helena , Hönes Georg Sebastian , Brix Klaudia , Köhrle Josef , Zwanziger Denise , Moeller, Lars Christian , Führer Dagmar , Führer-Sakel Dagmar
Published: February 2019

Clinical manifestation of hyperthyroidism and hypothyroidism vary with age, with an attenuated, oligosymptomatic presentation of thyroid dysfunction (TD) in older patients. We asked, whether in rodents TD phenotypes are influenced by age and whether this involves changes in systemic and/or organ thyroid hormone (TH) signaling. Chronic hyper- or hypothyroidism was induced in male mice at different life stages (5, 12, and 20 months). TH excess resulted in pronounced age-specific body weight changes (increase in youngest and decrease in old mice), neither explained by changes in food intake (similar increase at all ages), nor by thermogenic gene expression in brown adipose tissue (BAT) or TH serum concentrations. Relative increase in body temperature and activity were more pronounced in old compared to young hyperthyroid mice. An attenuated hypothyroid state was found in old mice for locomotor activity and in heart and BAT on functional (less bradycardia) and gene expression level (heart and BAT). In contrast, decrease in body weight was pronounced in old hypothyroid mice. Thus, age has divergent impact on features of TD in mice, whereby effects on highly complex systems, such as energy homeostasis are not proportional to serum TH state, in contrast to organ-specific responses in heart and BAT.
Reassessing the Cold War and the Far-Right: Fascist Legacies and the Making of the Liberal International Order after 1945
Authors: Anievas Alexander , Saull Richard
Published: February 2019

This article intervenes in IR debates on the origins and character of the postwar liberal international order. Dominant theorizations of the US-led Western order rest on a shared assumption of its essentially post-fascist character based on the liberal-democratic properties of its constitutive members. This article challenges this prevailing view. It does so through a critical historical and theoretical exploration of the role of far-right ideopolitical forces in the development of the liberal international order during the early Cold War period. Drawing on the concepts of “uneven and combined development” and “passive revolution” as alternative theoretical frames, the article focuses particular attention on the significance of former fascists in the workings and institutional fabric of a number of West European states and the relationship between the United States and NATO in far-right coup-plotting and violence that punctuated their national histories. Demonstrating these far-right “contributions” to the making and evolution of the Cold War order, the article offers a reconceptualization of liberal order construction and US hegemony that not only problematizes existing accounts of Cold War geopolitics but also demonstrates the structural interconnections between the far-right and liberal order-building projects that goes beyond the Cold War era.
PRECISE: A domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors
Authors: Mourragui Soufiane , Loog Marco , Reinders Marcel JT , Wessels Lodewyk FA
Published: February 2019

Motivation

Cell lines and patient-derived xenografts (PDX) have been used extensively to understand the molecular underpinnings of cancer. While core biological processes are typically conserved, these models also show important differences compared to human tumors, hampering the translation of findings from pre-clinical models to the human setting. In particular, employing drug response predictors generated on data derived from pre-clinical models to predict patient response, remains a challenging task. As very large drug response datasets have been collected for pre-clinical models, and patient drug response data is often lacking, there is an urgent need for methods that efficiently transfer drug response predictors from pre-clinical models to the human setting.

Results

We show that cell lines and PDXs share common characteristics and processes with human tumors. We quantify this similarity and show that a regression model cannot simply be trained on cell lines or PDXs and then applied on tumors. We developed PRECISE, a novel methodology based on domain adaptation that captures the common information shared amongst pre-clinical models and human tumors in a consensus representation. Employing this representation, we train predictors of drug response on pre-clinical data and apply these predictors to stratify human tumors. We show that the resulting domain-invariant predictors show a small reduction in predictive performance in the pre-clinical domain but, importantly, reliably recover known associations between independent biomarkers and their companion drugs on human tumors.

Availability

PRECISE and the scripts for running our experiments are available on our GitHub page (https://github.com/NKI-CCB/PRECISE).

Contact

l.wessels@nki.nl

Supplementary information

Supplementary data are available. online.
Identification of lncRNAs associated with early stage breast cancer and their prognostic implications
Authors: Magendhra Rao Arunagiri Kuha Deva , Patel Krishna , Jyothi Sunitha Korivi , Meenakumari Balaiah , Sundersingh Shirley , Sridevi Velusami , Rajkumar Thangarajan , Pandey Akhilesh , Chatterjee Aditi , Gowda Harsha , Mani Samson
Published: February 2019

Breast cancer is a common malignancy among women with the highest incidence rate worldwide. Dysregulation of long non-coding RNAs occurring in the preliminary stages of breast carcinogenesis is poorly understood. In this study, RNA sequencing was done to identify long non-coding RNA expression profiles associated with early-stage breast cancer. RNA sequencing was done in 6 invasive ductal carcinoma (IDC) tissues along with paired normal tissue samples, 7 ductal carcinomain situ(DCIS) tissues and 5 apparently normal breast tissues. We identified 375 differentially expressed lncRNAs (DElncRNAs) in IDC tissues compared to paired normal tissues. Antisense transcripts (∼58%) were the largest subtype among DElncRNAs. About 20% of the 375 DElncRNAs were supported by typical split readings leveraging their detection confidence. Validation was done in n=52 IDC and paired normal tissue by qRT-PCR for the identified targets (ADAMTS9-AS2, EPB41L4A-AS1, WDFY3-AS2, RP11-295M3.4, RP11-161M6.2, RP11-490M8.1, CTB-92J24.3 and FAM83H-AS)1. We evaluated the prognostic significance of DElncRNAs based on TCGA datasets and overexpression of FAM83H-AS1 was associated with patient poor survival. We confirmed that the down-regulation of ADAMTS9-AS2 in breast cancer was due to promoter hypermethylation through in-vitro silencing experiments and pyrosequencing.
When do big problems far away become smaller than the problems closer to home
Authors: Donker Tjibbe , Hopkins Katie L. , Hopkins Susan , Muller-Pebody Berit , Peto Tim E.A. , Johnson Alan P. , Woodford Neil , Crook Derrick W. , Walker A. Sarah , Robotham Julie V.
Published: February 2019

Infection prevention and control strategies aimed at reducing the occurrence of Carbapenemase-Producing Enterobacteriaceae (CPE) and other antimicrobial-resistant organisms often include advice about screening patients coming from hospitals with a known resistance problem, to prevent introductions into new hospitals by shared patients. We argue that, despite being an efficient method of identifying cases, admission screening for introduction prevention is only effective if the absolute number of imported cases from other hospitals outnumbers the cases coming from the hospital’s own patient population, and therefore is only a feasible control strategy during the start of an epidemic.
Intracortical dynamics underlying repetitive stimulation predicts changes in network connectivity
Authors: Huang Yuhao , Hajnal Boglárka , Entz László , Fabó Dániel , Herrero Jose L. , Mehta Ashesh D. , Keller Corey J.
Published: February 2019

Targeted stimulation can be used to modulate the activity of brain networks. Previously we demonstrated that direct electrical stimulation produces predictable post-stimulation changes in brain excitability. However, understanding the neural dynamics during stimulation and its relationship to post-stimulation effects is limited but critical for treatment optimization. Here, we applied 10Hz direct electrical stimulation across several cortical regions in 14 patients implanted with intracranial electrodes for seizure monitoring. The stimulation train was characterized by a consistent increase in high gamma (70-170Hz) power. Immediately post-train, low-frequency (1-8Hz) power increased, resulting in an evoked response that was highly correlated with the neural response during stimulation. Using two measures of network connectivity, cortico-cortical evoked potentials (indexing effective connectivity) and theta coherence (indexing functional connectivity), we found a stronger response to stimulation in regions that were highly connected to the stimulation site. In these regions, repeated cycles of stimulation trains and rest progressively altered the stimulation response. Finally, after just 2 minutes (10%) of repetitive stimulation, we were able to predict post-stimulation connectivity changes with high discriminability. Taken together, this work reveals a relationship between stimulation dynamics and post-stimulation connectivity changes in humans. Thus, measuring neural activity during stimulation can inform future plasticity-inducing protocols.
Executive control of positive and negative information and adolescent depressive symptoms: cross-sectional and longitudinal associations in a population-based cohort
Authors: Lewis Gemma , Button Katherine S. , Pearson Rebecca M , Munafo Marcus R , Lewis Glyn
Published: February 2019

Background

Large population-based studies of neuropsychological factors that characterize or precede depressive symptoms are rare. Most studies use small case-control or cross-sectional designs, which may cause selection bias and cannot test temporality. In a large UK population-based cohort we investigated cross-sectional and longitudinal associations between executive control of positive and negative information and adolescent depressive symptoms.

Methods

Cohort study of 2315 UK adolescents (ALSPAC) who completed an affective go/no-go task at age 18. Depressive symptoms were assessed with the Clinical Interview Schedule Revised (CIS-R) and short Mood and Feeling Questionnaire (sMFQ) at age 18, and with the sMFQ 15 months later. Analyses were linear multilevel regressions (for cross-sectional associations) and traditional linear regressions (for longitudinal associations), before and after adjustment for confounders.

Results

Cross-sectionally, at age 18, there was some evidence that adolescents with more depressive symptoms made more errors in executive control (after adjustments, errors increased by 0.17 of a point per 1 SD increase in sMFQ score, 95% CI 0.08 to 0.25). However, this cross-sectional association was not observed for the CIS-R (.03, 95% CI -.06 to .12). There was no evidence of a difference in executive control errors according to valence. Longitudinally, there was no evidence that reduced executive control was associated with future depressive symptoms.

Conclusions

Executive control of positive and negative information does not appear to be a marker of current or future depressive symptoms in adolescents and would therefore not be a useful target in interventions to prevent adolescent depression. According to our evidence, the affective go/no-go task is also not a good candidate for future neuroimaging studies of adolescent depression.
Pixel personality for dense object tracking in a 2D honeybee hive
Authors: Bozek Katarzyna , Hebert Laetitia , Mikheyev Alexander S , Stephens Greg J
Published: February 2019

Tracking large numbers of densely-arranged, interacting objects is challenging due to occlusions and the resulting complexity of possible trajectory combinations, as well as the sparsity of relevant, labeled datasets. Here we describe a novel technique of collective tracking in the model environment of a 2D honeybee hive in which sample colonies consist ofN∼ 103highly similar individuals, tightly packed, and in rapid, irregular motion. Such a system offers universal challenges for multiobject tracking, while being conveniently accessible for image recording. We first apply an accurate, segmentation-based object detection method to build initial short trajectory segments by matching object configurations based on class, position and orientation. We then join these tracks into full single object trajectories by creating an object recognition model which is adaptively trained to recognize honeybee individuals through their visual appearance across multiple frames, an attribute we denote as pixel personality. Overall, we reconstruct ∼ 46% of the trajectories in 5 min recordings from two different hives and over 71% of the tracks for at least 2 min. We provide validated trajectories spanning 3, 000 video frames of 876 unmarked moving bees in two distinct colonies in different locations and filmed with different pixel resolutions, which we expect to be useful in the further development of general-purpose tracking solutions.
Climate change is predicted to disrupt patterns of local adaptation in wild and cultivated maize
Authors: Aguirre-Liguori Jonás A , Ramírez-Barahona Santiago , Tiffin Peter , Eguiarte Luis E
Published: February 2019

Climate change is one of the most important threats to biodiversity and crop sustainability. The impact of climate change is often evaluated on the basis of expected changes in species’ geographical distributions. Genomic diversity, local adaptation, and migration are seldom integrated into projections of species’ responses to climate change. Here we predict that climate change will impact populations of two wild relatives of maize, the teosintesZea maysssp.mexicanaandZ. maysssp.parviglumis, by altering patterns of local adaptation and decreasing migration probabilities. These alterations appear to be geographically heterogeneous across populations, suggesting that the possible impacts of climate change will vary considerably among populations. This in spite that most populations exhibit high levels of genetic diversity and are predicted to lie within future suitable areas. The heterogeneous patterns of local adaptation uncovered in teosintes are also evident across maize landraces, which suggests that climate change may give way to future maladaptation of several landraces within currently cultivated areas, possibly leading to increased chances of production shocks under increased temperatures. The predicted alterations to habitat distribution, migration potential, and patterns of local adaptation in wild and cultivated maize, raises a red flag for the future of populations. This underscores the need for continued integration of agronomical practices, genomic data, and climate models to better understand the impacts of a rapidly changing climate on cultivated and wild species.
Detecting RyR clusters with CaCLEAN: influence of spatial distribution and structural heterogeneity
Authors: Ladd David , Tilunaite Agne , Soeller Christian , Roderick H. Llewelyn , Crampin Edmund , Rajagopal Vijay
Published: February 2019

In cardiomyocytes, the coordinated release of calcium ions from intracellular stores through ryanodine receptor (RyR) clusters is key to the generation of a calcium transient and induction of contraction. Recently, a deconvolution algorithm from radio astronomy was adapted and applied to analysis of calcium fluorescence imaging of cardiomyocytes. The algorithm, CaCLEAN, showed potential in revealing both the spatial locations of RyR clusters and their functional response in living cells. However, whether the RyR clusters identified by CaCLEAN analysis of the imaging data were true or false positives remained unvalidated in the absence of ground truth values. In this work, a structurally realistic finite element model was developed to simulate reaction-diffusion of calcium emanating from RyR clusters during the rising phase (first 30 ms) of the calcium transient. The effect of two sets of factors were examined with the model: (1) the number and spacing of simulated RyR clusters and (2) the effect of mitochondria acting as barriers to diffusion. Confocal fluorescence microscopy images were simulated from the model results and analysed using CaCLEAN. The performance of CaCLEAN was found to be sensitive to cluster spacing and distance from the imaging plane. In a case with sparsely-packed clusters, detection recall and precision were 0.82 for clusters up to 610 nm from the imaging plane; in a densely-packed cluster case, recall and precision were 0.69 for clusters up to 280 nm from the imaging plane. Users interested in applying CaCLEAN to their data should therefore consider the likely density of cluster distributions and the trade-off between precision and recall when determining the maximum relevant depth of RyR clusters in their application.
Enterococcus faeciumgenome dynamics during long-term asymptomatic patient gut colonization
Authors: Bayjanov Jumamurat R. , Baan Jery , Rogers Malbert R.C. , Troelstra Annet , Willems Rob J.L. , van Schaik Willem
Published: February 2019

Background

E. faeciumis a gut commensal of humans and animals. In addition, it has recently emerged as an important nosocomial pathogen through the acquisition of genetic elements that confer resistance to antibiotics and virulence. We performed a whole-genome sequencing based study on 96 multidrug-resistantE. faeciumstrains that asymptomatically colonized five patients with the aim to describe the genome dynamics of this species.

Results

The patients were hospitalized on multiple occasions and isolates were collected over periods ranging from 15 months to 6.5 years. Ninety-five of the sequenced isolates belonged toE. faeciumclade A1, which was previously determined to be responsible for the vast majority of clinical infections. The clade A1 strains clustered into six clonal groups of highly similar isolates, three of which entirely consisted of isolates from a single patient. We also found evidence of concurrent colonization of patients by multiple distinct lineages and transfer of strains between patients during hospitalisation. We estimated the evolutionary rate of two clonal groups that colonized a single patient at 12.6 and 25.2 single nucleotide polymorphisms (SNPs)/genome/year. A detailed analysis of the accessory genome of one of the clonal groups revealed considerable variation due to gene gain and loss events, including the chromosomal acquisition of a 37 kbp prophage and the loss of an element containing carbohydrate metabolism-related genes. We determined the presence and location of twelve different Insertion Sequence (IS) elements, with ISEfa5showing a unique pattern of location in 24 of the 25 isolates, suggesting widespread ISEfa5excision and insertion into the genome during gut colonization.

Conclusions

Our findings show that theE. faeciumgenome is highly dynamic during asymptomatic colonization of the patient gut. We observe considerable genomic flexibility due to frequent horizontal gene transfer and recombination, which can contribute to the generation of genetic diversity within the species and, ultimately, can contribute to its success as a nosocomial pathogen.
Stability of an adaptively controlled pathway maximising specific flux under varying conditions
Authors: Overal Gosse B. , Hulshof Josephus , Planqué Robert
Published: February 2019

Microbial cells need to adapt to changing environmental conditions to survive. There is an evolutionary advantage to grow fast; this requires high metabolic rates, and an efficient allocation of enzymatic resources. Here we study a general control theory called qORAC, developed previously, which allows cells to adaptively control their enzyme allocations to achieve maximal steady state flux. The control is robust to perturbations in the environment, but those perturbations themselves do not feature in the control. In this paper we focus on the archetypical pathway, the linear chain with reversible Michaelis-Menten kinetics, together with qORAC control. First we assume that the metabolic pathway is in quasi-steady state with respect to enzyme synthesis. Then we show that the map between steady state metabolite and enzyme concentrations is a smooth bijection. Using this information, we finally show that the unique (and hence flux-maximising) steady state of this system is locally stable. We provide further evidence that it may in fact be globally stable.
Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage
Authors: Lau Anna Katharina , Leimeister Chris-André , Morgenstern Burkhard
Published: February 2019

In many fields of biomedical research, it is important to estimate phylogenetic distances between taxa based on low-coverage sequencing reads. Major applications are, for example, phylogeny reconstruction, species identification from small sequencing samples, or bacterial strain typing in medical diagnostics. Herein, we adapt our previously developed software programFiltered Spaced-Word Matches (FSWM)for alignment-free phylogeny reconstruction to work on unassembled reads; we call this implementationRead-SpaM. Test runs on simulated reads from bacterial genomes show that our approach can estimate phylogenetic distances with high accuracy, even for large evolutionary distances and for very low sequencing coverage.

Contact:bmorgen@gwdg.de
NNAlign_MA; semi-supervised MHC peptidome deconvolution for accurate characterization of MHC binding motifs and improved T cell epitope prediction
Authors: Alvarez Bruno , Reynisson Birkir , Barra Carolina , Buus Søren , Ternette Nicola , Connelley Tim , Andreatta Massimo , Nielsen Morten
Published: February 2019

Antigen presentation by Major Histocompatibility Complex (MHC) is a cornerstone of the cellular immune system, and characterization of the rules defining which peptides are suitable for MHC presentation is of key interest for understanding T cell immunogenicity and the development of T cell driven therapeutics. The collective set of peptides presented on a cell surface by MHC molecules is known as the immunopeptidome. Due to the vast MHC polymorphism, this peptidome is unique between individuals. Current state-of-the-art liquid chromatography mass spectrometry (LC-MS) technologies allow the identification of large peptidomes specific for a given host or cell line, and numerous studies have proven this data to be a rich source of information for learning the rules of MHC-mediated antigen presentation. The data obtained with MS techniques is usually poly-specific – i.e. it contains multiple sequence motifs matching the different MHC molecules expressed in the system under investigation. Deconvolution of this poly-specificity has proven a challenge, and imposes a substantial limitation for learning MHC specific rules for antigen presentation from immunopeptidome data. This since each ligand first must be unambiguously associated to its presenting MHC molecule(s) within the haplotype of the cell line.

Here, we describe NNAlign_MA, a method that is able to address this challenge. NNAlign_MA is capable of taking a mixed training set composed of single-allele (SA) data (peptides assigned to single MHCs) and multi-allele (MA) data (peptides with multiple options for MHCs assignments) as input, and in a fully automated manner deconvolute the individual MHC restriction of all MA sequences while learning the binding specificities of all the MHCs present in the training set.

The NNAlign_MA method was benchmarked on a large and diverse dataset, covering human MHC class I and class II, and bovine class I (BoLA) data. For all cases, the method was demonstrated to have unprecedented performance compared to state-of-the-art methods, achieving a complete deconvolution of binding motifs contained within poly-specificity MS eluted ligand data and an improved predictive performance for identification of both eluted ligands and T cell epitopes.

Given its very high flexibility and ease of use, we expect NNAlign_MA to serve as an effective tool to increase our understanding of the rules for MHC antigen presentation and guide the development of novel T cell-based therapeutics.
Variable Genome Evolution in Fungi After Transposon-Mediated Amplification of a Housekeeping Gene
Authors: Dhillon Braham , Kema Gert H. J. , Hamelin Richard , Bluhm Burt H. , Goodwin Stephen B.
Published: February 2019

Background

Transposable elements (TEs) can be key drivers of evolution, but the mechanisms and scope of how they impact gene and genome function are largely unknown. Previous analyses revealed that TE-mediated gene amplifications can have variable effects on fungal genomes, from inactivation of function to production of multiple active copies. For example, a DNA methyltransferase gene in the wheat pathogenZymoseptoria tritici(synonymMycosphaerella graminicola) was amplified to tens of copies, all of which were inactivated by Repeat-Induced Point mutation (RIP) including the original, resulting in loss of cytosine methylation. In another wheat pathogen,Pyrenophora tritici-repentis, a histone H3 gene was amplified to tens of copies with little evidence of RIP, leading to many potentially active copies. To further test the effects of transposon-aided gene amplifications on genome evolution and architecture, the repetitive fraction of the significantly expandedPseudocercospora fijiensisgenome was analyzed in greater detail.

Results

These analyses identified a housekeeping gene, histone H3, which was captured and amplified to hundreds of copies by ahATDNA transposon, all of which were inactivated by RIP, except for the original. InP. fijiensisthe original H3 gene probably was not protected from RIP, but most likely was maintained intact due to strong purifying selection. Comparative analyses revealed that a similar event occurred in five additional genomes representing the fungal generaCercospora, PseudocercosporaandSphaerulina.

Conclusions

These results indicate that the interplay of TEs and RIP can result in different and unpredictable fates of amplified genes, with variable effects on gene and genome evolution.
HLA-C-restricted presentation of a conserved bacterial epitope to an innate NK cell receptor
Authors: Sim Malcolm J. W. , Rajagopalan Sumati , Altmann Daniel M. , Boyton Rosemary J. , Sun Peter D. , Long Eric O.
Published: February 2019

The killer-cell Ig-like receptor (KIR) family, expressed mainly in natural killer (NK) cells, includes an activation receptor of unknown function, KIR2DS4. Here we show that KIR2DS4 is restricted by HLA-C*05:01 with a strong preference for tryptophan at position 8 of 9-mer peptides. ‘Self’ peptides with Trp8 eluted from HLA-C*05:01 are rare and only one out of 12 bound KIR2DS4. An HLA-C*05:01-peptide complex that bound KIR2DS4 was sufficient for strong activation of primary KIR2DS4+NK cells, independently of coactivation by other receptors and of prior NK cell licensing. A highly conserved sequence in bacterial recombinase A, which is essential for DNA repair and survival, includes an epitope that bound to HLA-C*05:01 and activated KIR2DS4+NK cells. Thus, in addition to their established role in defense against viruses and cancer, NK cells may have also evolved to detect and respond to hundreds of bacterial species through recognition of a conserved RecA epitope.
Organizational properties of a functional mammalian cis-regulome
Authors: Chaudhri Virendra K. , Dienger-Stambaugh Krista , Wu Zhiguo , Shrestha Mahesh , Singh Harinder
Published: February 2019

Mammalian genomic states are distinguished by their chromatin and transcription profiles. Most genomic analyses rely on chromatin profiling to infer cis-regulomes controlling distinctive cellular states. By coupling FAIRE-seq with STARR-seq and integrating Hi-C we assemble a functional cis-regulome for activated murine B-cells. Within 55,130 accessible chromatin regions we delineate 9,989 active enhancers communicating with 7,530 promoters. The cis-regulome is dominated by long range enhancer-promoter interactions (>100kb) and complex combinatorics, implying rapid evolvability. Genes with multiple enhancers display higher rates of transcription and multi-genic enhancers manifest graded levels of H3K4me1 and H3K27ac in poised and activated states, respectively. Motif analysis of pathway-specific enhancers reveals diverse transcription factor (TF) codes controlling discrete processes. The cis-regulome strikingly enriches for combinatorial DNA binding regions of lineage determining TFs. Their genomic binding patterns reveal that onset of chromatin accessibility is associated with binding of simpler combinations whereas enhancer function requires greater complexity.
Iron activates microglia and directly stimulates indoleamine-2,3-dioxygenase activity in the N171-82Q mouse model of Huntington’s disease
Authors: Donley David W. , Realing Marley , Gigley Jason P. , Fox Jonathan H.
Published: February 2019

Huntington’s disease (HD) is a neurodegenerative disorder caused by a dominant CAG-repeat expansion in the huntingtin gene. Morphologic activation of microglia is a key marker of neuroinflammation that is present before clinical onset in HD patients. The kynurenine pathway of tryptophan degradation is restricted in part to microglia and is activated in HD, where it contributes to disease progression. Indoleamine-2,3-dioxygenase (IDO) is a microglial enzyme that catalyzes the first step in this pathway. HD brain microglial cells also accumulate iron; however, the role of iron in promoting microglial activation and the kynurenine pathway is unclear. Based on analyses of morphological characteristics of microglia, we showed that HD mice demonstrate an activated microglial morphology compared with controls. Neonatal iron supplementation resulted in additional microglial morphology changes compared with HD controls. Increased microglial activation in iron-supplemented HD mice was indicated by increased soma volume and decreased process length. In our assessment of whether iron can affect the kynurenine pathway, iron directly enhanced the activity of human recombinant IDO1 with an EC50 of 1.24 nM. We also detected elevated microglial cytoplasmic labile iron in N171-82Q HD mice, an increase that is consistent with the cellular location of IDO. We further demonstrated that neonatal iron supplementation, a model for studying the role of iron in neurodegeneration, activates IDO directly in the mouse brain and promotes neurodegeneration in HD mice. Kynurenine pathway metabolites were also modified in HD and by iron supplementation in wild-type mice. These findings indicate that iron dysregulation contributes to the activation of microglia and the kynurenine pathway in a mouse model of HD.
Mutant huntingtin protein alters the response of microglial cells to inflammatory stimuli
Authors: Donley David W. , Nelson Ryan , Gigley Jason P. , Fox Jonathan H.
Published: February 2019

Huntington’s disease (HD) is a progressive neurodegenerative disease that affects the striatum and cerebral cortex. It is caused by a dominant CAG trinucleotide expansion in exon 1 of theHTTgene. Mutant huntingtin protein (mHtt) is expressed in neurons and immune cells. HD patients demonstrate altered blood cytokine profiles and altered responses of peripheral immune cells to inflammatory stimuli. However, the effects of mHtt on microglial immune responses are not fully understood. Herein we discuss the current understanding of how mHtt alters microglial inflammatory responses. Using lentivirus, we expressed the N171 N-terminal fragment of wild-type or mhtt containing 18 and 82 glutamine repeats in cultured EOC-20 microglial cells. We then measured responses to lipopolysaccharide or interleukin-6. Mutant huntingtin-expressing microglial cells produced less interleukin-6 and nitric oxide in response to lipopolysaccharide stimulation than wild-type huntingtin-expressing cells. However, mHtt-expressing microglia stimulated with interleukin-6 produced more nitric oxide than wild-type cells. Mutant huntingtin-expressing cells had higher basal NF-κB and further elevations of NF-κB after interleukin-6 but not lipopolysaccharide stimulation. Thus we demonstrate the potential of mHtt to dampen responses to lipopolysaccharide but potentiate responses to interleukin-6. This work adds to the emerging understanding that mHtt alters not only baseline status of cells but may also result in altered immune responses dependent on the nature of the inflammatory stimuli. We also present our perspective that in human HD the extent of inflammation may depend, in part, on altered responses to varied inflammatory stimuli including environmental factors such as infection.
Introgressive and horizontal acquisition of Wolbachia byDrosophila yakuba-clade hosts and horizontal transfer of incompatibility loci between distantly related Wolbachia
Authors: Cooper Brandon S. , Vanderpool Dan , Conner William R. , Matute Daniel R. , Turelli Michael
Published: February 2019

Maternally transmitted Wolbachia infect about half of insect species, yet the predominant mode(s) of Wolbachia acquisition remains uncertain. Species-specific associations could be old, with Wolbachia and hosts co-diversifying (i.e., cladogenic acquisition), or relatively young and acquired by horizontal transfer or introgression. The threeDrosophila yakuba-clade hosts ((D. santomea, D. yakuba),D. teissieri) diverged about three million years ago and currently hybridize on Bioko and São Tomé, west African islands. Each species is polymorphic for nearly identical Wolbachia that cause weak cytoplasmic incompatibility (CI)–reduced egg hatch when uninfected females mate with infected males.D. yakuba-clade Wolbachia are closely related towMel, globally polymorphic inD. melanogaster. We use draft Wolbachia and mitochondrial genomes to demonstrate thatD. yakuba-clade Wolbachia and mitochondrial phylogenies tend to follow host nuclear phylogenies; however, roughly half ofD. santomeaindividuals, sampled both inside and outside of the São Tomé hybrid zone, have introgressedD. yakubamitochondria. Both mitochondria and Wolbachia possess far more recent common ancestors than the bulk of the host nuclear genomes, precluding cladogenic Wolbachia acquisition. General concordance of Wolbachia and mitochondrial phylogenies suggests that horizontal transmission is rare, but varying relative rates of molecular divergence complicate time-based statistical tests. Loci that cause CI inwMel are disrupted inD. yakuba-clade Wolbachia; however, a second set of loci predicted to cause CI are located in the same WO prophage region. These alternative CI loci seem to have been acquired horizontally from distantly related Wolbachia, with transfer mediated by flanking Wolbachia-specific ISWpi1 transposons.
Amino Sugars Modify Antagonistic Interactions between Commensal Oral Streptococci andStreptococcus mutans
Authors: Chen Lulu , Chakraborty Brinta , Zou Jing , Burne Robert A. , Zeng Lin
Published: February 2019

N-acetylglucosamine (GlcNAc) and glucosamine (GlcN) enhance the competitiveness of the laboratory strain DL1 ofStreptococcus gordoniiagainst the caries pathogenStreptococcus mutans. Here we examine how amino sugars affect the interaction of five low-passage clinical isolates of abundant commensal streptococci withS. mutansutilizing a dual-species biofilm model. Compared to glucose, growth on GlcN or GlcNAc significantly reduced the viability ofS. mutansin co-cultures with most commensals, shifting the proportions of species. Consistent with these results, production of H2O2was increased in most commensals when growing on amino sugars, and inhibition ofS. mutansbyStreptococcus cristatus, Streptococcus oralis,orS. gordoniiwas enhanced by amino sugars on agar plates. All commensals exceptS. oralishad higher arginine deiminase activities when grown on GlcN, and in some cases GlcNAc. Inex vivobiofilms formed using pooled cell-containing saliva (CCS), the proportions ofS. mutanswere drastically diminished when GlcNAc was the primary carbohydrate. Increased production of H2O2could account in large part for the inhibitory effects of CCS biofilms. Surprisingly, amino sugars appeared to improve mutacin production byS. mutanson agar plates, suggesting that the commensals have mechanisms to actively subvert antagonism byS. mutansin co-cultures. Collectively, these findings demonstrate that amino sugars can enhance the beneficial properties of low-passage commensal oral streptococci and highlight their potential for moderating the cariogenicity of oral biofilms.

SIGNIFICANCE

Dental caries is driven by dysbiosis of oral biofilms in which dominance by acid-producing and acid-tolerant bacteria results in loss of tooth mineral. Our previous work demonstrated the beneficial effects of amino sugars, GlcNAc and GlcN, in promoting the antagonistic properties of a health-associated oral bacterium,Streptococcus gordonii,in competition with the major caries pathogenStreptococcus mutans.Here we investigated 5 low-passage clinical isolates of the most common streptococcal species to establish how amino sugars may influence the ecology and virulence of oral biofilms. Using multiplein vitromodels, including a human saliva-derived microcosm biofilm, experiments showed significant enhancement by at least one amino sugar in the ability of most of these bacteria to suppress the caries pathogen. Therefore, our findings demonstrated the mechanism of action by which amino sugars may affect human oral biofilms to promote health.
Characterization of pyruvate dehydrogenase complex E1 alpha and beta subunits ofMycoplasma synoviae
Authors: Bao Shijun , Ding Xiaoqin , Yu Shengqing , Ding Chan
Published: February 2019

Mycoplasma synoviae(MS) is an important pathogen, causing enormous economic losses to the poultry industry worldwide every year. Therefore, the studies on MS will lay the foundation for diagnosis, prevention and treatment of MS infection. In this study, primers designed based on the sequences of pyruvate dehydrogenase complex (PDC) E1 alpha and beta subunit genes (pdhAandpdhB, respectively) of MS WVU1853 strain in GenBank were used to amplify thepdhAandpdhBgenes of MS WVU1853 strain through PCR. Then the prokaryotic expression vectors pET-pdhA and pET-pdhB were constructed and were expressed inEscherichia coliBL21(DE3) cells. Subsequently, the recombinant proteins rMSPDHA and rMSPDHB were purified and anti-rMSPDHA and anti-rMSPDHB sera were prepared by immunizing rabbits, respectively. Finally, the subcellular localization of PDHA and PDHB in MS, binding activity of rMSPDHA and rMSPDHB to chicken plasminogen (Plg) and human fibronectin (Fn), complement-dependent mycoplasmacidal assays, and adherence and adherence inhibition assays were accomplished. The results showed that PDHA and PDHB were distributed both on the surface membrane and within soluble cytosolic fractions of MS cells. The rMSPDHA and rMSPDHB presented binding activity with chicken Plg and human Fn. The rabbit anti-rMSPDHA and anti-rMSPDHB sera had distinct mycoplasmacidal efficacy in the presence of guinea pig complement, and the adherence of MS to DF-1 cells pretreated with Plg was effectively inhibited by treatment with anti-rMSPDHA or anti-rMSPDHB sera. Hence, the study indicates that the surface-associated MSPDHA and MSPDHB are the adhesion-related factors of MS that contributes to bind to Plg/Fn and adhesion to DF-1 cells.
Data-driven spatial filtering for improved measurement of cortical tracking of multiple representations of speech
Authors: Lesenfants D , Vanthornhout J , Verschueren E , Francart T
Published: February 2019

Objective

Measurement of the cortical tracking of continuous natural speech from electroencephalography (EEG) recordings using a forward model is becoming an important tool in auditory neuroscience. However, it requires a manual channel selection based on visual inspection or prior knowledge to obtain a summary measure of cortical tracking. In this study, we present a method to on the one hand remove non-stimulus-related activity from the EEG signals to be predicted, and on the other hand automatically select the channels of interest. We also aim to show that the EEG prediction from phonology-related speech features is possible in Dutch.

Approach

Eighteen participants listened to a Flemish story, while their EEG was recorded. Subject-specific and grand-average temporal responses functions were determined between the EEG activity in different frequency bands and several stimulus features: the envelope, spectrogram, phonemes, phonetic features or a combination. The temporal response functions were then used to predict EEG from the stimulus, and the predicted was compared with the recorded EEG, yielding a measure of cortical tracking of stimulus features. A spatial filter was calculated based on the generalized eigenvalue decomposition (GEVD), and the effect on EEG prediction accuracy was determined.

Main results

A model including both low- and high-level speech representations was able to better predict the brain responses to the speech than a model only including low-level features. The inclusion of a GEVD-based spatial filter in the model increased the prediction accuracy of cortical responses to each speech feature at both single-subject (270% improvement) and group-level (310 %).

Significance

We showed that the inclusion of acoustical and phonetic speech information and the addition of a data-driven spatial filter allow improved modelling of the relationship between the speech and its brain response and offer an automatic channel selection.

Highlights

Automatic channel selection for evaluating the cortical tracking of continuous natural speech

Data-driven spatial filtering for removing non-stimulus-related activity from the EEG signals

Improved prediction of brain responses to speech by combining acoustical and phonetic speech information in Dutch

Disclosure

The authors report no disclosures relevant to the manuscript.
Direct Evidence for Glucose Consumption Acceleration by Carbonates in Cultured Cells
Authors: Sorimachi Kenji
Published: February 2019

Established Py-3Y1-S2 rat fibroblast cells were used to evaluate whether NaHCO3or Na2CO3influences glucose metabolismin vitro, because factors that contribute to metabolic pathways are much simpler to evaluate in cultured cells than in whole animal bodies. The effects of the carbonates on glucose consumption decreased at high concentrations, >5 mg/ml for Na2CO3and >7 mg/ml for NaHCO3, because of the increased pH of the culture medium. The effects of the carbonates on glucose consumption were additive with those of vanadium and concanavalin A. Streptozotocin, alloxan, and nicotinamide, which induce diabetes in animals, reduced glucose consumption by Py-3Y1-S2 cells, and the inhibitory effects of these reagents were abolished by both Na2CO3and NaHCO3. Finally, the carbonates increased lactate production from glucose in the cells, followed by acceleration of lactate secretion into the culture medium. The present study clarified that NaHCO3and Na2CO3directly regulate glucose metabolism.
Rapid sperm capture: High-throughput flagellar waveform analysis
Authors: Gallagher M.T. , Cupples G. , Ooi E.H. , Kirkman-Brown J.C. , Smith D.J.
Published: February 2019

Flagella are critical across all eukaryotic life, and the human sperm flagellum is crucial to natural fertility. Existing automated sperm diagnostics (CASA) rely on tracking the sperm head and extrapolating measures. We describe fully-automated tracking and analysis of flagellar movement for large cell numbers. The analysis is demonstrated on freely-motile cells in low and high viscosity fluids, and validated on published data of tethered cells undergoing pharmacological hyperactivation. Direct analysis of the flagellar beat reveals that the CASA measure ‘beat cross frequency’, does not measure beat frequency. A new measurement, track centroid speed, is validated as an accurate differentiator of progressive motility. Coupled with fluid mechanics codes, waveform data enables extraction of experimentally intractable quantities such as energy dissipation, disturbance of the surrounding medium and viscous stresses. We provide a powerful and accessible research tool, enabling connection of the cell’s mechanical activity to its motility and effect on its environment.
Functional diversification of hybridoma produced antibodies by CRISPR/HDR genomic engineering
Authors: der Schoot Johan M.S. van , Fennemann Felix L. , Valente Michael , Dolen Yusuf , Hagemans Iris M. , Becker Anouk M.D. , Le Gall Camille M. , Dalen Duco van , Cevirgel Alper , van Bruggen J. Armando C. , Engelfriet M , Caval Tomislav , Bentlage Arthur E.H. , Fransen Marieke F. , Nederend Maaike , Leusen Jeanette H.W. , Heck Albert J.R. , Vidarsson Gestur , Figdor Carl G. , Verdoes Martijn , Scheeren Ferenc A.
Published: February 2019

Hybridoma technology is instrumental for the development of novel antibody therapeutics and diagnostics. Recent preclinical and clinical studies highlight the importance of antibody isotype for therapeutic efficacy. However, since the sequence encoding the constant domains is fixed, tuning antibody function in hybridomas has been restricted. Here, we demonstrate a versatile CRISPR/HDR platform to rapidly engineer the constant immunoglobulin domains to obtain recombinant hybridomas which secrete antibodies in the preferred format, species and isotype. Using this platform, we obtained recombinant hybridomas secreting Fab’ fragments, isotype switched chimeric antibodies, and Fc-silent mutants. These antibody products are stable, retain their antigen specificity, and display their intrinsic Fc-effector functions in vitro and in vivo. Furthermore, we can site-specifically attach cargo to these antibody products via chemo-enzymatic modification. We believe this versatile platform facilitates antibody engineering for the entire scientific community, empowering preclinical antibody research.

One Sentence Summary

We demonstrate a universal CRISPR/HDR based platform for rapid genetic engineering of hybridomas to obtain functionally diverse antibody isotype panels in the species and format of choice.