bluuebunny/crossref_metadata_2025 huggingface dataset:
Global connectivity and function of descending spinal input revealed by 3D microscopy and retrograde transduction
Authors: Wang Zimei , Maunze Brian , Wang Yufang , Tsoulfas Pantelis , Blackmore Murray G.
Published: May 2018

The brain communicates with the spinal cord through numerous axon tracts that arise from discrete nuclei, transmit distinct functions, and often collateralize to facilitate the coordination of descending commands. In efforts to restore supraspinal connectivity after injury or disease, this complexity presents a major challenge to interpreting functional outcomes, while the wide distribution of supraspinal nuclei complicates the delivery of therapeutics. Here we harness retrograde viral vectors to overcome these challenges. We demonstrate highly efficient retrograde transduction by AAV2-Retro in adult female mice, and employ tissue clearing to visualize descending tracts and create a mesoscopic projectome for the spinal cord. Moreover, chemogenetic silencing of supraspinal neurons with retrograde vectors results in complete and reversible forelimb paralysis, illustrating effective modulation of supraspinal function. Retrograde efficacy persists even after spinal injury, highlighting therapeutic potential. These data provide a global view of supraspinal connectivity and illustrate the potential of retrograde vectors to parse the functional contributions of supraspinal inputs.
Intersection of phosphate transport, oxidative stress and TOR signalling inCandida albicansvirulence
Authors: Liu Ning-Ning , Uppuluri Priya , Broggi Achille , Besold Angelique , Ryman Kicki , Kambara Hiroto , Solis Norma , Lorenz Viola , Qi Wanjun , Acosta-Zaldivar Maikel , Emami S. Noushin , Bao Bin , An Dingding , Bonilla Francisco A. , Sola-Visner Martha , Filler Scott G. , Luo Hongbo R. , Engström Ylva , Ljungdahl Per Olof , Culotta Valeria C. , Zanoni Ivan , Lopez-Ribot Jose L. , Köhler Julia R.
Published: May 2018

Phosphate is an essential macronutrient required for cell growth and division. Pho84 is the major high-affinity cell-surface phosphate importer ofSaccharomyces cerevisiaeand a crucial element in the phosphate homeostatic system of this model yeast. We found that loss ofCandida albicansPho84 attenuated virulence inDrosophilaand murine oropharyngeal and disseminated models of invasive infection, and conferred hypersensitivity to neutrophil killing. Susceptibility of cells lacking Pho84 to neutrophil attack depended on reactive oxygen species (ROS):pho84-/-cells were no more susceptible than wild typeC. albicansto neutrophils from a patient with chronic granulomatous disease, or to those whose oxidative burst was pharmacologically inhibited or neutralized.pho84-/-mutants hyperactivated oxidative stress signalling. They accumulated intracellular ROS in the absence of extrinsic oxidative stress, in high as well as low ambient phosphate conditions. ROS accumulation correlated with diminished levels of the unique superoxide dismutase Sod3 inpho84-/-cells, whileSOD3overexpression from a conditional promoter substantially restored these cells’ oxidative stress resistance in vitro. Repression ofSOD3expression sharply increased their oxidative stress hypersensitivity. Neither of these oxidative stress management effects of manipulatingSOD3transcription was observed inPHO84wild type cells. Sod3 levels were not the only factor driving oxidative stress effects onpho84-/-cells, though, because overexpressingSOD3did not ameliorate these cells’ hypersensitivity to neutrophil killing ex vivo, indicating Pho84 has further roles in oxidative stress resistance and virulence. Measurement of cellular metal concentrations demonstrated that diminished Sod3 expression was not due to decreased import of its metal cofactor manganese, as predicted from the function ofS. cerevisiaePho84 as a low-affinity manganese transporter. Instead of a role of Pho84 in metal transport, we found its role in TORC1 activation to impact oxidative stress management: overexpression of the TORC1-activating GTPase Gtr1 relieved the Sod3 deficit and ROS excess inpho84-/-null mutant cells, though it did not suppress their hypersensitivity to neutrophil killing or hyphal growth defect. Pharmacologic inhibition of Pho84 by small molecules including the FDA-approved drug foscarnet also induced ROS accumulation. Inhibiting Pho84 could hence support host defenses by sensitizingC. albicansto oxidative stress.
Neutrophil microvesicles drive atherosclerosis by deliveringmiR-155to atheroprone endothelium
Authors: Gomez Ingrid , Ward Ben , Souilhol Celine , Recarti Chiara , Ariaans Mark , Johnston Jessica , Burnett Amanda , Mahmoud Marwa , Luong Le Anh , West Laura , Long Merete , Parry Sion , Woods Rachel , Hulston Carl , Benedikter Birke , Bazaz Rohit , Francis Sheila , Kiss-Toth Endre , Zandvoort Marc van , Schober Andreas , Hellewell Paul , Evans Paul C. , Ridger Victoria
Published: May 2018

Neutrophils have been implicated in the pathogenesis of atherosclerosis, a lipid-driven disease of arteries, but they are seldom found in atherosclerotic plaques. To resolve this longstanding paradox, we investigated whether neutrophil-derived microvesicles may influence arterial pathophysiology. Clinical and pre-clinical studies revealed that levels of circulating neutrophil microvesicles were enhanced by exposure to a high fat diet, a known risk factor for atherosclerosis. Neutrophil microvesicles accumulated at disease-prone regions of arteries that are exposed to complex flow patterns, and they promoted vascular inflammation and atherosclerosis in a murine model. Using cultured endothelial cells exposed to disturbed flow, it was demonstrated that neutrophil microvesicles promoted inflammatory gene expression by delivering a microRNA (miR-155) that enhanced NF-κB activation. Similary, neutrophil microvesicles increased miR-155 and enhanced NF-κB at disease-prone sites of disturbed flow in arteries of mice. We conclude that delivery of microvesicles carrying miR-155 to disease-prone regions of arteries provides a novel mechanism by which neutrophils contribute to vascular inflammation and atherogenesis.
Neuronal morphologies built for reliable physiology in a rhythmic motor circuit
Authors: Otopalik Adriane G. , Marder Eve
Published: May 2018

The neurons of the crustacean stomatogastric ganglion (STG) exhibit highly-conserved firing patterns, voltage waveforms, and circuit functions despite quantifiable animal-to-animal variability in their neuronal morphologies. In recent work, we showed that one neuron type, the Gastric Mill (GM) neuron, is electrotonically compact and operates much like a single compartment, despite having thousands of branch points and a total cable length on the order of 10 mm. Here, we explore how STG neurite morphology shapes voltage signal propagation and summation in four STG neuron types. We use focal glutamate photo-uncaging in tandem with somatic intracellular recordings to examine passive electrotonic structure and voltage signal summation in the GM neuron and three additional STG neuron types: Lateral Pyloric (LP), Ventricular Dilator (VD), and Pyloric Dilator (PD) neurons. In each neuron, we measured the amplitudes and apparent reversal potentials (Erevs) of inhibitory responses evoked with focal glutamate photo-uncaging at more than 20 sites varying in their distance (100–800 μm) from the somatic recording site in the presence of TTX. Apparent Erevs were relatively invariant (mean CVs = 0.04, 0.06, 0.05, and 0.08 for 5–6 GM, LP, PD, VD neurons, respectively), suggesting that all four neuron types are similarly electrotonically uniform and compact. We then characterized the directional sensitivity and arithmetic of voltage summation (with fast sequential activation of 4–6 sites) in individual STG neurites. All four neuron types showed no directional bias in voltage signal summation and linear voltage summation. We motivate these experiments with a proof-of-concept computational model that suggests the immense tapering of STG neurite diameters: from 10–20 μm to sub-micron diameters at the terminal tips, may explain the uniform electrotonic structures experimentally observed and contribute to the robust nature of this central pattern-generating circuit.
Using set theory to reduce redundancy in pathway sets
Authors: Stoney Ruth , Schwartz Jean-Mark , Robertson David L , Nenadic Goran
Published: May 2018

1.

1.01

Background

The consolidation of pathway databases, such as KEGG[1], Reactome[2]and ConsensusPathDB[3], has generated widespread biological interest, however the issue of pathway redundancy impedes the use of these consolidated datasets. Attempts to reduce this redundancy have focused on visualizing pathway overlap or merging pathways, but the resulting pathways may be of heterogeneous sizes and cover multiple biological functions. Efforts have also been made to deal with redundancy in pathway data by consolidating enriched pathways into a number of clusters or concepts. We present an alternative approach, which generates pathway subsets capable of covering all of genes presented within either pathway databases or enrichment results, generating substantial reductions in redundancy.

1.02

Results

We propose a method that uses set cover to reduce pathway redundancy, without merging pathways. The proposed approach considers three objectives: removal of pathway redundancy, controlling pathway size and coverage of the gene set. By applying set cover to the ConsensusPathDB dataset we were able to produce a reduced set of pathways, representing 100% of the genes in the original data set with 74% less redundancy, or 95% of the genes with 88% less redundancy. We also developed an algorithm to simplify enrichment data and applied it to a set of enriched osteoarthritis pathways, revealing that within the top ten pathways, five were redundant subsets of more enriched pathways. Applying set cover to the enrichment results removed these redundant pathways allowing more informative pathways to take their place.

1.03

Conclusion

Our method provides an alternative approach for handling pathway redundancy, while ensuring that the pathways are of homogeneous size and gene coverage is maximised. Pathways are not altered from their original form, allowing biological knowledge regarding the data set to be directly applicable. We demonstrate the ability of the algorithms to prioritise redundancy reduction, pathway size control or gene set coverage. The application of set cover to pathway enrichment results produces an optimised summary of the pathways that best represent the differentially regulated gene set.
Bivariate GWAS scan identifies six novel loci associated with lipid levels and coronary artery disease
Authors: Siewert Katherine M. , Voight Benjamin F.
Published: May 2018

Background

Plasma lipid levels are heritable and genetically associated with risk of coronary artery disease (CAD). However, genome-wide association studies (GWAS) routinely analyze these traits independently of one another. Joint GWAS for two related phenotypes can lead to a higher-powered analysis to detect variants contributing to both traits.

Methods and Results

We performed a bivariate GWAS to discover novel loci associated with heart disease, using a CAD Meta-Analysis (122,733 cases and 424,528 controls), and lipid traits, using data from the Global Lipid Genetics Consortium (188,577 subjects). We identified six previously unreported loci at genome-wide significance (P < 5 × 10−8), three which were associated with Triglycerides and CAD, two which were associated with LDL cholesterol and CAD, and one associated with Total Cholesterol and CAD. At several of our loci, the GWAS signals jointly localize with genetic variants associated with expression level changes for one or more neighboring genes, indicating that these loci may be affecting disease risk through regulatory activity.

Conclusions

We discovered six novel variants individually associated with both lipids and coronary artery disease.
Large-scale RNA editing profiling in different adult chicken tissues
Authors: Shafiei Hamid , Bakhtiarizadeh Mohammad Reza , Salehi Abdolreza
Published: May 2018

RNA editing is a post-transcription maturation process that diversifies genomically encoded information and can lead to diversity and complexity of transcriptome, especially in the brain. Thanks to next-generation sequencing technologies, a large number of editing sites have been identified in different species, especially in human, mouse and rat. While this mechanism is well described in mammals, only a few studies have been performed in the chicken. Here, we developed a rigorous computational strategy to identify RNA editing sites in eight different tissues of the chicken (brain, spleen, colon, lung, kidney, heart, testes and liver), based on RNA sequencing data alone. We identified 68 A-to-G editing sites in 46 genes. Only two of these were previously reported in chicken. We found no C-to-U sites, attesting the lack of this type of editing mechanism in the chicken. Similar to mammals, the editing sites were enriched in non-coding regions, rarely resulted in change of amino acids, showed a critical role in nervous system and had a low guanosine level upstream of the editing site and some enrichment downstream from the site. Moreover, in contrast to mammals, editing sites were weakly enriched in interspersed repeats and the frequency and editing ratio of non-synonymous sites were higher than those of synonymous sites.

Interestingly, we found several tissue-specific edited genes including GABRA3, SORL1 and HTR1D in brain and RYR2 and FHOD3 in heart that were associated with functional processes relevant to the corresponding tissue. This finding highlighted the importance of the RNA editing in several chicken tissues, especially the brain. This study extends our understanding of RNA editing in chicken tissues and establish a foundation for further exploration of this process.
Bacteria are required for regeneration of the Xenopus tadpole tail
Authors: Bishop Thomas F. , Beck Caroline W.
Published: May 2018

The impressive regenerative capabilities of amphibians have been studied for over a century. Although we have learnt a great deal about regenerative processes, the factors responsible for the initiation of regeneration have remained elusive. A previous study implicated reactive oxygen species (ROS) and the ROS-generator, NADPH oxidase (Nox), in Xenopus tadpole tail regeneration. In this study we suggest that Nox is expressed as a consequence of NF-κB transcription factor activity and that ROS produced by Nox, in turn, help to maintain the activity of NF-κB, forming a positive-feedback loop. Microorganisms were found to be required for regeneration through binding to toll-like receptors (TLR). NF-κB is a downstream component of TLR pathways and its activation through TLR stimulation could jump-start the positive-feedback loop. These findings provide potential targets for the activation of regeneration in non-regenerative animals.
Baculovirus-inducing fast-acting innate immunity killsPlasmodiumliver stages
Authors: Emran Talha Bin , Iyori Mitsuhiro , Ono Yuki , Amelia Fitri , Yusuf Yenni , Islam Ashekul , Alam Asrar , Ogawa Ryohei , Matsuoka Hiroyuki , Yamamoto Daisuke , Yoshida Shigeto
Published: May 2018

Baculovirus (BV), an enveloped insect virus with a circular double-stranded DNA genome, possesses unique characteristics that induce strong innate immune responses in mammalian cells. Here, we show that BV administration not only sterilely protects BALB/c mice for at least 7 days from subsequentPlasmodium bergheisporozoite infection but also eliminates existing liver-stage parasites completely, effects superior to those of primaquine, and does so in a TLR9-independent manner. Six hours post-BV administration, IFN-α and IFN-γ were robustly produced in serum, and RNA transcripts of interferon-stimulated genes were drastically upregulated in the liver. Thein vivopassive transfer of post-BV administration serum effectively eliminated liver-stage parasites, and IFN-α neutralization abolished this effect, indicating that the BV liver-stage parasite killing mechanism is downstream of the type I IFN signaling pathway. Our results demonstrate that BV is a potent IFN-inducing prophylactic and therapeutic agent with great potential for further development as a new malaria vaccine and/or anti-hypnozoite drug.
The Evolution and Sequence Diversity of FhuA inSalmonellaandEscherichia
Authors: Wang Yejun , Chen Xiongbin , Zhu Guoqiang , White Aaron P. , Köster Wolfgang
Published: May 2018

ThefhuACDBoperon, present in a number ofEnterobacteriaceae, encodes components essential for the uptake of ferric hydroxamate type siderophores. FhuA acts not only as transporter for physiologically important chelated ferric iron, but also as receptor for various bacteriophages, toxins and antibiotics, which are pathogenic to bacterial cells. In this research, thefhuAgene distribution and sequence diversity were investigated inEnterobacteriaceae, especiallySalmonellaandEscherichia. Comparative sequence analysis resulted in afhuAphylogenetic tree that did not match the expected phylogeny based on housekeeping sequence analysis or trees offhuCDBgenes. ThefhuAsequences showed a unique mosaic-clustering pattern. On the other hand, the gene sequences showed high conservation for strains from the same serovar or serotype. In total, six clusters were identified from FhuA proteins inSalmonellaandEscherichia, among which typical peptide fragment variations could be defined. Six fragmental insertions / deletions and two substitution fragments were discovered, which could well classify the different clusters. Structure modeling demonstrated that all the six featured insertions/deletions and one substitution fragment are located at the apexes of the long loops of FhuA external pocket. These frequently mutated regions are likely under high selection pressure, and bacterial strains could have escaped from phage infection or toxin / antibiotics attack viafhuAgene mutations while maintaining the siderophore uptake activity essential for bacterial survival. The unusualfhuAclustering suggests that high frequency exchange offhuAgenes has occurred between enterobacterial strains after distinctive species were established.

IMPORTANCE

The enterobacterialfhuACDBoperon encodes proteins which mediate the uptake of siderophores to supply the cells with iron essential for bacterial survival. Here we show different evolutionary patterns for thefhugenes within the same operon. ThefhuAhas a phylogenetic tree that does not match the species phylogeny, whereas the rest of thefhugenes do. ThefhuAgenes showed inter-species sequence convergence and conservation within specific serovars and serotypes. Nearly all of the significant sequence differences among FhuA clusters are located in potential ligand-binding sites on the extracellular surface of fhuA-encoding receptors. The unusualfhuAclustering suggests the frequent recombination and exchange offhuAgenes between enterobacterial strains in the evolutionary state after distinctive species were established.

Our findings suggested either a new evolutionary mechanism or local gene recombination infhuAthat is in contrast to previous evolutionary hypotheses that have formed under the assumption of no recombination.
The genetic architecture of hair colour in the UK population
Authors: Morgan Michael D. , Pairo-Castineira Erola , Rawlik Konrad , Canela-Xandri Oriol , Rees Jonathan , Sims David , Tenesa Albert , Jackson Ian J.
Published: May 2018

We have extensively mapped the genes responsible for hair colour in the UK population. MC1R mutations are well established as the principal genetic cause of red hair colour, but with variable penetrance. We find variation at genes encoding its agonist (POMC), inverse agonist (ASIP) and other loci contribute to red hair and demonstrate epistasis between MC1R and some of these loci. Blonde hair is associated with over 200 loci, and we find a genetic continuum from black through dark and light brown to blonde. Many of the associated genes are involved in hair growth or texture, emphasising the cellular connections between keratinocytes and melanocytes in the determination of hair colour.
First report on Bacterial Diversity of Potable Spring water of Indian Himalayan Region
Authors: Singh Ashish Kumar , Das Saurav , Singh Samer , Gajamer Varsha Rani , Pradhan Nilu , Lepcha Yangchen D. , Tiwari Hare Krishna
Published: May 2018

Water quality of a region directly corroborates with the health index of people. People in the Himalayan hills mainly depend upon the spring water for potability. To determine the microbial ecology of the spring waters of Sikkim, the variable region of 16S rRNA has been sequenced using Illumina MiSeq. Phylum wise annotation showed the East and North district are mostly dominated byProteobacteria(41% and 35.80%), whereas West and South district is dominated byPlanctomycetes(38.46%) andVerrucomicrobia(33%). The consistent dominance phyla in the all the four districts wereBacteriodetes(34-24%) which was highest dominancy in North district and lowest in wets district. Genus wise distribution showed the abundance ofBrevifolis, Flavobacterium, Verrucomicrobia subdivision3, Emticica, Cytophaga, Prosthecobacter, Planctomycetes, Varivorax, Arcicella, Isosphera, Sedimunibacteriumetc. The East district showed highest dominancy of genusEmticiciawhereasPlanctomycetesin the West district. The North district was mainly dominated by genusArcicellaandBrevifollisin the South district. North on the antonymous showed totally different sets of microbial diversity. North district showed an abundance ofArcicella, Planctomycetes, SchlerensiaandAzohydromonas. The heat map produced by Bray Curtis distance method produced three clusters which showed the close relationship between West and East district microbiome that further related to South district. The sample of North district formed out group that showed different community structure from other three districts. The principle component analysis was showed that the east and South district samples are closely related and distantly correlated to the west Sikkim, but the North district showed completely different microbial community. The canonical correspondence analysis showed correlation between bacterial diversity and hydrochemistry and it was found that the bacterial diversity was influenced by the concentration of different metallic ions like sodium, calcium, barium and iron. This is a first report from the Eastern Himalayan region of India and it largely enhances our knowledge about the microbial structure of potable spring water of Eastern Himalayan. This study is useful for Government of India as well as the state government to adopt the different strategic treatment procedures to improve the quality of water that is supplied to the community resides in the Himalayan regions and solely dependent on this untreated spring water.
Bottlenecks in the transmission ofPorcine reproductive and respiratory syndrome virus(PRRSV1) to naïve pigs and quasi-species variation during infection in partially immune pigs
Authors: Cortey Martí , Arocena Gastón , Pileri Emanuela , Martín-Valls Gerard , Mateu Enric
Published: May 2018

The existence of bottlenecks during infection ofPorcine reproductive and respiratory syndrome virus(PRRSV) was studied in an experimental one-to-one model of transmission in pigs. Besides, the differences between viral quasi-species in vaccinated pigs that developed shorter or longer viremias after natural challenge were analysed. The results consistently reported the existence of bottlenecks during transmission. Several positions along the PRRSV genome were identified as being selected in partially immune animals that developed short viremias. Those positions accumulated in GP2, nsp9 and M proteins and resulted in changes in the protein structure and in the interactions of those proteins with their targets. The fact that the affected proteins are known targets of the immunity against PRRSV suggested that the immune response selected those changes. This pig model can be useful for the study of other pathogens of interest in animals and humans.

Author summary

Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically important disease of pigs. It is caused by PRRS virus (PRRSV), a positive-sense, single-stranded RNA virus in theArteriviridaefamily within the orderNidovirales. Here, we study the existence of bottlenecks during disease transmission and the differences between viral quasi-species in vaccinated pigs that developed shorter or longer viremias after natural challenge. Our results consistently report the existence of bottlenecks during PRRSV1 transmission and identify several mutations along the viral genome selected by the host immune response that can be clear targets for new vaccine development.
Detection of shared balancing selection in the absence of trans-species polymorphism
Authors: Cheng Xiaoheng , DeGiorgio Michael
Published: May 2018

Trans-species polymorphism has been widely used as a key sign of long-term balancing selection across multiple species. However, such sites are often rare in the genome, and could result from mutational processes or technical artifacts. Few methods are yet available to specifically detect footprints of trans-species balancing selection without using trans-species polymorphic sites. In this study, we develop summary- and model-based approaches that are each specifically tailored to uncover regions of long-term balancing selection shared by a set of species by using genomic patterns of intra-specific polymorphism and inter-specific fixed differences. We demonstrate that our trans-species statistics have substantially higher power than single-species approaches to detect footprints of trans-species balancing selection, and are robust to those that do not affect all tested species. We further apply our model-based methods to human and chimpanzee whole genome sequencing data. In addition to the previously-established MHC and malaria resistance-associatedFREM3/GYPEregions, we also find outstanding genomic regions involved in barrier integrity and innate immunity, such as theGRIK1/CLDN17intergenic region, and theSLC35F1andABCA13genes. Our findings not only echo the significance of pathogen defense, but also reveal novel candidates in maintaining balanced polymorphisms across human and chimpanzee lineages. Finally, we show that these trans-species statistics can be applied to and work well for an arbitrary number of species, and integrate them into open-source software packages for ease of use by the scientific community.
A hypothetical new role for single-stranded DNA binding proteins in the immune system
Authors: Vijay Nagarjun , Chande Ajit
Published: May 2018

The breadth of the host range of single-stranded DNA (ssDNA) viruses is roughly comparable to the host range of double-stranded DNA viruses (dsDNA). Yet, general ssDNA sensing receptors that activate the immune system have not been unequivocally identified while numerous dsDNA sensing receptors are known. Here, we hypothesize that some of the Single-Stranded DNA Binding (SSB) proteins may act as receptors that detect single-stranded DNA from pathogens and activate the innate immune system. As the first test of our hypothesis, we checked whether human genes that are known to bind to ssDNA are potentially interferon-regulated. Out of the 102 human genes that are known to have ssDNA binding ability 23 genes show a more than two-fold increase in gene expression upon interferon treatment. Single-stranded DNA viruses are pathogens of not only animals but also of plants and protozoans. We used this information to further prioritize our candidate list to ssDNA binding genes that are common between the model plant Arabidopsis thaliana and humans. Based on these strategies, we shortlist several promising candidate genes including the HMGB1 gene which could act as a ssDNA sensor that activates the immune system. Agreeably though we cannot establish a definitive role for these genes as ssDNA sensors of the immune system as yet, our preliminary analysis suggests the potential existence of ssDNA binding protein-like receptors (SLR’s) that are worth investigating further.
Changes in lipid and proteome composition accompany growth ofBacillus subterraneusMITOT1 under supercritical CO2and may promote acclimation to associated stresses
Authors: Peet Kyle C. , Ravindra Kodihalli C. , Wishnok John S. , Summons Roger E. , Thompson Janelle R.
Published: May 2018

Recent demonstration that multipleBacillusstrains grow in batch bioreactors containing supercritical (sc) CO2(i.e. >73 atm, >31°C) is surprising given the recognized roles of scCO2as a sterilant and solvent. Growth under scCO2is of interest for biotechnological applications and for microbially-enhanced geologic carbon sequestration. We hypothesize thatBacillusspp. may alter cell wall and membrane composition in response to scCO2-associated stresses. In this study, protein expression and membrane lipids ofB. subterraneusMITOT1 were profiled in cultures grown under headspaces of 1 and 100 atm of CO2or N2. Growth under 100 atm CO2revealed significantly decreased fatty acid branching and increased fatty acyl chain lengths relative to 1 atm cultures. Proteomes of MITOT1 grown under 1 and 100 atm pressures of CO2and N2were similar (Spearman R>0.65), and principal component analysis revealed variation by treatment with the first two principal components corresponding to headspace gas (CO2or N2) and pressure (1 atm and 100 atm), respectively. Amino acid metabolic proteins were enriched under CO2, including the glycine cleavage system, previously shown to be upregulated in acid stress response. These results provide insights into the stationary phase physiology of strains grown under scCO2, suggesting modifications of cell membranes and amino acid metabolism may be involved in response to acidic, high CO2conditions under scCO2.
In Vitro Growth Effects of Morphine and Naloxone on Various Head and Neck Squamous Cell Cancer Cell Lines
Authors: Denton Stephen R , Padia Reema , Shea Jill E. , Buchmann Luke O , Stoddard Gregory J , Firpo Matthew A , Call Tyler R
Published: May 2018

Understanding the potential effects of mu-agonism and antagonism on cancer cells is important for the perioperative physician. Previous studies suggest some tumor cells may have altered growth with mu-agonism or antagonism. This study investigates the effects of morphine (mu-agonist) and naloxone (mu-antagonist) in head and neck tumor cell lines (laryngeal squamous cell carcinoma (SCC), lateral tongue SCC and base of tongue SCC). Morphine showed no significant effect on tumor cell growth. Naloxone showed significant inhibition of growth in laryngeal SCC, but not in lateral or base of tongue SCC.
RNA polymerase organizes into distinct spatial clusters independent of ribosomal RNA transcription inE. coli
Authors: Weng Xiaoli , Bohrer Christopher H. , Bettridge Kelsey , Lagda Arvin Cesar , Cagliero Cedric , Jin Ding Jun , Xiao Jie
Published: May 2018

Recent studies have shown that RNA polymerase (RNAP) is spatially organized into distinct clusters inE. coliandB. subtiliscells. Spatially organized molecular components in prokaryotic systems imply compartmentalization without the use of membranes, which may offer new insights into pertinent functions and regulations. However, the function of RNAP clusters and whether its formation is driven by active ribosomal RNA (rRNA) transcription remain elusive. In this work, we investigated the spatial organization of RNAP inE. colicells using quantitative superresolution imaging. We observed that RNAP formed large, distinct clusters under a rich medium growth condition and preferentially located in the center of the nucleoid. Two-color superresolution colocalization imaging showed that under the rich medium growth condition, nearly all RNAP clusters were active in synthesizing rRNA, suggesting that rRNA synthesis may be spatially separated from mRNA synthesis that most likely occurs at the nucleoid periphery. Surprisingly, a large fraction of RNAP clusters persisted under conditions in which rRNA synthesis was reduced or abolished, or when only one out of the seven rRNA operons (rrn)remained. Furthermore, when gyrase activity was inhibited, we observed a similar rRNA synthesis level, but multiple dispersed, smaller rRNA and RNAP clusters occupying not only the center but also the periphery of the nucleoid, comparable to an expanded nucleoid. These results suggested that RNAP was organized into active transcription centers for rRNA synthesis under the rich medium growth condition; their presence and spatial organization, however, were independent of rRNA synthesis activity under the conditions used but were instead influenced by the structure and characteristics of the underlying nucleoid. Our work opens the door for further investigations of the function and molecular nature of RNAP clusters and points to a potentially new mechanism of transcription regulation by the spatial organization of individual molecular components.
Localizing and classifying adaptive targets with trend filtered regression
Authors: Mughal Mehreen R. , DeGiorgio Michael
Published: May 2018

Identifying genomic locations of natural selection from sequence data is an ongoing challenge in population genetics. Current methods utilizing information combined from several summary statistics typically assume no correlation of summary statistics regardless of the genomic location from which they are calculated. However, due to linkage disequilibrium, summary statistics calculated at nearby genomic positions are highly correlated. We introduce an approach termedTrendsetterthat accounts for the similarity of statistics calculated from adjacent genomic regions through trend filtering, while reducing the effects of multicollinearity through regularization. Our penalized regression framework has high power to detect sweeps, is capable of classifying sweep regions as either hard or soft, and can be applied to other selection scenarios as well. We find thatTrendsetteris robust to both extensive missing data and strong background selection, and has comparable power to similar current approaches. Moreover, the model learned byTrendsettercan be viewed as a set of curves modeling the spatial distribution of summary statistics in the genome. Application to human genomic data revealed positively-selected regions previously discovered such as LCT in Europeans and EDAR in East Asians. We also identified a number of novel candidates and show that populations with greater relatedness share more sweep signals.
Human Sensitivity to Perturbations Constrained by a Model of the Natural Image Manifold
Authors: Fruend Ingo , Stalker Elee
Published: May 2018

Humans are remarkably well tuned to the statistical properties of natural images. However, quantitative characterization of processing within the domain of natural images has been difficult because most parametric manipulations of a natural image make that image appear less natural. We used generative adversarial networks (GANs) to constrain parametric manipulations to remain within an approximation of the manifold of natural images. In the first experiment, 7 observers decided which one of two synthetic perturbed images matched a synthetic unperturbed comparison image. Observers were significantly more sensitive to perturbations that were constrained to an approximate manifold of natural images than they were to perturbations applied directly in pixel space. Trial by trial errors were consistent with the idea that these perturbations disrupt configural aspects of visual structure used in image segmentation. In a second experiment, 5 observers discriminated paths along the image manifold as recovered by the GAN. Observers were remarkably good at this task, confirming that observers were tuned to fairly detailed properties of an approximate manifold of natural images. We conclude that human tuning to natural images is more general than detecting deviations from natural appearance, and that humans have, to some extent, access to detailed interrelations between natural images.
High throughput single cell sequencing of bothT-cell-receptor-betaalleles
Authors: Hosoya Tomonori , Li Hongyang , Ku Chia-Jui , Wu Qingqing , Guan Yuanfang , Engel James Douglas
Published: May 2018

Allelic exclusion is a vital mechanism for the generation of monospecificity to foreign antigens in B- and T-lymphocytes. Here we developed a high-throughput barcoded method to simultaneously analyze the VDJ recombination status of both mouseT cell receptor betaalleles in hundreds of single cells using Next Generation Sequencing.
Peripheral blood DNA methylation and autism spectrum disorder
Authors: Andrews Shan V. , Sheppard Brooke , Windham Gayle C. , Schieve Laura A. , Schendel Diana E. , Croen Lisa A. , Chopra Pankaj , Alisch Reid S. , Newschaffer Craig J. , Warren Stephen T. , Feinberg Andrew P. , Fallin M. Daniele , Ladd-Acosta Christine
Published: May 2018

Background

Several reports have suggested a role for epigenetic mechanisms in ASD etiology. Epigenome-wide association studies (EWAS) in autism spectrum disorder (ASD) may shed light on particular biological mechanisms. However, studies of ASD cases versus controls have been limited by post-mortem timing and severely small sample sizes. Reports from in-life sampling of blood or saliva have also been very limited in sample size, and/or genomic coverage. We present the largest case-control EWAS for ASD to date, combining data from population-based case-control and case-sibling pair studies.

Methods

DNA from 968 blood samples from children in the Study to Explore Early Development (SEED 1) was used to generate epigenome-wide array DNA methylation (DNAm) data at 485,512 CpG sites for 453 cases and 515 controls, using the Illumina 450K Beadchip. The Simons Simplex Collection (SSC) provided 450K array DNAm data on an additional 343 cases and their unaffected siblings. We performed EWAS meta-analysis across results from the two data sets, with adjustment for sex and surrogate variables that reflect major sources of biological variation and technical confounding such as cell type, batch, and ancestry. We compared top EWAS results to those from a previous brain-based analysis. We also tested for enrichment of ASD EWAS CpGs for being targets of meQTL associations using available SNP genotype data in the SEED sample.

Findings

In this meta-analysis of blood-based DNA from 796 cases and 858 controls, no single CpG met a Bonferroni discovery threshold of p < 1.12×10−7. Seven CpGs showed differences at p < 1×10−5and 48 at 1×10−4. Of the top 7, 5 showed brain-based ASD associations as well, often with larger effect sizes, and the top 48 overall showed modest concordance (r = 0.31) in direction of effect with cerebellum samples. Finally, we observed suggestive evidence for enrichment of CpG sites controlled by SNPs (meQTL targets) among the EWAS CpGs hits, which was consistent across EWAS and meQTL discovery p-value thresholds.

Conclusions

We report the largest case-control EWAS study of ASD to date. No single CpG site showed a large enough DNAm difference between cases and controls to achieve epigenome-wide significance in this sample size. However, our results suggest the potential to observe disease associations from blood-based samples. Among the 7 sites achieving suggestive statistical significance, we observed consistent, and stronger, effects at the same sites among brain samples. Discovery-oriented EWAS for ASD using blood samples will likely need even larger samples and unified genetic data to further understand DNAm differences in ASD.
Stiffness Sensing and Cell Motility: Durotaxis and Contact Guidance
Authors: Feng Jingchen , Levine Herbert , Mao Xiaoming , Sander Leonard M.
Published: May 2018

Mechanical properties of the substrate plays a vital role in cell motility. Cells are shown to migrate up stiffness gradient (durotaxis) and along aligned fibers in the substrate (contact guidance). Here we present a simple mechanical model for cell migration, by placing a cell on lattice models for biopolymer gels and hydrogels. In our model cells attach to the substrate via focal adhesions (FAs). As the cells contract, forces are generated at the FAs, determining their maturation and detachment. At the same time, the cell also allowed to move and rotate to maintain force and torque balance. Our model, in which the cells only take the information of forces at the FAs, without a prior knowledge of the substrate stiffness or geometry, is able to reproduce both durotaxis and contact guidance.
Label propagation defines signaling networks associated with recurrently mutated cancer genes
Authors: Cakir Merve , Mukherjee Sayan , Wood Kris C.
Published: May 2018

Each different tumor type has a distinct profile of genomic perturbations and each of these alterations causes unique changes to cellular homeostasis. Detailed analyses of these changes would reveal downstream effects of genomic alterations, contributing to our understanding of their roles in tumor development and progression. Across a range of tumor types, including bladder, lung, and endometrial carcinoma, we determined genes that are frequently altered in The Cancer Genome Atlas patient populations to study the effects of these alterations on signaling and regulatory pathways. To achieve this, we used a label propagation-based methodology to generate networks from gene expression signatures of mutations. Individual networks offered a comprehensive view of signaling changes represented by gene signatures, which in turn reflect the scope of molecular events that are perturbed in the presence of a given genomic alteration. Comparing different networks to each other revealed commonalities between them and biological pathways distinct genomic alterations converge on, highlighting the critical signaling events tumor dysregulate through multiple mechanisms. Finally, mutations inducing common changes to the signaling network were used to search for genomic markers of drug response, connecting shared perturbations to differential drug response.
Developmental system drift in motor ganglion patterning between distantly related tunicates
Authors: Lowe Elijah K. , Stolfi Alberto
Published: May 2018

The larval nervous system of the solitary tunicateCionais a simple model for the study of chordate neurodevelopment. The development and connectivity of theCionaMotor Ganglion (MG) has been studied in fine detail, but how this important structure develops in other tunicates is not well known. By comparing gene expression patterns in the developing MG of the distantly related tunicateMolgula occidentalis, we found that its patterning is highly conserved compared to theCionaMG. MG neuronal subtypes inMolgulawere specified in the exact same positions as inCiona, though the timing of subtype-specific gene expression onset was slightly shifted to begin earlier, relative to mitotic exit and differentiation. In transgenicMolgulaembryos electroporated withDmbxreporter plasmids, we were also able to characterize the morphology of the lone pair of descending decussating neurons (ddNs) inMolgula, revealing the same unique contralateral projection seen inCionaddNs and their putative vertebrate homologs the Mauthner cells. AlthoughDmbxexpression labels the ddNs in both species, cross-species transgenic assays revealed significant changes to thecis-regulatory logic underlyingDmbxtranscription. We found thatDmbx cis-regulatory DNAs fromCionacan drive highly specific reporter gene expression inMolguladdNs, butMolgulasequences are not active inCionaddNs. This acute divergence in the molecular mechanisms that underlie otherwise functionally conservedcis-regulatory DNAs supports the recently proposed idea that the extreme genetic plasticity observed in tunicates may be attributed to the extremerigidityof the spatial organization of their embryonic cell lineages.
Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations
Authors: Nguyen Quan H. , Lukowski Samuel W. , Chiu Han Sheng , Senabouth Anne , Bruxner Timothy J.C. , Christ Angelika N. , Palpant Nathan J. , Powell Joseph E.
Published: May 2018

Heterogeneity of cell states represented in pluripotent cultures has not been described at the transcriptional level. Since gene expression is highly heterogeneous between cells, single-cell RNA sequencing can be used to identify how individual pluripotent cells function. Here, we present results from the analysis of single-cell RNA sequencing data from 18,787 individual WTC-CRISPRi human induced pluripotent stem cells. We developed an unsupervised clustering method and, through this, identified four subpopulations distinguishable on the basis of their pluripotent state, including a core pluripotent population (48.3%), proliferative (47.8%), early primed for differentiation (2.8%), and late primed for differentiation (1.1%). For each subpopulation, we were able to identify the genes and pathways that define differences in pluripotent cell states. Our method identified four transcriptionally distinct predictor gene sets composed of 165 unique genes that denote the specific pluripotency states; using these sets, we developed a multigenic machine learning prediction method to accurately classify single cells into each of the subpopulations. Compared against a set of established pluripotency markers, our method increases prediction accuracy by 10%, specificity by 20%, and explains a substantially larger proportion of deviance (up to threefold) from the prediction model. Finally, we developed an innovative method to predict cells transitioning between subpopulations and support our conclusions with results from two orthogonal pseudotime trajectory methods.