bluuebunny/crossref_metadata_2025 huggingface dataset:
Parasite insight: assessing fitness costs, infection risks and foraging benefits relating to gastrointestinal nematodes in wild mammalian herbivores
Authors: Coulson Graeme , Cripps Jemma K. , Garnick Sarah , Bristow Verity , Beveridge Ian
Published: June 2018

Mammalian herbivores are typically infected by parasitic nematodes, which are acquired through direct, faecal–oral transmission. These parasites can cause significant production losses in domestic livestock, but much less is known about impacts on wild mammalian hosts. We review three elements of parasitism from the host's perspective: fitness costs of infection, risks of infection during foraging and benefits of nutritious pasture. The majority of wildlife studies have been observational, but experimental manipulation is increasing. Treatment with anthelmintics to manipulate parasite load has revealed varied impacts of parasites on fitness variables across host species, but has not produced consistent evidence for parasite-induced anorexia or impaired body condition. Some experimental studies of infection risk have manipulated faecal contamination and detected faecal avoidance by hosts. Only two field studies have explored the trade-off between infection risk and nutritional benefit generated by avoidance of contaminated patches. Overall, field studies of costs, risks and benefits of the host–parasite relationship are limited and few have examined more than one of these elements. Parasitism has much in common with predation, and future insights into anti-parasite responses by wild hosts could be gained from the conceptual and technical developments in research on anti-predator behaviour.

This article is part of the Theo Murphy meeting issue ‘Evolution of pathogen and parasite avoidance behaviours’.
Ectoparasite defence in humans: relationships to pathogen avoidance and clinical implications
Authors: Kupfer Tom R. , Fessler Daniel M. T.
Published: June 2018

Currently, disgust is regarded as the main adaptation for defence against pathogens and parasites in humans. Disgust's motivational and behavioural features, including withdrawal, nausea, appetite suppression and the urge to vomit, defend effectively against ingesting or touching sources of pathogens. However, ectoparasites do not attack their hosts via ingestion, but rather actively attach themselves to the body surface. Accordingly, by itself, disgust offers limited defence against ectoparasites. We propose that, like non-human animals, humans have a distinct ectoparasite defence system that includes cutaneous sensory mechanisms, itch-generation mechanisms and grooming behaviours. The existence of adaptations for ectoparasite defence is supported by abundant evidence from non-human animals, as well as more recent evidence concerning human responses to ectoparasite cues. Several clinical disorders may be dysfunctions of the ectoparasite defence system, including some that are pathologies of grooming, such as skin picking and trichotillomania, and others, such as delusory parasitosis and trypophobia, which are pathologies of ectoparasite detection. We conclude that future research should explore both distinctions between, and overlap across, ectoparasite defence systems and pathogen avoidance systems, as doing so will not only illuminate proximate motivational systems, including disgust, but may also reveal important clinical and social consequences.

This article is part of the Theo Murphy meeting issue ‘Evolution of pathogen and parasite avoidance behaviours'.
Machine learning for randomised controlled trials: identifying treatment effectheterogeneity with strict control of type I error
Authors: Holmes Chris C. , Watson James A.
Published: June 2018

Background

It is widely acknowledged that retrospective exploratory analyses of randomised controlled trials (RCTs) seeking to identify treatment effect heterogeneity (TEH) are prone to bias and false positives. Yet the increasing availability of multiple data modalities on subjects and the desire to learn all we can from trial participants motivates the inclusion of such analyses within RCTs. Coupled to this, widespread advances in AI and machine learning (ML) methods hold great potential to utilise such data to characterise subjects exhibiting heterogeneous treatment response.

Methods

We present new learning strategies for RCT ML discovery methods that ensure strict control of the false positive reporting rate at a pre-specified level. Our approach uses randomised data partitioning and statistical or ML based prediction on held-out data. This can test for both crossover and non-crossover TEH. The former is done via a two-sample hypothesis test measuring overall predictive performance of the ML method. The latter is done via ‘stacking’ the ML predictors alongside a classical statistical model to formally test the added benefit of the ML algorithm. An adaptation of recent statistical theory allows for the construction of a valid aggregate p-value. This learning strategy is agnostic to the choice of ML method.

Results

We demonstrate our approach with a re-analysis of the SEAQUAMAT trial. We find no evidence for any crossover subgroup who would benefit from a change in treatment from the current standard-of-care, artesunate, but strong evidence for significant noncrossover TEH within the artesunate treatment group. We find that artesunate provides a differential benefit to patients with high numbers of circulating ring stage parasites.

Conclusions

Our ML approach combined with the use of computational notebooks and version control can improve the robustness and transparency of RCT exploratory analyses. The methods allow researchers to apply the latest ML techniques safe in the knowledge that any declared associations are statistically significant at a user defined level.
Collagen assembly and turnover imaged with a CRISPR-Cas9 engineered Dendra2 tag
Authors: Pickard Adam , Adamson Antony , Lu Yinhui , Chang Joan , Garva Richa , Hodson Nigel , Kadler Karl E.
Published: June 2018

Electron microscopy has been the “gold standard” for studying collagen networks but dynamic information on how cells synthesise the networks has been lacking. Live imaging methods have been unable to distinguish newly-synthesised fibrils from pre-existing fibrils and intracellular collagen. Here, we tagged endogenous collagen-I using CRISPR-Cas9 with photoswitchable Dendra2 and demonstrate live cells synthesising, migrating on, and interacting with, collagen fibrils. This strategy is applicable for other long half-life proteins.
Isolating and Quantifying the Role of Developmental Noise in Generating Phenotypic Variation
Authors: Kiskowski Maria , Glimm Tilmann , Moreno Nickolas , Gamble Tony , Chiari Ylenia
Published: June 2018

Phenotypic variation in organisms is typically attributed to genotypic variation, environmental variation, and their interaction. Developmental noise, which arises from stochasticity in cellular and molecular processes occurring during development when genotype and environment are fixed, also contributes to phenotypic variation. The potential influence of developmental noise is likely underestimated in studies of phenotypic variation due to intrinsic mechanisms within organisms that stabilize phenotypes and decrease variation. Since we are just beginning to appreciate the extent to which phenotypic variation due to stochasticity is potentially adaptive, the contribution of developmental noise to phenotypic variation must be separated and measured to fully understand its role in evolution. Here, we show that phenotypic variation due to genotype and environment, versus the contribution of developmental noise, can be distinguished for leopard gecko (Eublepharis macularius) head color patterns using mathematical simulations that model the role of random variation (corresponding to developmental noise) in patterning. Specifically, we modified the parameters of simulations corresponding to genetic and environmental variation to generate the full range of phenotypic variation in color pattern seen on the heads of eight leopard geckos. We observed that over the range of these parameters, the component of variation due to genotype and environment exceeds that due to developmental noise in the studied gecko cohort. However, the effect of developmental noise on patterning is also substantial. This approach can be applied to any regular morphological trait that results from self-organized processes such as reaction-diffusion mechanisms, including the frequently found striped and spotted patterns of animal pigmentation patterning, patterning of bones in vertebrate limbs, body segmentation in segmented animals. Our approach addresses one of the major goals of evolutionary biology: to define the role of stochasticity in shaping phenotypic variation.
Image Scanning Microscopy with Single-Photon Detector Array
Authors: Castello Marco , Tortarolo Giorgio , Buttafava Mauro , Deguchi Takahiro , Villa Federica , Koho Sami , Bianchini Paolo , Sheppard Colin J. R. , Diaspro Alberto , Tosi Alberto , Vicidomini Giuseppe
Published: June 2018

Image scanning microscopy (ISM) improves the spatial resolution of conventional confocal laser-scanning microscopy (CLSM), but current implementations reduce versatility and restrict its combination with fluorescence spectroscopy techniques, such as fluorescence lifetime. Here, we describe a natural design of ISM based on a fast single-photon detector array, which allows straightforward upgrade of an existing confocal microscope, without compromising any of its functionalities. In contrast to all-optical ISM implementations, our approach provides access to the raw scanned images, opening the way to adaptive reconstruction methods, capable of considering different imaging conditions and distortions. We demonstrate its utility in the context of fluorescence lifetime, deep, multicolor and live-cell imaging. This implementation will pave the way for a transparent and massive transition from conventional CLSM to ISM.

confocal microscopy | time-resolved spectroscopy | image scanning microscopy | single-photon detector array
Long-range order from local interactions: organization and development of distributed cortical networks
Authors: Smith Gordon B. , Hein Bettina , Whitney David E. , Fitzpatrick David , Kaschube Matthias
Published: June 2018

The cortical networks that underlie behavior exhibit an orderly functional organization at local and global scales, which is readily evident in the visual cortex of carnivores and primates1-6. Here, neighboring columns of neurons represent the full range of stimulus orientations and contribute to distributed networks spanning several millimeters2,7-11. However, the principles governing functional interactions that bridge this fine-scale functional architecture and distant network elements are unclear, and the emergence of these network interactions during development remains unexplored. Here, by using in vivo wide-field and 2-photon calcium imaging of spontaneous activity patterns in mature ferret visual cortex, we find widespread and specific modular correlation patterns that accurately predict the local structure of visually-evoked orientation columns from the spontaneous activity of neurons that lie several millimeters away. The large-scale networks revealed by correlated spontaneous activity show abrupt ‘fractures’ in continuity that are in tight register with evoked orientation pinwheels. Chronic in vivo imaging demonstrates that these large-scale modular correlation patterns and fractures are already present at early stages of cortical development and predictive of the mature network structure. Silencing feed-forward drive through either retinal or thalamic blockade does not affect network structure suggesting a cortical origin for this large-scale correlated activity, despite the immaturity of long-range horizontal network connections in the early cortex. Using a circuit model containing only local connections, we demonstrate that such a circuit is sufficient to generate large-scale correlated activity, while also producing correlated networks showing strong fractures, a reduced dimensionality, and an elongated local correlation structure, all in close agreement with our empirical data. These results demonstrate the precise local and global organization of cortical networks revealed through correlated spontaneous activity and suggest that local connections in early cortical circuits may generate structured long-range network correlations that underlie the subsequent formation of visually-evoked distributed functional networks.
pH-mediated inhibition of a bumble bee parasite by an intestinal symbiont
Authors: Palmer-Young Evan C , Raffel Thomas R , McFrederick Quinn S
Published: June 2018

Non-pathogenic microbes can provide multiple benefits to their hosts, including pathogen inhibition. Gut symbionts can augment resistance to pathogens by stimulating host immune responses, competing for space and nutrients, or producing antimicrobial metabolites. The gut microbiota of social bees, which pollinate many crops and wildflowers, has demonstrated benefits against diverse infections and might help protect against pathogen-related declines. The bumble bee gut microbiota, consisting chiefly of five taxa common to corbiculate bees, has been shown to enhance resistance to the trypanosomatid parasiteCrithidia bombi. Specifically, infection intensity was negatively correlated with abundance ofLactobacillus“Firm-5” bacteria. However, the mechanism underlying this relationship remains unknown. We tested the hypothesis that the Firm-5 bacteriumLactobacillus bombicola, which produces lactic acid, inhibitsC. bombivia a pH-mediated effect.

Consistent with our hypothesis,Lactobacillus bombicolaspent medium inhibitedC. bombigrowth via a reduction in pH that was both necessary and sufficient for inhibition. Inhibition of all parasite strains occurred within the pH range previously observed in honey bee guts, though sensitivity to acidity varied among parasite strains. Spent medium was slightly more potent than HCl, D-, and L-lactic acids for a given pH, suggesting that other metabolites also contribute to inhibitory effects. Our results implicate symbiont-mediated reduction in gut pH as a key determinant of trypanosomatid infection in bees. Future investigation intoin vivoeffects of gut microbial composition on pH and infection intensity would help determine the relevance of these findings for bees threatened by trypanosomatids.

Importance

Pollinators such as honey and bumble bees provide services to plants in agricultural and wild ecosystems, but both wild and managed bees are threatened by infection-related declines. The symbiotic gut microbiota of bees provides a naturally occurring defense against infection. For example, the bumble bee microbiota reduces infection with trypanosomatid parasites, but how inhibition occurs remains unknown. We show that the acidic spent medium from a common bumble bee gut symbiont,Lactobacillus bombicola,inhibitsin vitrogrowth of the trypanosomatid gut parasite,Crithidia bombi.The acidity of the spent medium was both necessary and sufficient for parasite inhibition. Inhibitory pH values were within the range documented in honey bee guts, suggesting that pH-mediated parasite inhibition is plausible in live bees. Results suggest that production of acids by sugar-fermenting symbionts confers pH-mediated resistance to infection in bees, whereas depletion of core microbiota could result in low-acid conditions that favor parasite growth.
Cross-feeding between Bifidobacterium infantis and Anaerostipes caccae on lactose and human milk oligosaccharides
Authors: Chia Loo Wee , Mank Marko , Blijenberg Bernadet , Bongers Roger S. , Aalvink Steven , Limpt Kees van , Wopereis Harm , Tims Sebastian , Stahl Bernd , Belzer Clara , Knol Jan
Published: June 2018

The establishment of the gut microbiota immediately after birth is a dynamic process that may impact lifelong health. At this important developmental stage in early life, human milk oligosaccharides (HMOS) serve as specific substrates to promote the growth of gut microbes, particularly the group of Actinobacteria (bifidobacteria). Later in life, this shifts to the colonisation of Firmicutes and Bacteroidetes, which generally dominate the human gut throughout adulthood. The well-orchestrated transition is important for health, as an aberrant microbial composition and/or SCFA production are associated with colicky symptoms and atopic diseases in infants. Here, we study the trophic interactions between an HMOS-degrader, Bifidobacterium longum subsp. infantis and the butyrogenic Anaerostipes caccae using carbohydrate substrates that are relevant in this early life period, i.e. lactose and HMOS. Mono-and co-cultures of these bacterial species were grown at pH 6.5 in anaerobic bioreactors supplemented with lactose or total human milk carbohydrates (containing both lactose and HMOS). A cac was not able to grow on these substrates except when grown in co-culture with B. inf, leading concomitant butyrate production. Cross-feeding was observed, in which A. cac utilised the liberated monosaccharides as well as lactate and acetate produced by B. inf. This microbial cross-feeding is indicative of the key ecological role of bifidobacteria in providing substrates for other important species to colonise the infant gut. The symbiotic relationship between these key species contributes to the gradual production of butyrate early in life that could be important for host-microbial cross-talk and gut maturation.

Importance

The establishment of a healthy infant gut microbiota is crucial for the immune, metabolic and neurological development of infants. Recent evidence suggests that an aberrant gut microbiota early in life could lead to discomfort and predispose infants to the development of immune related diseases. This paper addresses the ecosystem function of two resident microbes of the infant gut. The significance of this research is the proof of cross-feeding interactions between HMOS-degrading bifidobacteria and a butyrate-producing microorganism. Bifidobacteria in the infant gut that support the growth and butyrogenesis of butyrate-producing bacteria, could orchestrated an important event of maturation for both the gut ecosystem and physiology of infant.
Innate visual preferences and behavioral flexibility inDrosophila
Authors: Grabowska Martyna J. , Steeves James , Alpay Julius , Poll Matthew Van De , Ertekin Deniz , Swinderen Bruno van
Published: June 2018

Visual decision-making in animals is influenced by innate preferences as well as experience. Interaction between hard-wired responses and changing motivational states determines whether a visual stimulus is attractive, aversive, or neutral. It is however difficult to separate the relative contribution of nature versus nurture in experimental paradigms, especially for more complex visual parameters such as the shape of objects. We used a closed-loop virtual reality paradigm for walkingDrosophilaflies to uncover innate visual preferences for the shape and size of objects, in a recursive choice scenario allowing the flies to reveal their visual preferences over time. We found thatDrosophilaflies display a robust attraction / repulsion profile for a range of objects sizes in this paradigm, and that this visual preference profile remains evident under a variety of conditions and persists into old age. We also demonstrate a level of flexibility in this behavior: innate repulsion to certain objects could be transiently overridden if these were novel, although this effect was only evident in younger flies. Finally, we show that a reward circuit in the fly brain,Drosophilaneuropeptide F (dNPF), can be recruited to guide visual decision-making. Optogenetic activation of dNPF-expressing neurons converted a visually repulsive object into a more attractive object. This suggests that dNPF activity in theDrosophilabrain guides ongoing visual choices, to override innate preferences and thereby provide a necessary level of behavioral flexibility in visual decision-making.
A domestication history of dynamic adaptation and genomic deterioration in sorghum
Authors: Smith Oliver , Nicholson William V , Kistler Logan , Mace Emma , Clapham Alan , Rose Pamela , Stevens Chris , Ware Roselyn , Samavedam Siva , Barker Guy , Jordan David , Fuller Dorian Q , Allaby Robin G
Published: June 2018

The evolution of domesticated cereals was a complex interaction of shifting selection pressures and repeated introgressions. Genomes of archaeological crops have the potential to reveal these dynamics without being obscured by recent breeding or introgression. We report a temporal series of archaeogenomes of the crop sorghum (Sorghum bicolor) from a single locality in Egyptian Nubia. These data indicate no evidence for the effects of a domestication bottleneck but instead suggest a steady decline in genetic diversity over time coupled with an accumulating mutation load. Dynamic selection pressures acted sequentially on architectural and nutritional domestication traits, and adaptation to the local environment. Later introgression between sorghum races allowed exchange of adaptive traits and achieved mutual genomic rescue through an ameliorated mutation load. These results reveal a model of domestication in which genomic adaptation and deterioration was not focused on the initial stages of domestication but occurred throughout the history of cultivation.
Jag1 modulates an oscillatory Dll1-Notch-Hes1 signaling module to coordinate growth and fate of pancreatic progenitors
Authors: Seymour Philip A. , Collin Caitlin A. , Egeskov-Madsen Anuska l. R. , Jørgensen Mette C. , Shimojo Hiromi , Imayoshi Itaru , de Lichtenberg Kristian H. , Kopan Raphael , Kageyama Ryoichiro , Serup Palle
Published: June 2018

Notch signaling controls proliferation of multipotent pancreatic progenitor cells (MPCs) and their segregation intobipotentprogenitors (BPs) and unipotentpro-acinar cells (PACs). Here we uncover fast ultradian oscillations in the ligand Dll1, and the transcriptional effector Hes1, which proved crucial for MPC expansion. Conversely Jag1, a uniformly expressed ligand, curbed MPC growth, but as expression later segregated to PACs it proved critical for specifying all but the most proximal 5% of BPs, while BPs were entirely lost inJag1,Dll1double mutants. Moreover, experimentally induced changes in Hes1 oscillation parameters was associated with selective adoption of BP or PAC fates. Anatomically, ductal morphogenesis and organ architecture is minimally perturbed inJag1mutants until later stages, when ductal remodeling fails and signs of acinar-to-ductal metaplasia appear. Our study uncovers oscillating Notch activity in the developing pancreas, which along with modulation by Jag1 is required to coordinate MPC growth and fate.
IL-11 is a therapeutic target in idiopathic pulmonary fibrosis
Authors: Ng Benjamin , Dong Jinrui , Viswanathan Sivakumar , D’Agostino Giuseppe , Widjaja Anissa A. , Lim Wei-Wen , Ko Nicole SJ. , Tan Jessie , Chothani Sonia P. , Huang Benjamin , Xie Chen , Chacko Ann-Marie , Guimarães-Camboa Nuno , Evans Sylvia M. , Byrne Adam J. , Maher Toby M. , Liang Jiurong , Noble Paul W. , Schafer Sebastian , Cook Stuart A.
Published: June 2018

Idiopathic pulmonary fibrosis (IPF) remains a progressive disease despite best medical management. We previously identified IL-11 as a critical factor for cardiovascular fibrosis and examine here its role in pulmonary fibrosis.IL-11is consistently upregulated in IPF genomic datasets, which we confirmed by histology. Pulmonary fibroblasts stimulated with IL-11 transform into invasive myofibroblasts whereas fibroblasts fromIl11radeleted mice did not respond to pro-fibrotic stimuli. In the mouse, injection of recombinant Il-11 or fibroblast-specific expression of Il-11 caused pulmonary fibrosis. We then generated a neutralising IL-11 binding antibody that blocks lung fibroblast activation across species. In a mouse model of IPF, anti-IL-11 therapy attenuated lung fibrosis and specifically blocked Erk activation. These data prioritise IL-11 as an accessible drug target in IPF.

One Sentence Summary

Non-canonical IL-11 signalling is a central hallmark of idiopathic pulmonary fibrosis and represents a novel target for antibody therapies.
Hook-length of the bacterial flagellum is optimized for maximal stability of the flagellar bundle
Authors: Spöring Imke , Martinez Vincent A. , Hotz Christian , Schwarz-Linek Jana , Grady Keara L. , Nava-Sedeño Josué M. , Vissers Teun , Singer Hanna M. , Rohde Manfred , Bourquin Carole , Hatzikirou Haralampos , Poon Wilson C. K. , Dufour Yann S. , Erhardt Marc
Published: June 2018

Most bacteria swim in liquid environments by rotating one or several flagella. The long external filament of the flagellum is connected to a membrane-embedded basal-body by a flexible universal joint, the hook, which allows the transmission of motor torque to the filament. The length of the hook is controlled on a nanometer-scale by a sophisticated molecular ruler mechanism. However, why its length is stringently controlled has remained elusive. We engineered and studied a diverse set of hook-length variants ofSalmonella enterica. Measurements of plate-assay motility, single-cell swimming speed and directional persistence in quasi 2D and population-averaged swimming speed and body angular velocity in 3D revealed that the motility performance is optimal around the wild type hook-length. We conclude that too short hooks may be too stiff to function as a junction and too long hooks may buckle and create instability in the flagellar bundle. Accordingly, peritrichously flagellated bacteria move most efficiently as the distance travelled per body rotation is maximal and body wobbling is minimized. Thus, our results suggest that the molecular ruler mechanism evolved to control flagellar hook growth to the optimal length consistent with efficient bundle formation. The hook-length control mechanism is therefore a prime example of how bacteria evolved elegant, but robust mechanisms to maximize their fitness under specific environmental constraints.

Author summary

Many bacteria use flagella for directed movement in liquid environments. The flexible hook connects the membrane-embedded basal-body of the flagellum to the long, external filament. Flagellar function relies on self-assembly processes that define or self-limit the lengths of major parts. The length of the hook is precisely controlled on a nanometer-scale by a molecular ruler mechanism. However, the physiological benefit of tight hook-length control remains unclear. Here, we show that the molecular ruler mechanism evolved to control the optimal length of the flagellar hook, which is consistent with efficient motility performance. These results highlight the evolutionary forces that enable flagellated bacteria to optimize their fitness in diverse environments and might have important implications for the design of swimming micro-robots.
Nociceptor translational profiling reveals the RagA-mTORC1 network as a critical generator of neuropathic pain
Authors: Megat Salim , Ray Pradipta R. , Moy Jamie K. , Lou Tzu-Fang , Barragan-Iglesias Paulino , Li Yan , Pradhan Grishma , Wangzhou Andi , Ahmad Ayesha , North Robert Y. , Dougherty Patrick M. , Khoutorsky Arkady , Sonenberg Nahum , Webster Kevin R. , Dussor Gregory , Campbell Zachary T. , Price Theodore J.
Published: June 2018

Pain sensing neurons, nociceptors, are key drivers of neuropathic pain. We used translating ribosome affinity purification (TRAP) to comprehensively characterize up-and down-regulated mRNA translation in Scn10a-positive nociceptors in chemotherapy-induced neuropathic pain. We provide evidence that an underlying mechanism driving these changes in gene expression is a sustained mTORC1 activation driven by MNK1-eIF4E signaling. RagA, a GTPase controlling mTORC1 activity, is identified as a novel target of MNK1-eIF4E signaling, demonstrating a new link between these distinct signaling pathways. Neuropathic pain and RagA translation are strongly attenuated by genetic ablation of eIF4E phosphorylation, MNK1 elimination or treatment with the MNK inhibitor eFT508. We reveal a novel translational circuit for the genesis of neuropathic pain with important implications for next generation neuropathic pain therapeutics.

One Sentence Summary

Cell-specific sequencing of translating mRNAs elucidates signaling pathology that can be targeted to reverse neuropathic pain
Ataxia Telangiectasia triggers deficits in Reelin pathway
Authors: Canet-Pons Júlia , Schubert Ralf , Duecker Ruth Pia , Schrewe Roland , Wölke Sandra , Schnölzer Martina , Auburger Georg , Zielen Stefan , Warnken Uwe
Published: June 2018

Autosomal recessive Ataxia Telangiectasia (A-T) is characterized by radiosensitivity, immunodeficiency and cerebellar neurodegeneration. A-T is caused by inactivating mutations in the Ataxia-Telangiectasia-Mutated (ATM) gene, a serine-threonine protein kinase involved in DNA-damage response and excitatory neurotransmission. The selective vulnerability of cerebellar Purkinje neurons (PN) to A-T is not well understood.

Employing global proteomic profiling of cerebrospinal fluid from patients at ages around 15 years we detected reduced Calbindin, Reelin, Cerebellin-1, Cerebellin-3, Protocadherin Fat 2, Sempahorin 7A and increased Apolipoprotein -B, -H, -J peptides. Bioinformatic enrichment was observed for pathways of chemical response, locomotion, calcium binding and complement immunity. This seemed important, since secretion of Reelin from glutamatergic afferent axons is crucial for PN radial migration and spine homeostasis. Reelin expression is downregulated by irradiation and its deficiency is a known cause of ataxia. Validation efforts in 2-month-oldAtm-/- mice before onset of motor deficits confirmed transcript reductions for Reelin receptorsApoer2/Vldlrwith increases for their ligandsApoe/Apohand cholesterol 24-hydroxylaseCyp46a1. Concomitant dysregulations were found forVglut2/Sema7aas climbing fiber markers, glutamate receptors likeGrin2band calcium homeostasis factors (Atp2b2, Calb1, Itpr1), while factors involved in DNA damage, oxidative stress, neuroinflammation and cell adhesion were normal at this stage.

These findings show that deficient levels of Reelin signaling factors reflect the neurodegeneration in A-T in a sensitive and specific way. As an extracellular factor, Reelin may be accessible for neuroprotective interventions.
Selecting precise reference normal tissue samples for cancer research using a deep learning approach
Authors: Zeng William , Glicksberg Benjamin S. , Li Yangyan , Chen Bin
Published: June 2018

Background

Normal tissue samples are often employed as a control for understanding disease mechanisms, however, collecting matched normal tissues from patients is difficult in many instances. In cancer research, for example, the open cancer resources such as TCGA and TARGET do not provide matched tissue samples for every cancer or cancer subtype. The recent GTEx project has profiled samples from healthy individuals, providing an excellent resource for this field, yet the feasibility of using GTEx samples as the reference remains unanswered.

Methods

We analyze RNA-Seq data processed from the same computational pipeline and systematically evaluate GTEx as a potential reference resource. We use those cancers that have adjacent normal tissues in TCGA as a benchmark for the evaluation. To correlate tumor samples and normal samples, we explore top varying genes, reduced features from principal component analysis, and encoded features from an autoencoder neural network. We first evaluate whether these methods can identify the correct tissue of origin from GTEx for a given cancer and then seek to answer whether disease expression signatures are consistent between those derived from TCGA and from GTEx.

Results

Among 32 TCGA cancers, 18 cancers have less than 10 matched adjacent normal tissue samples. Among three methods, autoencoder performed the best in predicting tissue of origin, with 12 of 14 cancers correctly predicted. The reason for misclassification of two cancers is that none of normal samples from GTEx correlate well with any tumor samples in these cancers. This suggests that GTEx has matched tissues for the majority cancers, but not all. While using autoencoder to select proper normal samples for disease signature creation, we found that disease signatures derived from normal samples selected via an autoencoder from GTEx are consistent with those derived from adjacent samples from TCGA in many cases. Interestingly, choosing top 50 mostly correlated samples regardless of tissue type performed reasonably well or even better in some cancers.

Conclusions

Our findings demonstrate that samples from GTEx can serve as reference normal samples for cancers, especially those do not have available adjacent tissue samples. A deep-learning based approach holds promise to select proper normal samples.
Increased Cerebral Blood Flow after single dose of antipsychotics in healthy volunteers depends on dopamine D2 receptor density profiles
Authors: Selvaggi Pierluigi , Hawkins Peter C.T. , Dipasquale Ottavia , Rizzo Gaia , Bertolino Alessandro , Dukart Juergen , Sambataro Fabio , Pergola Giulio , Williams Steven C.R. , Turkheimer Federico , Zelaya Fernando , Veronese Mattia , Mehta Mitul A.
Published: June 2018

As a result of neuro-vascular coupling, the functional effects of antipsychotics in human brain have been investigated in both healthy and clinical populations using haemodynamic markers such as regional Cerebral Blood Flow (rCBF). However, the relationship between observed haemodynamic effects and the pharmacological action of these drugs has not been fully established. Here, we analysed MRI-based rCBF data from a placebo-controlled study in healthy volunteers, who received a single dose of three different D2 receptor antagonists and tested the association of the main effects of the drugs on rCBF against normative population maps of D2R protein density and gene-expression data. In particular, we correlated CBF changes after antipsychotic administration with non-displaceable binding potential (BPND) template maps of the high affinity D2-antagonist Positron Emission Tomography (PET) ligand [18F]Fallypride and brain post-mortem microarray mRNA expression data for the DRD2 gene. For all antipsychotics, rCBF changes were directly proportional to brain D2R densities and DRD2 mRNA expression measures, although PET BPND spatial profiles explained more variance as compared with mRNA profiles (PET R2 range= 0.20-0.60, mRNA PET R2 range 0.04-0.20, pairwise-comparisons all p<0.05). In addition, the spatial coupling between ΔCBF and D2R profiles varied between the different antipsychotics tested, possibly reflecting differential affinities. Overall, these results indicate that the functional effects of antipsychotics as measured with rCBF are tightly correlated with the distribution of their target receptors in striatal and extra-striatal regions. Our results further demonstrate the link between neurotransmitter targets and haemodynamic changes reinforcing rCBF as a robust in-vivo marker of drug effects. This work is important in bridging the gap between pharmacokinetic and pharmacodynamics of novel and existing compounds.
Tissue-specific Gene Expression Prediction Associates Vitiligo with SUOX through an Active Enhancer
Authors: Qi Zhihua , Xie Shiqi , Chen Rui , Aisa Haji A. , Hon Gary C. , Guan Yongtao
Published: June 2018

Vitiligo is an autoimmune disease featuring destruction of melanocytes, which results in patchy depigemtation of skin and hair; two vitiligo GWAS studies identified multiple significant associations, including SNPs in 12q13.2 region. But one study ascribed the association to IKZF4 because it encodes a regulator of T cell activation and is associated with two autoimmune diseases; while the other study ascribed the association to PMEL because it encodes melanocyte protein and has the strongest differential expression between vitiligo lesions and perilesional normal skins. Here we show that vitiligo associated gene in 12q13.2 region is SUOX. Reanalyzing one GWAS dataset, we predicted tissue-specific gene-expression by leveraging Genotype-Tissue Expression (GTEx) datasets, and performed association mapping between the predicted gene-expressions and vitiligo status. SUOX expression is significantly associated with vitiligo in both Nerve (tibia) and Skin (sun exposed) tissues. Epigenetic marks encompass the most significant eQTL of SUOX in both nerve and skin tissues suggest a putative enhancer 3Kb downstream of SUOX. We silenced the putative enhancer using the CRISPR interference system and observed 50% decrease in SUOX expression in K562 cells, a cell line that has similar DNase hypersensitive sites and gene expression pattern to the skin tissue at SUOX locus. Our work provided an example to make sense GWAS hits through examining factors that affect gene expression both computationally and experimentally.
Lightweight bioinformatics: evaluating the utility of Single Board Computer (SBC) clusters for portable, scalable Real-Time Bioinformatics in fieldwork environments via benchmarking
Authors: Parker Joe
Published: June 2018

The versatility of the current DNA sequencing platforms and the development of portable, nanopore sequencers means that it has never been easier to collect genetic data for unknown sample ID. In fact, the distinction between fieldwork and the laboratory is becoming blurred since genome-scale data can now be collected in challenging conditions in a matter of hours. However, the full scientific and societal benefits of these new methods can only be realised with equally rapid and portable analyses. At present, field-based analyses of genomic data, despite advances in computing technology, remain problematic; laptop computers are relatively expensive and limited in scalability, while cloud- and cluster-based analyses depend, for the time being, on sufficiently reliable high-bandwidth data uplinks to transmit primary data for analysis.

Single board computers (SBCs), such as the Raspberry Pi, offer a potential solution to this problem: while less powerful than their laptop cousins, their very individual low cost and power consumption mean modest arrays of SBCs could be used for field-based preprocessing, or complete analyses or primary data. In this study we investigate the performance of one SBC, the Pi 3 Model B+, on a range of typical field-sequencing tasks versus laptop and cloud-based form-factors. Our data analysis pipeline has been made available as a workflow on Github for simple, scalable deployment for a range of uses.
PARP10 promotes cellular proliferation and tumorigenesis by alleviating replication stress
Authors: Schleicher Emily M. , Galvan Adri M. , Moldovan George-Lucian , Nicolae Claudia M.
Published: June 2018

During carcinogenesis, cells are exposed to increased replication stress due to replication fork arrest at sites of DNA lesions and other difficult to replicate regions. Efficient fork restart and DNA repair are important for cancer cell proliferation. We previously showed that the ADP-ribosyltransferase PARP10 interacts with the replication protein PCNA and promotes lesion bypass by recruiting specialized, non-replicative DNA polymerases. Here, we show that PARP10 is overexpressed in a large proportion of human tumors. To understand the role of PARP10 in cellular transformation, we inactivated PARP10 in HeLa cancer cells by CRISPR/Cas9-mediated gene knockout, and overexpressed it in non-transformed RPE-1 cells. We found that PARP10 promotes cellular proliferation and replication fork elongation. Mechanistically, PARP10 overexpression alleviated cellular sensitivity to replication stress by fostering the restart of stalled replication forks. Importantly, mouse xenograft studies indicated that loss of PARP10 reduces the tumorigenesis activity of HeLa cells, while its overexpression results in tumor formation by non-transformed RPE-1 cells. Our findings indicate that PARP10 promotes cellular transformation by alleviating replication stress, and suggest that targeting PARP10 may represent a novel therapeutic approach.
Evaluating cell lines as models for metastatic cancer through integrative analysis of open genomic data
Authors: Liu Ke , Newbury Patrick A. , Glicksberg Benjamin S. , Zeng William ZD , Andrechek Eran R. , Chen Bin
Published: June 2018

Metastasis is the most common cause of cancer-related death and, as such, there is an urgent need to discover new therapies to treat metastasized cancers. Cancer cell lines are widely-used models to study cancer biology and test drug candidates. However, it is still unknown to what extent they adequately resemble the disease in patients. The recent accumulation of large-scale genomic data in cell lines, mouse models, and patient tissue samples provides an unprecedented opportunity to evaluate the suitability of cell lines for metastatic cancer research. In this work, we used breast cancer as a case study. The comprehensive comparison of the genetic profiles of 57 breast cancer cell lines with those of metastatic breast cancer samples revealed substantial genetic differences. In addition, we identified cell lines that more closely resemble different subtypes of metastatic breast cancer. Surprisingly, a combined analysis of mutation, copy number variation and gene expression data suggested that MDA-MB-231, the most commonly used triple negative cell line for metastatic breast cancer research, had little genomic similarity with Basal-like metastatic breast cancer samples. We further compared cell lines with organoids, a new type of preclinical model which are becoming more popular in recent years. We found that organoids outperformed cell lines in resembling the transcriptome of metastatic breast cancer samples. However, additional differential expression analysis suggested that both types of models could not mimic the effects of tumor microenvironment and meanwhile had their own bias towards modeling specific biological processes. Our work provides a guide of cell line selection in metastasis-related study and sheds light on the potential of organoids in translational research.
An expanded toolkit for gene tagging based on MiMIC and scarless CRISPR tagging in Drosophila
Authors: Li-Kroeger David , Kanca Oguz , Lee Pei-Tseng , Cowan Sierra , Lee Michael , Jaiswal Manish , Salazar Jose Luis , He Yuchun , Bellen Hugo J.
Published: June 2018

We generated new genetic tools to efficiently tag genes in Drosophila. Double Header (DH) utilizes intronic MiMIC/CRIMIC insertions to generate artificial exons for GFP mediated protein trapping or T2A-GAL4 gene trapping in vivo based on CRE recombinase to avoid embryo injections. DH significantly increases integration efficiency compared to previous strategies and faithfully reports the expression pattern of genes and proteins. The second technique targets genes lacking coding introns using a two-step cassette exchange. First, we replace the endogenous gene with an excisable compact dominant marker using CRISPR making a null allele. Second, the insertion is replaced with a protein::tag cassette.

This sequential manipulation allows the generation of numerous tagged alleles or insertion of other DNA fragments that facilitates multiple downstream applications. Both techniques allow precise gene manipulation and facilitate detection of gene expression, protein localization and assessment of protein function, as well as numerous other applications.
Enhanced Synthesis of Poly Gamma Glutamic Acid by Increasing the Intracellular Reactive Oxygen Species in the Bacillus licheniformis Δ1-pyrroline-5-carboxylate Dehydrogenase Gene ycgN Deficient Strain
Authors: Li Bichan , Cai Dongbo , Hu Shiying , Zhu Anting , He Zhili , Chen Shouwen
Published: June 2018

Poly gamma glutamic acid (γ-PGA) is an anionic polyamide with numerous applications. Proline metabolism influences the formation of reactive oxygen species (ROS), and is involved in a wide range of cellular processes. However, the relation between proline metabolism and γ-PGA synthesis has not yet been analyzed. In this study, our results indicated that the deletion of Δ1-pyrroline-5-carboxylate dehydrogenase encoded gene ycgN resulted in 85.22% higher yield of γ-PGA in B. licheniformis WX-02. But the deletion of proline dehydrogenase encoded gene ycgM had no effect on γ-PGA synthesis. Meanwhile, a 2.92-fold higher level of P5C was detected in ycgN deficient strain WXΔycgN, while the P5C levels in WXΔycgM and double mutant strain WXΔycgMN remained the same, compared to WX-02. The ROS level of WXΔycgN was 1.18-fold higher than that of WX-02, and the addition of n-acetylcysteine (antioxidant) into medium could decrease its ROS level, further reduced the γ-PGA yield. Our results showed that proline catabolism played an important role in maintaining ROS homeostasis, and the deletion of ycgN caused P5C accumulation, which induced a transient ROS signal to promote γ-PGA synthesis in B. licheniformis.

Importance

γ-PGA is an anionic polyamide with various applications in biomedical and industrial fields. Proline metabolism influences the intracellular reactive oxygen species (ROS) and is involved in a wide range of cellular processes. Here, we report the effects of proline metabolism on γ-PGA synthesis. Our results indicated that deletion of ycgN promoted the synthesis of γ-PGA by increasing the intracellular levels of Δ1-pyrroline-5-carboxylate to generate a transient ROS signal in B. licheniformis WX-02. This study provides the valuable information that enhanced synthesis of γ-PGA by knocking out of ycgN.
Deregulation of LRSAM1 expression impairs the levels of TSG101, UBE2N, VPS28, MDM2 and EGFR
Authors: Minaidou Anna , Nicolaou Paschalis , Christodoulou Kyproula
Published: June 2018

CMT is the most common hereditary neuromuscular disorder of the peripheral nervous system with a prevalence of 1/2500 individuals and it is caused by mutations in more than 80 genes. LRSAM1, a RING finger ubiquitin ligase also known as TSG101-associated ligase (TAL), has been associated with Charcot-Marie-Tooth disease type 2P (CMT2P) and to date eight causative mutations have been identified. Little is currently known on the pathogenetic mechanisms that lead to the disease. We investigated the effect of LRSAM1 deregulation on possible LRSAM1 interacting molecules in cell based models. Possible LRSAM1 interacting molecules were identified using protein-protein interaction databases and literature data. Expression analysis of these molecules was performed in both CMT2P patient and control lymphoblastoid cell lines as well as in LRSAM1 and TSG101 downregulated SH-SY5Y cells.TSG101, UBE2N, VPS28, EGFR and MDM2 levels were significantly decreased in the CMT2P patient lymphoblastoid cell line as well as in LRSAM1 downregulated cells. TSG101 downregulation had a significant effect only on the expression of VPS28 and MDM2 and it did not affect the levels of LRSAM1. This study confirms that LRSAM1 is a regulator of TSG101 expression. Furthermore, deregulation of LRSAM1 significantly affects the levels of UBE2N, VPS28, EGFR and MDM2.