bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential Sustained and Transient Temporal Processing Across Visual Streams
Authors: Stigliani Anthony , Jeska Brianna , Grill-Spector Kalanit
Published: June 2018

How do high-level visual regions process the temporal aspects of our visual experience? While the temporal sensitivity of early visual cortex has been studied with fMRI in humans, temporal processing in high-level visual cortex is largely unknown. By modeling neural responses with millisecond precision in separate sustained and transient channels, and introducing a flexible encoding framework that captures differences in neural temporal integration time windows and response nonlinearities, we predict fMRI responses across visual cortex for stimuli ranging from 33 ms to 20 s. Using this innovative approach, we discovered that lateral category-selective regions respond to visual transients associated with stimulus onsets and offsets but not sustained visual information. Thus, lateral category-selective regions compute moment-tomoment visual transitions, but not stable features of the visual input. In contrast, ventral category-selective regions respond to both sustained and transient components of the visual input. Responses to sustained stimuli exhibit adaptation, whereas responses to transient stimuli are surprisingly larger for stimulus offsets than onsets. This large offset transient response may reflect a memory trace of the stimulus when it is no longer visible, whereas the onset transient response may reflect rapid processing of new items. Together, these findings reveal previously unconsidered, fundamental temporal mechanisms that distinguish visual streams in the human brain. Importantly, our results underscore the promise of modeling brain responses with millisecond precision to understand the underlying neural computations.

AUTHOR SUMMARY

How does the brain encode the timing of our visual experience? Using functional magnetic resonance imaging (fMRI) and a temporal encoding model with millisecond resolution, we discovered that visual regions in the lateral and ventral processing streams fundamentally differ in their temporal processing of the visual input. Regions in lateral temporal cortex process visual transients associated with stimulus onsets and offsets but not the unchanging aspects of the visual input. That is, they compute moment-to-moment changes in the visual input. In contrast, regions in ventral temporal cortex process both stable and transient components, with the former exhibiting adaptation. Surprisingly, in these ventral regions responses to stimulus offsets were larger than onsets. We suggest that the former may reflect a memory trace of the stimulus, when it is no longer visible, and the latter may reflect rapid processing of new items at stimulus onset. Together, these findings (i) reveal a fundamental temporal mechanism that distinguishes visual streams and (ii) highlight both the importance and utility of modeling brain responses with millisecond precision to understand the temporal dynamics of neural computations in the human brain.
Amyloidogenic Proteins Drive Hepatic Proteostasis Remodeling in an Induced Pluripotent Stem Cell Model of Systemic Amyloid Disease
Authors: Giadone Richard M. , Liberti Derek C. , Matte Taylor M. , Rosarda Jessica D. , Torres-Arancivia Celia , Ghosh Sabrina , Diedrich Jolene K. , Pankow Sandra , Skvir Nicholas , Jean J.C. , Yates John R. , Wilson Andrew A. , Connors Lawreen H. , Kotton Darrell N. , Wiseman R. Luke , Murphy George J.
Published: June 2018

Systemic amyloidosis represents a class of disorders in which misfolded proteins are secreted by effector organs and deposited as proteotoxic aggregates at downstream target tissues. Despite being well-described clinically, the contribution of effector organs such as the liver to the pathogenesis of these diseases is poorly understood. Here, we utilize a patient-specific induced pluripotent stem cell (iPSC)-based model of hereditary transthyretin (TTR) amyloid disease (ATTR amyloidosis) in order to define the contributions of hepatic cells to the distal proteotoxicity of secreted TTR. To this end, we employ a gene correction strategy to generate isogenic, ATTR amyloidosis patient-specific iPSCs expressing either amyloidogenic or wild-type TTR. We further utilize this gene editing strategy in combination with single cell RNAseq to identify multiple hepatic proteostasis factors, including many components of adaptive unfolded protein response (UPR) signaling pathways, whose expression correlates with the production of destabilized TTR variants in iPSC-derived hepatic cells. We further demonstrate that enhancing ER proteostasis within ATTR amyloidosis iPSC-derived hepatic lineages via stress-independent activation of aforementioned adaptive UPR signaling preferentially reduces the secretion of destabilized amyloidogenic TTR. Together, these results suggest the potential of the liver to chaperone-at-a-distance and impact pathogenesis at downstream target cells in the context of systemic amyloid disease, and further highlight the promise of UPR modulating therapeutics for the treatment of TTR-mediated and other amyloid diseases.
Breakdown of spatial coding and neural synchronization in epilepsy
Authors: Shuman Tristan , Aharoni Daniel , Cai Denise J. , Lee Christopher R. , Chavlis Spyridon , Taxidis Jiannis , Flores Sergio E. , Cheng Kevin , Javaherian Milad , Kaba Christina C. , Shtrahman Matthew , Bakhurin Konstantin I. , Masmanidis Sotiris , Khakh Baljit S. , Poirazi Panayiota , Silva Alcino J. , Golshani Peyman
Published: June 2018

Temporal lobe epilepsy causes significant cognitive deficits in both human patients and rodent models, yet the specific circuit mechanisms that alter cognitive processes remain unknown. There is dramatic and selective interneuron death and axonal reorganization within the hippocampus of both humans and animal models, but the functional consequences of these changes on information processing at the neuronal population level have not been well characterized. To examine spatial representations of epileptic and control mice, we developed a novel wire-free miniature microscope to allow for unconstrained behavior during in vivo calcium imaging of neuronal activity. We found that epileptic mice running on a linear track had severely impaired spatial processing in CA1 within a single session, as place cells were less precise and less stable, and population coding was impaired. Long-term stability of place cells was also compromised as place cells in epileptic mice were highly unstable across short time intervals and completely remapped across a week. Because of the large-scale reorganization of inhibitory circuits in epilepsy, we hypothesized that degraded spatial representations were caused by dysfunctional inhibition. To test this hypothesis, we examined the temporal dynamics of hippocampal interneurons using silicon probes to simultaneously record from CA1 and dentate gyrus during head-fixed virtual navigation. We found that epileptic mice had a profound reduction in theta coherence between the dentate gyrus and CA1 regions and altered interneuron synchronization. In particular, dentate interneurons of epileptic mice had altered phase preferences to ongoing theta oscillations, which decorrelated inhibitory population firing between CA1 and dentate gyrus. To assess the specific contribution of desynchronization on spatial coding, we built a CA1 network model to simulate hippocampal desynchronization. Critically, we found that desynchronized inputs reduced the information content and stability of CA1 neurons, consistent with the experimental data. Together, these results demonstrate that temporally precise intra-hippocampal communication is critical for forming the spatial code and that desynchronized firing of hippocampal neuronal populations contributes to poor spatial processing in epileptic mice.
Mouse Models ofGNAO1-Associated Movement Disorder: Allele- and sex-specific differences in phenotypes
Authors: Feng Huijie , Larrivee Casandra L. , Demireva Elena , Xie Huirong , Leipprandt Jeff , Neubig Richard R.
Published: June 2018

Background

Infants and children with dominantde novomutations inGNAO1exhibit movement disorders, epilepsy, or both. Children with loss-of-function (LOF) mutations exhibit Epileptiform Encephalopathy 17 (EIEE17). Gain-of-function (GOF) mutations or those with normal function are found in patients with Neurodevelopmental Disorder with Involuntary Movements (NEDIM). There is no animal model with a human mutantGNAO1allele.

Objectives

Here we develop a mouse model carrying a humanGNAO1mutation and determine whether clinical features of theGNAO1mutation including movement disorder would be evident in the mouse model.

Methods

A mouseGnao1knock-in GOF mutation (G203R) was created by CRISPR/Cas9 methods. The resulting offspring and littermate controls were subjected to a battery of behavioral tests. A previously reported GOF mutant mouse knock-in (Gnao1+/G184S) was also studied for comparison.

Results

Gnao1+/G203Rmutant mice are viable and gain weight comparably to controls. Homozygotes are non-viable. Grip strength was decreased in both males and females. MaleGnao1+/G203Rmice were strongly affected in movement assays (RotaRod and DigiGait) while females were not. MaleGnao1+/G203Rmice also showed enhanced seizure propensity in the pentylenetetrazole kindling test. Mice with a G184S GOF knock-in also showed movement-related behavioral phenotypes but females were more strongly affected than males.

Conclusions

Gnao1+/G203Rmice phenocopy children with heterozygousGNAO1G203R mutations, showing both movement disorder and a relatively mild epilepsy pattern. This mouse model should be useful in mechanistic and preclinical studies ofGNAO1-related movement disorders.
Validating genome-wide CRISPR-Cas9 function in the non-conventional yeast Yarrowia lipolytica
Authors: Schwartz Cory , Cheng Jan-Fang , Evans Robert , Schwartz Christopher A. , Wagner James M. , Anglin Scott , Beitz Adam , Pan Weihua , Lonardi Stefano , Blenner Mark , Alper Hal S. , Yoshikuni Yasuo , Wheeldon Ian
Published: June 2018

Genome-wide mutational screens are central to understanding the genetic underpinnings of evolved and engineered phenotypes. The widespread adoption of CRISPR-Cas9 genome editing has enabled such screens in many organisms, but identifying functional sgRNAs still remains a challenge. To address this limitation, we developed a methodology to quantify the cutting efficiency of each sgRNA in a genome-scale library in the biotechnologically important yeast Yarrowia lipolytica. Screening in the presence and absence of native DNA repair enabled high-throughput quantification of sgRNA function leading to the identification of high efficiency sgRNAs that cover 94% of genes. Library validation enhanced the classification of essential genes by identifying inactive guides that create false negatives and mask the effects of successful disruptions. Quantification of guide effectiveness also creates a dataset from which functional determinants of CRISPR-Cas9 can be identified. Finally, application of the library identified mutations that led to high lipid accumulation and eliminated pseudohyphal morphology.
Rice Galaxy: an open resource for plant science
Authors: Juanillas Venice , Dereeper Alexis , Beaume Nicolas , Droc Gaetan , Dizon Joshua , Mendoza John Robert , Perdon Jon Peter , Mansueto Locedie , Triplett Lindsay , Lang Jillian , Zhou Gabriel , Ratharanjan Kunalan , Plale Beth , Haga Jason , Leach Jan E. , Ruiz Manuel , Thomson Michael , Alexandrov Nickolai , Larmande Pierre , Kretzschmar Tobias , Mauleon Ramil P.
Published: June 2018

Background

Rice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies and high density genotyping platforms for genome variation analysis and gene discovery. Germplasm collections representing rice diversity, improved varieties and elite breeding materials are accessible through rice gene banks for use in research and breeding, with many having genome sequences and high density genotype data available. Combining phenotypic and genotypic information on these accessions enables genome-wide association analysis, which is driving quantitative trait loci (QTL) discovery and molecular marker development. Comparative sequence analyses across QTL regions facilitate the discovery of novel alleles. Analyses involving DNA sequences and large genotyping matrices for thousands of samples, however, pose a challenge to non-computer savvy rice researchers.

Findings

We adopted the Galaxy framework to build the federated Rice Galaxy resource, with shared datasets, tools, and analysis workflows relevant to rice research. The shared datasets include high density genotypes from the 3,000 Rice Genomes project and sequences with corresponding annotations from nine published rice genomes. Rice Galaxy includes tools for designing single nucleotide polymorphism (SNP) assays, analyzing genome-wide association studies, population diversity, rice-bacterial pathogen diagnostics, and a suite of published genomic prediction methods. A prototype Rice Galaxy compliant to Open Access, Open Data, and Findable, Accessible, Interoperable, and Reproducible principles is also presented.

Conclusions

Rice Galaxy is a freely available resource that empowers the plant research community to perform state-of-the-art analyses and utilize publicly available big datasets for both fundamental and applied science.
The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates
Authors: Sarver Brice A. J. , Pennell Matthew W. , Brown Joseph W. , Keeble Sara , Hardwick Kayla M. , Sullivan Jack , Harmon Luke J.
Published: June 2018

Comparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. However, the effect that the selection of these priors has on the inference of comparative parameters has not been thoroughly investigated. Such uncertainty may systematically bias phylogenetic reconstruction and, subsequently, parameter estimation. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we use BEAST to simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation rates and extinction rates) from these trees. When substitution rate heterogeneity is large, parameter estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate.
The Vibrio H-ring facilitates the outer membrane penetration of polar-sheathed flagellum
Authors: Zhu Shiwei , Nishikino Tatsuro , Kojima Seiji , Homma Michio , Liu Jun
Published: June 2018

The bacterial flagellum has evolved as one of the most remarkable nanomachines in nature. It provides swimming and swarming motilities that are often essential for the bacterial life cycle and for pathogenesis. Many bacteria such as Salmonella and Vibrio species use flagella as an external propeller to move to favorable environments, while spirochetes utilize internal periplasmic flagella to drive a serpentine movement of the cell bodies through tissues. Here we use cryo-electron tomography to visualize the polar-sheathed flagellum of Vibrio alginolyticus with particular focus on a Vibrio specific feature, the H-ring. We characterized the H-ring by identifying its two components FlgT and FlgO. Surprisingly, we discovered that the majority of flagella are located within the periplasmic space in the absence of the H-ring, which are dramatically different from external flagella in wild-type cells. Our results indicate the H-ring has a novel function in facilitating the penetration of the outer membrane and the assembly of the external sheathed flagella. This unexpected finding is however consistent with the notion that the flagella have evolved to adapt highly diverse needs by receiving or removing accessary genes.

Significance Statement

Flagellum is the major organelle for motility in many bacterial species. While most bacteria possess external flagella such as the multiple peritrichous flagella found in Escherichia coli and Salmonella enterica or the single polar-sheathed flagellum in Vibrio spp., spirochetes uniquely assemble periplasmic flagella, which are embedded between their inner and outer membranes. Here, we show for the first time that the external flagella in Vibrio alginolyticus can be changed as periplasmic flagella by deleting two flagellar genes. The discovery here may provide a new paradigm to understand the molecular basis underlying flagella assembly, diversity, and evolution.
Insight into relationship between micro-consortia, nitrogen source and petroleum degradation at low temperature anaerobic condition
Authors: Yu Jicheng , Chen Chao , Liu Changjian , Yu Dongning , Chen Shuai , Yuan Fenghao , Fu Yang , Liu Qiu
Published: June 2018

Biostimulation by addition nutrients has been proved to be an effective bioremediation strategies. Revealing response law of nitrogen source and structure characteristics of anaerobic petroleum degrading microorganisms microbial population will help us optimize nutrient to promote oil degradation. Anaerobic micro-consortia characteristics in the enrichment marine sediment samples with different nitrogen source, combining with analysis of the oil degradation rates were studied in this paper, as well as functional genes involved in petroleum degradation were also analyzed. On the basis of optimizing the best inorganic nitrogen sources and organic nitrogen sources, an effective medium was designed by response surface methodology that used for enriching petroleum degradation micro-consortia. Amplicon sequencing analysis showed that the population of microorganisms migrated obviously when enriched with different nitrogen sources. With the increase of oil degradation rate, the microbial diversity was significantly decreased, and concentrated on a limited number of genera. The reasonable proportions of GammaProteobacteria, Bacteroidetes and Fusobacteria made the greatest contribution to petroleum degradation. Metagenomic analysis unveiled the mixed nitrogen source promoted the expression of functional genes related to petroleum degradation such as the transfer of succinyl-CoA, synthesis of acetyl CoA and β-oxidation cycle, and was beneficial to degradation of petroleum at low temperature anaerobic condition.

Originality Significance Statement

Addition of nutrients can promote growth of indigenous petroleum degradation-related bacteria and be helpful to the rapid degradation of petroleum. Previous studies accurately characterized aerobic microorganisms on petroleum degradation. However, we still known little about anaerobic microorganisms in marine environment. Most biostimulation methods use inorganic salt as the main nutritional supplement to improve the efficiency of petroleum degradation, but effects of different nitrogen sources on diversity of microorganisms and distribution of functional genes related to petroleum degradation at anaerobic conditions are still unknown. In this research, the effects of nitrogen on petroleum biodegradation, anaerobic microconsortium structure and distribution of genes related to petroleum degradation were unveiled by using amplicon sequencing and metagenomic analysis.
Development and analytical validation of an enzyme-linked immunosorbent assay based on baculovirus recombinant LipL32 protein antigen for the accurate detection of canine leptospirosis
Authors: Orozco-Cabrera Carolina , López-Valencia Gilberto , Cueto-González Sergio Arturo , Guerrero-Velázquez José Guadalupe , Moreno-Torres Kattya , Espinoza-Blandón Kelvin Orlando , Campo Nohemí Castro-Del , Gaxiola-Camacho Soila Maribel , Gómez-Gómez Sergio Daniel , Trasviña-Muñoz Enrique , Torres-Guzmán Cinthya , Monge-Navarro Francisco Javier
Published: June 2018

Leptospirainfects a wide range of companion, domestic and wild animal species, shedding the spirochetes into the environment via urine. Dogs become infected by direct or indirect contact with wild or domestic infected animal reservoirs increasing the risk of zoonotic transmission of the disease. The microscopic agglutination test has been used as the gold standard for the diagnosis of leptospirosis but has low sensitivity and is technically complex. Several ELISA tests have been developed based on recombinant proteins ofLeptospirafor the diagnosis of leptospirosis with similar or higher specificity and sensitivity levels than the microscopic agglutination test. Here, we developed and analytically validated an ELISA test based on recombinant LipL32 protein ofLeptospiraexpressed in baculovirus. The LipL32 protein was successfully adapted in an indirect ELISA using dog plasma samples. Optimization of the ELISA resulted in a P/N ratio of 7.18 using only 5 ng of rLipL32 per well. Inter-assay and intra-assay variation showed a CV of 3.96% and 6.98% respectively, suggesting that the ELISA-LipL32 is highly reproducible. When tested with field samples, concordance of the ELISA-LipL32 with a real-time PCR, positive concordance was 100%. Our results indicate that the ELISA-LipL32 has the potential to be used by veterinarians and public health investigators as a safe, rapid, inexpensive and reliable method for the early diagnosis ofLeptospirainfection in dogs. Additional studies are still required for clinical validation on field samples under different epidemiological scenarios.
NudCL2 is an Hsp90 cochaperone to regulate sister chromatid cohesion by stabilizing cohesin subunits
Authors: Yang Yuehong , Wang Wei , Li Min , Zhang Wen , Huang Yuliang , Gao Ya , Zhuo Wei , Yan Xiaoyi , Liu Wei , Wang Fangwei , Chen Dingwei , Zhou Tianhua
Published: June 2018

Sister chromatid cohesion plays a key role in ensuring precise chromosome segregation during mitosis, which is mediated by the multisubunit complex cohesin. However, the molecular regulation of cohesin subunits stability remains unclear. Here, we show that NudCL2 (NudC-like protein 2) is essential for the stability of cohesin subunits by regulating Hsp90 ATPase activity in mammalian cells. Depletion of NudCL2 induces mitotic defects and premature sister chromatid separation and destabilizes cohesin subunits that interact with NudCL2. Similar defects are also observed upon inhibition of Hsp90 ATPase activity. Interestingly, ectopic expression of Hsp90 efficiently rescues the protein instability and functional deficiency of cohesin induced by NudCL2 depletion, but not vice versa. Moreover, NudCL2 not only binds to Hsp90, but also significantly modulates Hsp90 ATPase activity and promotes the chaperone function of Hsp90. Taken together, these data suggest that NudCL2 is a previously undescribed Hsp90 cochaperone to modulate sister chromatid cohesion by stabilizing cohesin subunits, providing a hitherto unrecognized mechanism that is crucial for faithful chromosome segregation during mitosis.
Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors
Authors: Salmén Fredrik , Vickovic Sanja , Larsson Ludvig , Stenbeck Linnea , Vallon-Christersson Johan , Ehinger Anna , Häkkinen Jari , Borg Åke , Frisén Jonas , Ståhl Patrik L , Lundeberg Joakim
Published: June 2018

The comprehensive analysis of tumor tissue heterogeneity is crucial for determining specific disease states and establishing suitable treatment regimes. Here, we analyze tumor tissue sections from ten patients diagnosed with HER2+ breast cancer. We obtain and analyze multidimensional, genome-wide transcriptomics data to resolve spatial immune cell distribution and identity within the tissue sections. Furthermore, we determine the extent of immune cell infiltration in different regions of the tumor tissue, including invasive cancer regions. We combine cross-sectioning and computational alignment to build three-dimensional images of the transcriptional landscape of the tumor and its microenvironment. The three-dimensional data clearly demonstrates the heterogeneous nature of tumor-immune interactions and reveal interpatient differences in immune cell infiltration patterns. Our study shows the potential for an improved stratification and description of the tumor-immune interplay, which is likely to be essential in treatment decisions.
Three-dimensional culture of chicken primordial germ cells in chemically defined media containing the functional polymer FP003
Authors: Chen Yi-Chen , Chang Wei-Che , Lin Shau-Ping , Minami Masataka , Jean Christian , Hayashi Hisato , Rival-Gervier Sylvie , Kanaki Tatsuro , Wu Shinn-Chih , Pain Bertrand
Published: June 2018

Scalable production of avian suspension cell exhibits a valuable potential on therapeutic application by producing recombinant protein and as the substrate for virus growth. This study sought to establish a system with chemically defined components for three-dimensional (3D) culture of chicken primordial germ cells (cPGCs), a pluripotent avian cell type. cPGCs were cultured in medium supplemented with the functional polymer FP003. Viscoelasticity was low in this medium, and cPGCs did not sediment,and consequently their expansion was improved. The total number of cPGCs increased by 17-fold after 1week of culture in 3D-FAot medium, an aseric chemically defined medium containing FP003, indicating that this medium enhances the expansion of cPGCs. Moreover, cPGC cell lines stably expressed the germline-specific reporter VASA:tdTOMATO, as well as other markers of cPGCs, for more than 1 month upon culture in 3D-FAot medium, indicating that the characteristics of these cells are maintained. cPGCs harboring both PGK:EGFP and VASA:tdTOMATO robustly expressed both fluorescent proteins upon culture in 3D-FAot, suggesting that this approach is perspective for recombinant protein production. In summary,this novel 3D culture system can be used to efficiently expand cPGCs in suspension without mechanical stirring or loss of cellular properties. This system provides a platform for large-scale culture ofcPGCs in industry.
MRI-related anxiety in healthy individuals, intrinsic BOLD oscillations at 0.1 Hz and heart rate variability in low frequency bands
Authors: Pfurtscheller Gert , Schwerdtfeger Andreas , Fink David , Brunner Clemens , Aigner Christoph Stefan , Brito Joana , Andrade Alexandre
Published: June 2018

Participation in a MRI scan is associated with increased anxiety, thus possibly impacting baseline recording for functional MRI studies. We investigated in 23 healthy individuals without any former MRI experience (scanner-naïve) the relations between anxiety, 0.1-Hz BOLD oscillations and heart rate variability (HRV) in two separate resting state sessions (R1, R2). BOLD signals were recorded from precentral gyrus (PCG) and insula in both hemispheres. Phase-locking and time delays were computed in the frequency band 0.07–0.13 Hz. Positive (pTD) and negative time delays (nTD) were found. The pTD characterize descending neural BOLD oscillations spreading from PCG to insula and nTD characterize ascending vascular BOLD oscillations related to blood flow in the middle cerebral artery. HRV power in two low frequency bands 0.06–0.1 Hz and 0.1–0.14 Hz was computed. Based on the drop rate of the anxiety level from R1 to R2, two groups could be identified: one with a strong anxiety decline (large drop group) and one with a moderate decline or even anxiety increase (small drop group). A significant correlation was found only between the left-hemispheric time delay (pTD, nTD) of BOLD oscillations and anxiety drop, with a dominance of nTD in the large drop group. The analysis of within-scanner HRV revealed a pronounced increase of low frequency power between both resting states, dominant in the band 0.06–0.1 Hz in the large drop group and in the band 0.1–0.14 Hz in the small drop group. These results suggest different mechanisms related to anxiety processing in healthy individuals. One mechanism (large drop group) could embrace an increase of blood circulation in the territory of the left middle cerebral artery (vascular BOLD) and another (small drop group) translates to rhythmic central commands (neural BOLD) in the frequency band 0.1–0.14 Hz.
A system for gene expression noise control in yeast
Authors: Mundt Max , Anders Alexander , Murray Seán , Sourjik Victor
Published: June 2018

Gene expression noise arises from stochastic variation in the synthesis and degradation of mRNA and protein molecules and creates differences in protein numbers across populations of genetically identical cells. Such variability can lead to imprecision and reduced performance of both native and synthetic networks. In principle, gene expression noise can be controlled through the rates of transcription, translation and degradation, such that different combinations of those rates lead to the same protein concentrations but at different noise levels. Here, we present a “noise tuner” which allows orthogonal control over the transcription and the mRNA degradation rates by two different inducer molecules. Combining experiments with theoretical analysis, we show that in this system the noise is largely determined by the transcription rate whereas mean expression can be independently adjusted by mRNA stability. This noise tuner enables twofold changes in gene expression noise over a fivefold range of mean protein levels. We demonstrated the efficacy of the noise tuner in a complex regulatory network by varying gene expression noise in the mating pathway of Saccharomyces cerevisiae, which allowed us to control the output noise and the mutual information transduced through the pathway. The noise tuner thus represents an effective tool of gene expression noise control, both to interrogate noise sensitivity of natural networks and enhance performance of synthetic circuits.
Within-host infectious disease models accommodating cellular coinfection, with an application to influenza
Authors: Koelle Katia , Farrell Alex , Brooke Christopher , Ke Ruian
Published: June 2018

Within-host models are useful tools for understanding the processes regulating viral load dynamics. While existing models have considered a wide range of within-host processes, at their core these models have shown remarkable structural similarity. Specifically, the structure of these models generally consider target cells to be either uninfected or infected, with the possibility of accommodating further resolution (for example, cells that are refractory to infection and cells that are in an eclipse phase). Recent findings, however, indicate that cellular coinfection is the norm rather than the exception for many viral infectious diseases, and that cells with high multiplicity of infection are present over at least some duration of an infection. The reality of these cellular coinfection dynamics is not accommodated in current within-host models although it may be critical for understanding within-host dynamics. This is particularly the case if multiplicity of infection impacts infected cell phenotypes such as their death rate and their viral production rates. Here, we present a new class of within-host disease models that allow for cellular coinfection in a scalable manner by retaining the low-dimensionality that is a desirable feature of many current within-host models. The models we propose adopt the general structure of epidemiological ‘macroparasite’ models that allow hosts to be variably infected by parasites such as nematodes and host phenotypes to flexibly depend on parasite burden. Specifically, our within-host models consider target cells as ‘hosts’ and viral particles as ‘macroparasites’, and allow viral output and infected cell lifespans, among other phenotypes, to depend on a cell’s multiplicity of infection. We show with an application to influenza that these models can be statistically fit to viral load and other within-host data, that they can reproduce notable features of within-host viral dynamics, and that importantin vivoquantities such as the mean multiplicity of cellular infection can be easily quantified with these models once parameterized. The within-host model structure we develop here provides an alternative approach for modeling within-host viral load dynamics and allows for a new class of questions to be addressed that consider the effects of cellular coinfection, collective viral interactions, and viral complementation in within-host viral dynamics and evolution.
The Therapeutic Antibody Profiler (TAP): Five Computational Developability Guidelines
Authors: Raybould Matthew I. J. , Marks Claire , Krawczyk Konrad , Taddese Bruck , Nowak Jaroslaw , Lewis Alan P. , Bujotzek Alexander , Shi Jiye , Deane Charlotte M.
Published: June 2018

Therapeutic monoclonal antibodies (mAbs) must not only bind to their target but must also be free from 'developability issues', such as poor stability or high levels of aggregation. While small molecule drug discovery benefits from Lipinski's rule of five to guide the selection of molecules with appropriate biophysical properties, there is currently no in silico analog for antibody design. Here, we model the variable domain structures of a large set of post-Phase I clinical-stage antibody therapeutics (CSTs), and calculate an array of metrics to estimate their typical properties. In each case, we contextualize the CST distribution against a snapshot of the human antibody gene repertoire. We describe guideline values for five metrics thought to be implicated in poor developability: the total length of the Complementarity-Determining Regions (CDRs), the extent and magnitude of surface hydrophobicity, positive charge and negative charge in the CDRs, and asymmetry in the net heavy and light chain surface charges. The guideline cut-offs for each property were derived from the values seen in CSTs, and a flagging system is proposed to identify nonconforming candidates. On two mAb drug discovery sets, we were able to selectively highlight sequences with developability issues. We make available the Therapeutic Antibody Profiler (TAP), an open-source computational tool that builds downloadable homology models of variable domain sequences, tests them against our five developability guidelines, and reports potential sequence liabilities and canonical forms. TAP is freely available at http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/TAP.php.
Capturing auxin response factors syntax using DNA binding models
Authors: Stigliani Arnaud , Martin-Arevalillo Raquel , Lucas Jérémy , Bessy Adrien , Vinos-Poyo Thomas , Mironova Victoria , Vernoux Teva , Dumas Renaud , Parcy François
Published: June 2018

Auxin is a key hormone performing a wealth of functions throughout the plant life cycle. It acts largely by regulating genes at the transcriptional level through a family of transcription factors (TF) called auxin response factors (ARF). Even if all ARF monomers analysed so far bind a similar DNA sequence, there is evidence that ARFs differ in their target genomic regions and regulated genes. Here we use position weight matrices (PWM) to model ARF DNA binding specificity based on published DNA affinity purification sequencing (DAP-seq) data. We find that the genome binding of two ARFs (ARF2 and ARF5/Monopteros/MP) differ largely because these two factors have different preferred ARF binding site (ARFbs) arrangements (orientation and spacing). We illustrate why PWMs are more versatile to reliably identify ARFbs than the widely used consensus sequences and demonstrate their power with biochemical experiments on the regulatory regions of the IAA19 model gene. Finally, we combined gene regulation by auxin with ARF-bound regions and identified specific ARFbs configurations that are over-represented in auxin up-regulated genes, thus deciphering the ARFbs syntax functional for regulation. This provides a general method to exploit the potential of genome-wide DNA binding assays and decode gene regulation.
Evolution of salivary glue genes inDrosophilaspecies
Authors: Da Lage Jean-Luc , Thomas Gregg W. C. , Bonneau Magalie , Courtier-Orgogozo Virginie
Published: June 2018

Background

At the very end of the larval stage Drosophila expectorate a glue secreted by their salivary glands to attach themselves to a substrate while pupariating. The glue is a mixture of apparently unrelated proteins, some of which are highly glycosylated and possess internal repeats. Because species adhere to distinct substrates (i.e. leaves, wood, rotten fruits), glue genes are expected to evolve rapidly.

Results

We used available genome sequences and PCR-sequencing of regions of interest to investigate the glue genes in 20Drosophilaspecies. We discovered a new gene in addition to the seven glue genes annotated inD. melanogaster.We also identified a phase 1 intron at a conserved position present in five of the eight glue genes ofD. melanogaster, suggesting a common origin for those glue genes. A slightly significant rate of gene turnover was inferred. Both the number of repeats and the repeat sequence were found to diverge rapidly, even between closely related species. We also detected high repeat number variation at the intrapopulation level inD. melanogaster.

Conclusion

Most conspicuous signs of accelerated evolution are found in the repeat regions of several glue genes.
Integration of accessibility data from structure probing into RNA-RNA interaction prediction
Authors: Miladi Milad , Montaseri Soheila , Backofen Rolf , Raden Martin
Published: June 2018

Experimental structure probing data has been shown to improve thermodynamics-based RNA secondary structure prediction. To this end, chemical reactivity information (as provided e.g. by SHAPE) is incorporated, which encodes whether or not individual nucleotides are involved in intra-molecular structure. Since inter-molecular RNA-RNA interactions are often confined to unpaired RNA regions, SHAPE data is even more promising to improve interaction prediction. Here we show how such experimental data can be incorporated seamlessly into accessibility-based RNA-RNA interaction prediction approaches, as implemented in IntaRNA. This is possible via the computation and use of unpaired probabilities that incorporate the structure probing information. We show that experimental SHAPE data can significantly improve RNA-RNA interaction prediction. We evaluate our approach by investigating interactions of a spliceosomal U1 snRNA transcript with its target splice sites. When SHAPE data is incorporated, known target sites are predicted with increased precision and specificity.

Availability

https://github.com/BackofenLab/IntaRNA
OTUB1 non-catalytically regulates the stability of the E2 ubiquitin conjugating enzyme UBE2E1
Authors: Pasupala Nagesh , Morrow Marie E. , Que Lauren T. , Malynn Barbara A. , Ma Averil , Wolberger Cynthia
Published: June 2018

OTUB1 is a deubiquitinating enzyme that cleaves K48-linked polyubiquitin chains and also regulates ubiquitin signaling through a unique, non-catalytic mechanism. OTUB1 binds to a subset of E2 ubiquitin conjugating enzymes and inhibits their activity by trapping the E2~ubiquitin thioester and preventing ubiquitin transfer. The same set of E2s stimulate the deubiquitinating activity of OTUB1 when the E2 is not charged with ubiquitin. Previous studies have shown that, in cells, OTUB1 binds to members of the UBE2D (UBCH5) and UBE2E families, as well as to UBC13 (UBE2N). Cellular roles have been identified for the interaction of OTUB1 with UBC13 and members of the UBE2D family, but not for UBE2E E2 enzymes. We report here a novel role for OTUB1-E2 interactions in modulating E2 protein ubiquitination. We find that depletion of OTUB1 dramatically destabilizes the E2 conjugating enzyme UBE2E1 (UBE2E1) in cells and that this effect is independent of the catalytic activity of OTUB1 but depends on the ability of OTUB1 to bind to UBE2E1. We show that OTUB1 suppresses UBE2E1 autoubiquitinationin vitroand in cells, thereby preventing UBE2E1 from being targeted to the proteasome for degradation. Taken together, we have found a new role for OTUB1 in rescuing specific E2s from degradationin vivo.
TEsmall identifies small RNAs associated with targeted inhibitor resistance in melanoma
Authors: O’Neill Kathryn , Liao Wen-Wei , Patel Ami , Hammell Molly Gale
Published: June 2018

MicroRNAs (miRNAs) are small 21-22nt RNAs that act to regulate the expression of mRNA target genes through direct binding to mRNA targets. While miRNAs typically dominate small RNA transcriptomes, many other classes are present including tRNAs, snoRNAs, snRNAs, Y-RNAs, piRNAs, and siRNAs. Interactions between processing machinery and targeting networks of these various small RNA classes remains unclear, largely because these small RNAs are typically analyzed separately. Here we present TEsmall, a tool that allows for the simultaneous processing and analysis of small RNAs from each annotated class in a single integrated workflow. The pipeline begins with raw fastq reads and proceeds all the way to producing count tables formatted for differential expression. Several interactive charts are also produced to look at overall distributions in length and annotation classes. We next applied the TEsmall pipeline to small RNA libraries generated from melanoma cells responding to targeted inhibitors of the MAPK pathway. Targeted oncogene inhibitors have emerged as way to tailor cancer therapies to the particular mutations present in a given tumor. While these targeted strategies are typically effective for short intervals, the emergence of resistance is extremely common, limiting the effectiveness of single-agent therapeutics and driving the need for a better understanding of resistance mechanisms. Using TEsmall, we identified several microRNAs and other small RNA classes that are enriched in inhibitor resistant melanoma cells in multiple melanoma cell lines and may be able to serve as markers of resistant populations more generally.
In situtranscriptome characteristics are lost following culture adaptation of adult cardiac stem cells
Authors: Kim Taeyong , Echeagaray Oscar H. , Wang Bingyan J , Casillas Alexandria , Broughton Kathleen M. , Kim Bong-Hyun , Sussman Mark A
Published: June 2018

Regenerative therapeutic approaches for myocardial diseases often involve adoptive transfer of stem cells expandedex vivo. Prior studies indicate that cell culture conditions affect functional and phenotypic characteristics, but relationship(s) of cultured cells derived from freshly isolated populations and the heterogeneity of the cultured population remain poorly defined. Functional and phenotypic characteristics of adoptively donated cells will determine outcomes of interventional treatment for disease, necessitating characterization of the impact thatex vivoexpansion has upon isolated stem cell populations. Single-cell RNA-Seq profiling (scRNA-Seq) was performed to determine consequences of culture expansion upon adult cardiac progenitor cells (CPCs) as well as relationships with other cell populations. Bioinformatic analyses reveal loss of identity marker genes in cultured CPCs while simultaneously acquiring thousands of additional genes. Cultured CPCs exhibited decreased transcriptome variability within their population relative to their freshly isolated cells. Findings were validated by comparative analyses using scRNA-Seq datasets of various cell types generated by multiple scRNA-Seq technology. Increased transcriptome diversity and decreased population heterogeneity in the cultured cell population relative to freshly isolated cells may help account for reported outcomes associated with experimental and clinical use of CPCs for treatment of myocardial injury.
A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex
Authors: de Vries Saskia E. J. , Lecoq Jerome , Buice Michael A. , Groblewski Peter A. , Ocker Gabriel K. , Oliver Michael , Feng David , Cain Nicholas , Ledochowitsch Peter , Millman Daniel , Roll Kate , Garrett Marina , Keenan Tom , Kuan Leonard , Mihalas Stefan , Olsen Shawn , Thompson Carol , Wakeman Wayne , Waters Jack , Williams Derric , Barber Chris , Berbesque Nathan , Blanchard Brandon , Bowles Nicholas , Caldejon Shiella , Casal Linzy , Cho Andrew , Cross Sissy , Dang Chinh , Dolbeare Tim , Edwards Melise , Galbraith John , Gaudreault Nathalie , Griffin Fiona , Hargrave Perry , Howard Robert , Huang Lawrence , Jewell Sean , Keller Nika , Knoblich Ulf , Larkin Josh , Larsen Rachael , Lau Chris , Lee Eric , Lee Felix , Leon Arielle , Li Lu , Long Fuhui , Luviano Jennifer , Mace Kyla , Nguyen Thuyanh , Perkins Jed , Robertson Miranda , Seid Sam , Shea-Brown Eric , Shi Jianghong , Sjoquist Nathan , Slaughterbeck Cliff , Sullivan David , Valenza Ryan , White Casey , Williford Ali , Witten Daniela , Zhuang Jun , Zeng Hongkui , Farrell Colin , Ng Lydia , Bernard Amy , Phillips John W. , Reid R. Clay , Koch Christof
Published: June 2018

To understand how the brain processes sensory information to guide behavior, we must know how stimulus representations are transformed throughout the visual cortex. Here we report an open, large-scale physiological survey of neural activity in the awake mouse visual cortex: the Allen Brain Observatory Visual Coding dataset. This publicly available dataset includes cortical activity from nearly 60,000 neurons collected from 6 visual areas, 4 layers, and 12 transgenic mouse lines from 221 adult mice, in response to a systematic set of visual stimuli. Using this dataset, we reveal functional differences across these dimensions and show that visual cortical responses are sparse but correlated. Surprisingly, responses to different stimuli are largely independent, e.g. whether a neuron responds to natural scenes provides no information about whether it responds to natural movies or to gratings. We show that these phenomena cannot be explained by standard local filter-based models, but are consistent with multi-layer hierarchical computation, as found in deeper layers of standard convolutional neural networks.
Low MSH2 protein levels identify muscle-invasive bladder cancer resistant to cisplatin
Authors: Goodspeed Andrew , Jean Annie , Costello James C.
Published: June 2018

Background

The response to first-line, platinum-based treatment of muscle-invasive bladder cancer has not improved in three decades.

Objective

The objective of this study is to identify genes that predict cisplatin resistance in bladder cancer.

Design

We performed a whole-genome, CRISPR-based screen in a bladder cancer cell line treated with cisplatin to identify genes that mediate response to cisplatin. Targeted validation was performed in vitro across two bladder cancer cell lines. The top gene candidate was validated in a publicly available bladder cancer dataset containing 340 bladder cancer patients with treatment, protein, and survival information.

Results and limitations

The cisplatin resistance screen suggested the mismatch repair pathway through the loss of MSH2 and MLH1 contribute to cisplatin resistance. Bladder cancer cells depleted of MSH2 are resistant to cisplatin in vitro, in part due to a reduction in apoptosis. These cells maintain sensitivity to the cisplatin-analog, oxaliplatin. Bladder tumors with low protein levels of MSH2 have poorer overall survival when treated with cisplatin- or carboplatin-based therapy.

Conclusions

We generated in vitro and clinical support that bladder cancer cell lines and tumors with low levels of MSH2 are more resistant to cisplatin-based therapy. Further studies are warranted to determine the ability of MSH2 protein levels to serve as a prospective biomarker of chemotherapy response in bladder cancer.

Patient summary

We report the first evidence that the protein level of MSH2 may contribute to chemotherapy resistance observed in bladder cancer. MSH2 levels has the potential to serve as a biomarker of treatment response.