bluuebunny/crossref_metadata_2025 huggingface dataset:
Heterogeneous origins of human sleep spindles in different cortical layers
Authors: Hagler Donald J. , Ulbert Istvan , Wittner Lucia , Erőss Lorand , Madsen Joseph R. , Devinsky Orrin , Doyle Werner , Fabo Daniel , Cash Sydney S. , Halgren Eric
Published: November 2017

Sleep spindles are a cardinal feature in human slow wave sleep and may be important for memory consolidation. We studied the intracortical organization of spindles in humans by recording spontaneous sleep spindles from different cortical layers using linear microelectrode arrays. Two patterns of spindle generation were identified using visual inspection, and confirmed with factor analysis. Spindles were largest and most common in upper and middle channels, with limited involvement of deep channels. Many spindles were observed in only upper or only middle channels, but about half occurred in both. In spindles involving both middle and upper channels, the spindle envelope onset in middle channels led upper by ∼25-50ms on average. The phase relationship between spindle waves in upper and middle channels varied dynamically within spindle epochs, and across individuals. Current source density analysis demonstrated that upper and middle channel spindles were both generated by an excitatory supragranular current sink while an additional deep source was present for middle channel spindles only. Only middle channel spindles were accompanied by deep gamma activity. These results suggest that upper channel spindles are generated by supragranular pyramids, and middle channel by infragranular. Possibly, middle channel spindles are generated by core thalamocortical afferents, and upper channel by matrix. The concurrence of these patterns could reflect engagement of cortical circuits in the integration of more focal (core) and distributed (matrix) aspects of memory. These results demonstrate that at least two distinct intracortical systems generate human sleep spindles.

Significance Statement

Bursts of ∼14Hz oscillations, lasting about a second, have been recognized for over 80 years as cardinal features of mammalian sleep. Recent findings suggest that they play a key role in organizing cortical activity during memory consolidation. We used linear microelectrode arrays to study their intracortical organization in humans. We found that spindles could be divided into two types. One mainly engages upper layers of the cortex, which are considered to be specialized for associative activity. The other engages both upper and middle layers, including those devoted to sensory input. The interaction of these two spindle types may help organize the interaction of sensory and associative aspects of memory consolidation.
Oxidative stress and loss of Fe-S proteins in Friedreich ataxia induced pluripotent stem cell-derived PSNs can be reversed by restoring FXN expression with a benzamide HDAC inhibitor
Authors: Hu Amelié , Rai Myriam , Donatello Simona , Pandolfo Massimo
Published: November 2017

Epigenetic suppression of frataxin (FXN) expression caused by the presence of expanded GAA repeats at theFXNlocus is the key pathogenic event in Friedreich ataxia (FRDA), a recessive neurodegenerative and systemic disease. FXN is involved in iron-sulfur (Fe-S) cluster biogenesis in mitochondria, its deficiency causes multiple Fe-S protein deficiencies, mitochondrial dysfunction and oxidative stress. Primary sensory neurons (PSNs) in the dorsal root ganglia (DRGs) are the most vulnerable cells in FRDA, whose abnormal development and degeneration leads to the onset and early progression of ataxia. We generated PSNs from induced pluripotent stem cells (iPSCs) from FRDA patients and showed that they recapitulate the key pathogenic events in FRDA, including low FXN levels, loss of Fe-S proteins and impaired antioxidant responses. We also showed that FXN deficiency in these cells may be partially corrected by a pimelic benzamide histone deacetylase inhibitor, a class of potential therapeutics for FRDA. We generated and validated a cellular model of the most vulnerable neurons in FRDA, which can be used for further studies on pathogenesis and treatment approaches.
LEM-3 is a midbody-tethered DNA nuclease that resolves chromatin bridges during cytokinesis
Authors: Hong Ye , Sonneville Remi , Wang Bin , Scheidt Viktor , Meier Bettina , Woglar Alexander , Demetriou Sarah , Labib Karim , Jantsch Verena , Gartner Anton
Published: November 2017

Faithful chromosome segregation and genome maintenance requires the removal of all DNA bridges that physically link chromosomes before cells divide. Using C. elegans embryos we show that the LEM-3/Ankle1 nuclease defines a new genome integrity mechanism by processing DNA bridges right before cells divide. LEM-3 acts at the midbody, the structure where abscission occurs at the end of cytokinesis. LEM-3 localization depends on factors needed for midbody assembly, and LEM-3 accumulation is increased and prolonged when chromatin bridges are trapped at the cleavage plane. LEM-3 locally processes chromatin bridges that arise from incomplete DNA replication, unresolved recombination intermediates or the perturbance of chromosome structure. Proper LEM-3 midbody localization and function is regulated by AIR-2/Aurora B kinase. Strikingly, LEM-3 act cooperatively with the BRC-1/BRCA1 homologous recombination factor to promote genome integrity. These findings provide a molecular basis for the suspected role of the LEM-3 orthologue Ankle1 in human breast cancer.
Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data
Authors: Abu-Jamous Basel , Kelly Steven
Published: November 2017

Identification of co-expressed gene clusters can provide evidence for genetic or physical interactions between genes. Thus, co-expression clustering is a routine step in large-scale analyses of gene expression data. We show that commonly used clustering methods produce results that substantially disagree with each other, and do not match the biological expectations of co-expressed gene clusters. Furthermore, these clusters can contain up to 50% unreliably assigned genes. Consequently, downstream analyses of these clusters (e.g. functional term enrichment analysis) suffer from high error rates. We present clust, an automated method that solves these problems by extracting clusters that match the biological expectations of co-expressed genes. Using 100 datasets from five model organisms we demonstrate that clusters generated by clust are better than those produced by other methods, both numerically and for use in functional analysis. Finally, we show that clust can simultaneously cluster multiple datasets, enabling users to leverage the large quantity of public expression data for novel comparative analysis.
Tn-Core: context-specific reconstruction of core metabolic models using Tn-seq data
Authors: diCenzo George C , Mengoni Alessio , Fondi Marco
Published: November 2017

Motivation

Tn-seq (transposon mutagenesis and sequencing) and constraint-based metabolic modelling represent highly complementary approaches. They can be used to probe the core genetic and metabolic networks underlying a biological process, revealing invaluable information for synthetic biology engineering of microbial cell factories. However, while algorithms exist for integration of –omics data sets with metabolic models, no method has been explicitly developed for integration of Tn-seq data with metabolic reconstructions.

Results

We report the development of Tn-Core, a Matlab toolbox designed to generate gene-centric, context-specific core reconstructions consistent with experimental Tn-seq data. Extensions of this algorithm allow: i) the generation of context-specific functional models through integration of both Tn-seq and RNA-seq data; ii) to visualize redundancy in core metabolic processes; and iii) to assist in curation ofde novodraft metabolic models. The utility of Tn-Core is demonstrated primarily using aSinorhizobium melilotimodel as a case study.

Availability and implementation

The software can be downloaded fromhttps://github.com/diCenzo-GC/Tn-Core. All results presented in this work have been obtained with Tn-Core v. 1.0.

Contact

georgecolin.dicenzo@unifi.it,marco.fondi@unifi.it

Supplementary information

Supplementary data are available at Bioinformatics online.
CRISPys: Optimal sgRNA design for editing multiple members of a gene family using the CRISPR system
Authors: Hyams Gal , Abadi Shiran , Avni Adi , Halperin Eran , Shani Eilon , Mayrose Itay
Published: November 2017

The discovery and development of the CRISPR-Cas9 system in the past few years has made eukaryotic genome editing, and specifically gene knockout for reverse genetics, a simpler, efficient, and effective task. The system is directed to the genomic target site by a programmed single-guide RNA (sgRNA) that base-pairs with the DNA target, subsequently leading to site-specific double-strand breaks. However, many gene families in eukaryotic genomes exhibit partially overlapping functions and, thus, the knockout of one gene might be concealed by the function of the other. In such cases, the reduced specificity of the CRISPR-Cas9 system, which may lead to the cleavage of genomic sites that are not identical to the sgRNA, can be harnessed for the simultaneous knockout of multiple homologous genes. Here, we introduce CRISPys, an algorithm for the optimal design of sgRNAs that would potentially target multiple members of a given gene family. CRISPys first clusters all the potential targets in the input sequences into a hierarchical tree structure that specifies the similarity among them. Then, sgRNAs are proposed in the internal nodes of the tree by embedding mismatches where needed, such that the cleavage efficiencies of the induced targets are maximized. We suggest several approaches for designing the optimal individual sgRNA, and an approach that provides a set of sgRNAs that also accounts for the homologous relationships among gene-family members. We further show by in-silico examination over all gene families in theSolanum lycopersicumgenome that our suggested approach outperforms simpler alignment-based techniques.

Graphical abstract

Highlights

Many genes in eukaryotic genomes exhibit partially overlapping functions. This imposes difficulties on reverse-genetics, as the knockout of one gene might be concealed by the function of the other.

We present CRISPys, a graph-based algorithm for the optimal design of CRISPR systems given a set of redundant genes.

CRISPys harnesses the lack of specificity of the CRISPR-Cas9 genome editing technique, providing researchers the ability to simultaneously mutate multiple genes.

We show that CRISPys outperforms existing approaches that are based on simple alignment of the input gene family.
Hominin-specific NOTCH2 paralogs expand human cortical neurogenesis through regulation of Delta/Notch interactions
Authors: Suzuki Ikuo K. , Gacquer David , Van Heurck Roxane , Kumar Devesh , Wojno Marta , Bilheu Angéline , Herpoel Adèle , Chéron Julian , Polleux Franck , Detours Vincent , Vanderhaeghen Pierre
Published: November 2017

The human cerebral cortex has undergone rapid expansion and increased complexity during recent evolution. Hominid-specific gene duplications represent a major driving force of evolution, but their impact on human brain evolution remains unclear. Using tailored RNA sequencing (RNAseq), we profiled the spatial and temporal expression of Hominid-specific duplicated (HS) genes in the human fetal cortex, leading to the identification of a repertoire of 36 HS genes displaying robust and dynamic patterns during cortical neurogenesis. Among these we focused on NOTCH2NL, previously uncharacterized HS paralogs of NOTCH2. NOTCH2NL promote the clonal expansion of human cortical progenitors by increasing self-renewal, ultimately leading to higher neuronal output. NOTCH2NL function by activating the Notch pathway, through inhibition of Delta/Notch interactions. Our study uncovers a large repertoire of recently evolved genes linking genomic evolution to human brain development, and reveals how hominin-specific NOTCH paralogs may have contributed to the expansion of the human cortex.
Giant flagellins form thick flagellar filaments in two species of marine γ-proteobacteria
Authors: Thomson Nicholas M. , Ferreira Josie L. , Matthews-Palmer Teige R. , Beeby Morgan , Pallen Mark J.
Published: November 2017

Flagella, the primary means of motility in bacteria, are helical filaments that function as microscopic propellers composed of thousands of copies of the protein flagellin. Here, we show that many bacteria encode “giant” flagellins, greater than a thousand amino acids in length, and that two species that encode giant flagellins, the marine γ- proteobacteria Bermanella marisrubri and Oleibacter marinus, produce monopolar flagellar filaments considerably thicker than filaments composed of shorter flagellin monomers. We confirm that the flagellum from B. marisrubri is built from its giant flagellin. Phylogenetic analysis reveals that the mechanism of evolution of giant flagellins has followed a stepwise process involving an internal domain duplication followed by insertion of an additional novel insert. This work illustrates how “the” bacterial flagellum should not be seen as a single, idealised structure, but as a continuum of evolved machines adapted to a range of niches.
Synaptic m6A Epitranscriptome Reveals Functional Partitioning of Localized Transcripts for Dynamic Tripartite Synapse Modulation
Authors: Merkurjev Daria , Hong Wan-Ting , lida Kei , Goldie Belinda J , Yamaguti Hitoshi , Oomoto Ikumi , Ohara Takayuki , Kawaguchi Shin-ya , Hirano Tomoo , Martin Kelsey C , Pellegrini Matteo , Wang Dan Ohtan
Published: November 2017

A localized transcriptome at the synapse facilitates synapse-, stimulus-, and transcript-specific synthesis of the local proteome in response to neuronal activity. While enzyme-mediated mRNA modifications have been shown to regulate cellular mRNA turnover and translation, the role of these modifications in regulating synaptic RNA has not been studied. We established low-input m6A-seq of synaptosomal RNA to determine the chemically modified local transcriptome in healthy adult mouse forebrain and identified 4,329 selectively enriched m6A RNA peaks in 2,987 genes, which we refer to as the synaptic m6A epitranscriptome (SME). SME is functionally enriched in synthesis and modulation of tripartite synapses, and in pathways implicated in neurodevelopmental and neuropsychiatric diseases. Interrupting m6A-mediated regulation via knockdown of reader YTHDF1 in hippocampal neurons alters expression of SME member Apc, and causes synaptic malfunctions manifesting immature spine morphology and dampened excitatory synaptic transmission concomitant with decreased PSD-95 clustering and GluA1 surface expression. Our findings indicate that chemical modifications of synaptic mRNAs critically contribute to synaptic function.
Partitioning of semisynthetic lipidated N-Ras in lipid raft nanodomains determined by FRET to lipid domain markers
Authors: Shishina Anna K. , Kovrigina Elizaveta A. , Galiakhmetov Azamat R. , Rathore Rajendra , Kovrigin Evgenii L.
Published: November 2017

Cellular membranes are heterogeneous planar lipid bilayers displaying lateral phase separation with the nanometer-scale liquid-ordered phase (aka “lipid rafts” or Lo) surrounded by the liquid-disordered phase (Ld). Many membrane-associated proteins were found to stably integrate in the rafts, which is critical for their biological function. Isoforms H and N of Ras GTPase possess a unique ability to switch their lipid domain preference depending on the type of bound guanine nucleotide (GDP or GTP). This behavior, however, has never been reproducedin vitroin model bilayers with recombinant proteins, and therefore has been attributed to action of other proteins binding Ras at the membrane surface. In this paper, we report the observation of the nucleotide-dependent switch of lipid domain preferences of the semisynthetic lipidated N-Ras in raft lipid vesiclesin the absence of other proteins. To detect segregation of Ras molecules in raft and disordered lipid domains, we measured Förster Resonance Energy Transfer (FRET) between the donor fluorophore, mant, attached to the protein-bound guanine nucleotides, and the acceptor, rhodamine-conjugated lipid, localized to the liquid-disordered domains. We demonstrated that N-Ras preferentially populated raft domains when bound to mant-GDP, while losing preference for rafts when it was associated with a GTP mimic, mant-GppNHp. At the same time, the isolated lipidated C-terminal peptide of N-Ras was found localized outside of the liquid-ordered rafts, most likely—in the bulk disordered lipid.
Evolution at the edge of expanding populations
Authors: Deforet Maxime , Carmona-Fontaine Carlos , Korolev Kirill S. , Xavier Joao B.
Published: November 2017

Predicting evolution of expanding populations is critical to control biological threats such as invasive species and cancer metastasis. Expansion is primarily driven by reproduction and dispersal, but nature abounds with examples of evolution where organisms pay a reproductive cost to disperse faster. When does selection favor this ‘survival of the fastest?’ We searched for a simple rule, motivated by evolution experiments where swarming bacteria evolved into an hy-perswarmer mutant which disperses∼100% faster but pays a growth cost of ∼ 10% to make many copies of its flagellum. We analyzed a two-species model based on the Fisher equation to explain this observation: the population expansion rate (v) results from an interplay of growth (r) and dispersal (D) and is independent of the carrying capacity:. A mutant can take over the edge only if its expansion rate (v2) exceeds the expansion rate of the established species’ (v1); this simple condition (v2>v1) determines the maximum cost in slower growth that a faster mutant can pay and still be able to take over. Numerical simulations and time-course experiments where we tracked evolution by imaging bacteria suggest that our findings are general: less favorable conditions delay but do not entirely prevent the success of the fastest. Thus, the expansion rate defines a traveling wave fitness, which could be combined with trade-offs to predict evolution of expanding populations.
A de novo approach to disentangle partner identity and function in holobiont systems
Authors: Meng Arnaud , Marchet Camille , Corre Erwan , Peterlongo Pierre , Alberti Adriana , Da Silva Corinne , Wincker Patrick , Pelletier Eric , Probert Ian , Decelle Johan , Le Crom Stéphane , Not Fabrice , Bittner Lucie
Published: November 2017

Background

Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. The study of holobiont transcriptomes shares similarities with meta-transcriptomic, and hence, is also affected by challenges invoked above. Here we propose an innovative approach to tackle such difficulties which was applied to the study of marine holobiont models as a proof of concept.

Results

We considered three holobionts models, of which two transcriptomes were previously assembled and published, and a yet unpublished transcriptome, to analyze their raw reads and assign them to the host and/or to the symbiont(s) using Short Read Connector, a k-mer based similarity method. We were able to define four distinct categories of reads for each holobiont transcriptome: host reads, symbiont reads, shared reads and unassigned reads. The result of the independent assemblies for each category within a transcriptome led to a significant diminution of de novo assembled chimeras compared to classical assembly methods. Combining independent functional and taxonomic annotations of each partner’s transcriptome is particularly convenient to explore the functional diversity of an holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts and a first transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is limited. Conclusions

In contrast to classical assembly approaches, our bioinformatic strategy not only allows biologists to studying separately host and symbiont data from a holobiont mixture, but also generates improved transcriptome assemblies. The use of Short Read Connector has proven to be an effective way to tackle meta-transcriptomic challenges to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages such as the newly sequenced marine plankton Radiolaria-Dinophyta symbiosis and ultimately expand our knowledge about these marine symbiotic associations.
Diel predator activity drives a dynamic landscape of fear
Authors: Kohl Michel T. , Stahler Daniel R. , Metz Matthew C. , Forester James D. , Kauffman Matthew J. , Varley Nathan , White P.J. , Smith Douglas W. , MacNulty Daniel R.
Published: November 2017

Abstract

A ‘landscape of fear’ (LOF) is a map that describes continuous spatial variation in an animal’s perception of predation risk. The relief on this map reflects, for example, places that an animal avoids to minimize risk. Although the LOF concept is a potential unifying theme in ecology that is often invoked to explain the ecological and conservation significance of fear, quantified examples of a LOF over large spatial scales are lacking as is knowledge about the daily dynamics of a LOF. Despite theory and data to the contrary, investigators often assume, implicitly or explicitly, that a LOF is a static consequence of a predator’s mere presence. We tested the prediction that a LOF in a large-scale, free-living system is a highly-dynamic map with ‘peaks’ and ‘valleys’ that alternate across the diel (24-hour) cycle in response to daily lulls in predator activity. We did so with extensive data from the case study of Yellowstone elk(Cervus elaphus)and wolves(Canis lupus)that was the original basis for the LOF concept. We quantified the elk LOF, defined here as spatial allocation of time away from risky places and times, across nearly 1000-km2of northern Yellowstone National Park and found that it fluctuated with the crepuscular activity pattern of wolves, enabling elk to use risky places during wolf downtimes. This may help explain evidence that wolf predation risk has no effect on elk stress levels, body condition, pregnancy, or herbivory. The ability of free-living animals to adaptively allocate habitat use across periods of high and low predator activity within the diel cycle is an underappreciated aspect of animal behavior that helps explain why strong antipredator responses may trigger weak ecological effects, and why a LOF may have less conceptual and practical importance than direct killing.
Stoichiometric homeostasis of wetland vegetation along a nutrient gradient in a subtropical wetland. Understanding stoichiometric mechanisms of nutrient retention in wetland macrophytes
Authors: Julian Paul , Gerber Stefan , Bhomia Rupesh K. , King Jill , Osborne Todd Z. , Wright Alan L.
Published: November 2017

Nutrient homeostasis relates ambient stoichiometric conditions in an environment to the stoichiometry of living entities of the ecosystem. In wetland ecosystems, vegetation can be a large, highly variable and dynamic sink of nutrients. This study investigated stoichiometric homeostasis of dominant emergent and submerged aquatic vegetation (EAV and SAV, respectively) within two treatment flow-ways (FW) of Everglades Stormwater Treatment Area 2 (STA-2). These FW encompass a large gradient in plant nutrient availability. The hypotheses of this study is that wetland vegetation is non-homeostatic relative to ambient nutrients and consequently nutrient resorption will not vary along the nutrient gradient. We developed a framework to investigate how vegetation uptake and resorption of nutrients contribute separately to homeostasis. Overall, the wetland vegetation in this study was non-homeostatic with respect to differential uptake of nitrogen (N) vs. phosphorus (P). Resorption evaluated for EAV was high for P and moderate for N, resorption efficiency did not significantly vary along the gradient and therefore did not affect overall homeostatic status. Nutrient addition experiments may help to compensate for some of the limitation of our study, especially with respect to resolving the primary nutrient source (organic vs. inorganic sources, water vs. soil compartment) and nutrient utilization rates.
Insights into platypus population structure and history from whole-genome sequencing
Authors: Martin Hilary C. , Batty Elizabeth M. , Hussin Julie , Westall Portia , Daish Tasman , Kolomyjec Stephen , Piazza Paolo , Bowden Rory , Hawkins Margaret , Grant Tom , Moritz Craig , Grutzner Frank , Gongora Jaime , Donnelly Peter
Published: November 2017

The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly-improved reference genome, we called over 6.7M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative amongst other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated thede novomutation rate in the platypus at 7.0×10−9/bp/generation (95% CI 4.1×10−9− 1.2×10−8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species.
Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data
Authors: Davis Nicole M. , Proctor Diana M. , Holmes Susan P. , Relman David A. , Callahan Benjamin J.
Published: November 2017

Background

The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants — DNA sequences not truly present in the sample. Contaminants come from various sources, including reagents. Appropriate laboratory practices can reduce contamination, but do not eliminate it. Here we introduce decontam (https://github.com/benjjneb/decontam), an open-source R package that implements a statistical classification procedure that identifies contaminants in MGS data based on two widely reproduced patterns: contaminants appear at higher frequencies in low-concentration samples, and are often found in negative controls.

Results

decontam classified amplicon sequence variants (ASVs) in a human oral dataset consistently with prior microscopic observations of the microbial taxa inhabiting that environment and previous reports of contaminant taxa. In metagenomics and marker-gene measurements of a dilution series, decontam substantially reduced technical variation arising from different sequencing protocols. The application of decontam to two recently published datasets corroborated and extended their conclusions that little evidence existed for an indigenous placenta microbiome, and that some low-frequency taxa seemingly associated with preterm birth were contaminants.

Conclusions

decontam improves the quality of metagenomic and marker-gene sequencing by identifying and removing contaminant DNA sequences. decontam integrates easily with existing MGS workflows, and allows researchers to generate more accurate profiles of microbial communities at little to no additional cost.
The relationship between varicella (chickenpox) and scarlet fever in contemporary Hong Kong
Authors: Coleman S.
Published: November 2017

Scarlet fever epidemics have reemerged in China, the UK, and Hong Kong. This research tests whether scarlet fever epidemics in Hong Kong are linked to varicella epidemics. Varicella infection is a known risk for invasive Group A Streptococcal infections, and historical research shows a connection between varicella and scarlet fever. This analysis examines the relationship between these two disease in Hong Kong from 2011 to 2015 and compares varicella rates before and after the reintroduction of scarlet fever. Analysis shows that scarlet fever and varicella have synchronous annual epidemic cycles, and a mathematical model of the relationship between scarlet fever and varicella is estimated. Varicella rates were unchanged by the return of scarlet fever, but annual varicella cycles may have influenced the size and timing of scarlet fever outbreaks. Vaccination policies for varicella may need to be adjusted to limit scarlet fever epidemics.
Validating Antibodies for Quantitative Western Blot Measurements with Microwestern Array
Authors: Koch Rick J. , Barrette Anne Marie , Stern Alan D. , Hu Bin , Azeloglu Evren U. , Iyengar Ravi , Birtwistle Marc R.
Published: November 2017

Western blotting is often considered a semi-quantitative or even qualitative assay for assessing changes in protein or protein post-translational modification levels. Fluorescence-based measurement enables acquisition of quantitative data in principal, but requires determining the linear range of detection for each antibody—a labor-intensive task. Here, we describe the use of a high-throughput western blotting technique called microwestern array to more rapidly evaluate suitable conditions for quantitative western blotting with particular antibodies. We can evaluate up to 192 antibody/dilution/replicate combinations on a single standard size gel with a seven-point, two-fold lysate dilution series (~100-fold range). Pilot experiments demonstrate a surprisingly high proportion of investigated antibodies (17/22) are suitable for quantitative use, and that lack of validity might often be a consequence of lysate composition rather than antibody quality. Linear range for all validated antibodies is at least 8-fold, and in some cases nearly two orders of magnitude. That range could be greater as the presented tests did not find a limit for many antibodies. We find that phospho-specific and total antibodies do not have discernable trend differences in linear range or limit of detection, but total antibodies generally required higher working concentrations, suggesting phospho-specific antibodies may be generally higher affinity. Importantly, we demonstrate that results from microwestern analyses scale to normal “macro” western for a subset of antibodies. These data indicate that with initial validation, many antibodies can be readily used quantitatively in a reproducible manner. Antibody validation data and standard operating procedures are available online (www.birtwistlelab.com/protocols and www.dtoxs.org).
TKSA-MC: A Web Server for rational mutation through the optimization of protein charge interactions
Authors: Contessoto Vinícius G. , de Oliveira Vinícius M. , Fernandes Bruno R. , Slade Gabriel G. , Leite Vitor B. P.
Published: November 2017

The TKSAMC is a web server which calculates protein charge-charge interactions via the Tanford-Kirkwood Surface Accessibility model with the Monte Carlo method for sampling different protein protonation states. The optimization of charge-charge interactions via directed mutations has successfully enhanced the thermal stability of different proteins and could be a key to protein engineering improvement. The server presents the electrostatic free energy contribution of each polar-charged residue to protein native state stability. The server also indicates which residues contribute to destabilizing the protein native state with positive energy and the side chain exposed to solvent. This residue is a candidate for mutation to increase protein thermostability as a function of the chosen pH condition. The web server is freely available at UNESP (São Paulo State University - DF/IBILCE): http://tksamc.df.ibilce.unesp.br.
Estimating the effects of variation in viremia on mosquito susceptibility, infectiousness, andR0of Zika inAedes aegypti
Authors: Tesla Blanka , Demakovsky Leah R. , Packiam Hannah S. , Mordecai Erin A. , Rodríguez Américo D. , Bonds Matthew H. , Brindley Melinda A. , Murdock Courtney C.
Published: November 2017

Zika virus (ZIKV) is an arbovirus primarily transmitted byAedesmosquitoes. Like most viral infections, ZIKV viremia varies over several orders of magnitude, with unknown consequences for transmission. To determine the effect of viral concentration on ZIKV transmission risk, we exposed field-derivedAe. aegyptimosquitoes to four doses (103, 104, 105, 106PFU/mL) representative of potential variation in the field. We demonstrate that increasing ZIKV dose in the blood-meal significantly increases the probability of mosquitoes becoming infected and infectious, as well as the rate at which virus spreads to the saliva, but found no effect on dissemination efficiency or mosquito mortality. We also demonstrate that determining infection using RT-qPCR approaches rather than plaque assays potentially over-estimates key pathogen parameters, including the time at which mosquitoes become infectious and viral burden. Finally, using these data to parameterize anR0model, we demonstrate that variation in viremia substantially affects transmission risk.
Integrating co-expression networks with GWAS to prioritize causal genes in maize
Authors: Schaefer Robert J. , Michno Jean-Michel , Jeffers Joseph , Hoekenga Owen , Dilkes Brian , Baxter Ivan , Myers Chad L.
Published: November 2017

Background

Genome wide association studies (GWAS) have identified thousands of loci linked to hundreds of traits in many different species. However, because linkage equilibrium implicates a broad region surrounding each identified locus, the causal genes often remain unknown. This problem is especially pronounced in non-human, non-model species where functional annotations are sparse and there is frequently little information available for prioritizing candidate genes.

Results

To address this issue, we developed a computational approach called Camoco (Co-Analysis of Molecular Components) that systematically integrates loci identified by GWAS with gene co-expression networks to prioritize putative causal genes. We applied Camoco to prioritize candidate genes from a large-scale GWAS examining the accumulation of 17 different elements in maize seeds. Camoco identified statistically significant subnetworks for the majority of traits examined, producing a prioritized list of high-confidence causal genes for several agronomically important maize traits. Two candidate genes identified by our approach were validated through analysis of mutant phenotypes. Strikingly, we observed a strong dependence in the performance of our approach on the type of co-expression network used: expression variation across genetically diverse individuals in a relevant tissue context (in our case, maize roots) outperformed other alternatives.

Conclusions

Our study demonstrates that co-expression networks can provide a powerful basis for prioritizing candidate causal genes from GWAS loci, but suggests that the success of such strategies can highly depend on the gene expression data context. Both the Camoco software and the lessons on integrating GWAS data with co-expression networks generalize to species beyond maize.
CapsidMesh: atomic-detail structured mesh representation of icosahedral viral capsids and the study of their mechanical properties
Authors: Alonzo-Velázquez José Luis , Botello-Rionda Salvador , Herrera-Guzmán Rafael , Carrillo-Tripp Mauricio
Published: November 2017

Viruses are the most abundant pathogens affecting all forms of life. A major component of a virus is a protein shell, known as the viral capsid, that encapsulates the genomic material. The fundamental functions of the capsid are to protect and transport the viral genome, and recognize the host cell. Descriptions of this macromolecular complex have been proposed at different scales of approximation. Here, we introduce a methodology to generate a structured volumetric mesh of icosahedral viral capsids (CapsidMesh) based on the atomic positions of their constituents. Material properties of the capsid proteins can be set on every mesh element individually. Hence, we have control over all levels of protein structure (atoms, amino acids, subunits, oligomers,capsid). The CapsidMesh models are suitable for numerical simulations and analysis of a physical process using a third-party package. In particular, we used our methodology to generate a CapsidMesh of several capsids previously characterized by Atomic Force Microscopy experiments, and then simulated the mechanical nanoindentation through the Finite Element Method. By fitting to the experimental linear elastic response, we estimated the elastic modulus and mechanical stresses produced on the capsids. Our results show that the atomic detail of the CapsidMesh is sufficient to reproduce anisotropic properties of the particle.
Flex ddG: Rosetta ensemble-based estimation of changes in protein-protein binding affinity upon mutation
Authors: Barlow Kyle A. , Conchúir Shane O , Thompson Samuel , Suresh Pooja , Lucas James E. , Heinonen Markus , Kortemme Tanja
Published: November 2017

Computationally modeling changes in binding free energies upon mutation (interface ΔΔG) allows large-scale prediction and perturbation of protein-protein interactions. Additionally, methods that consider and sample relevant conformational plasticity should be able to achieve higher prediction accuracy over methods that do not. To test this hypothesis, we developed a method within the Rosetta macromolecular modeling suite (flex ddG) that samples conformational diversity using “backrub” to generate an ensemble of models, then applying torsion minimization, side chain repacking and averaging across this ensemble to estimate interface ΔΔGvalues. We tested our method on a curated benchmark set of 1240 mutants, and found the method outperformed existing methods that sampled conformational space to a lesser degree. We observed considerable improvements with flex ddG over existing methods on the subset of small side chain to large side chain mutations, as well as for multiple simultaneous non-alanine mutations, stabilizing mutations, and mutations in antibody-antigen interfaces. Finally, we applied a generalized additive model (GAM) approach to the Rosetta energy function; the resulting non-linear reweighting model improved agreement with experimentally determined interface DDG values, but also highlights the necessity of future energy function improvements.
Deleterious variation mimics signatures of genomic incompatibility and adaptive introgression
Authors: Kim Bernard Y. , Huber Christian D. , Lohmueller Kirk E.
Published: November 2017

While it is appreciated that population size changes can impact patterns of deleterious variation in natural populations, less attention has been paid to how population admixture affects the dynamics of deleterious variation. Here we use population genetic simulations to examine how admixture impacts deleterious variation under a variety of demographic scenarios, dominance coefficients, and recombination rates. Our results show that gene flow between populations can temporarily reduce the genetic load of smaller populations, especially if deleterious mutations are recessive. Additionally, when fitness effects of new mutations are recessive, between-population differences in the sites at which deleterious variants exist creates heterosis in hybrid individuals. This can lead to an increase in introgressed ancestry, particularly when recombination rates are low. Under certain scenarios, introgressed ancestry can increase from an initial frequency of 5% to 30-75% and fix at many loci, even in the absence of beneficial mutations. Further, deleterious variation and admixture can generate correlations between the frequency of introgressed ancestry and recombination rate or exon density, even in the absence of other types of selection. The direction of these correlations is determined by the specific demography and whether mutations are additive or recessive. Therefore, it is essential that null models include both demography and deleterious variation before invoking reproductive incompatibilities or adaptive introgression to explain unusual patterns of genetic variation.
Identification and characterisation of the cryptic Golgi Apparatus in Naegleria gruberi
Authors: Herman Emily K. , Yiangou Lyto , Cantoni Diego M. , Miller Christopher N. , Marciano-Cabral Francine , Anthonyrajah Erin , Dacks Joel B. , Tsaousis Anastasios D.
Published: November 2017

Although the Golgi apparatus has a conserved morphology of flattened stacked cisternae in the vast majority of eukaryotes, the organelle has lost the stacked organization in several eukaryotic lineages raising the question of what range of morphologies is possible for the Golgi. In order to understand this range of organellar diversity, it is necessary to characterise the Golgi in many different lineages. Here we identify the Golgi apparatus in Naegleria, the first description of an unstacked Golgi organelle in a non-parasitic eukaryote, other than fungi. We provide a comprehensive list of Golgi-associated membrane trafficking genes encoded in two separate species of Naegleria and transcriptomic support to show that nearly all are expressed in mouse-passaged N. fowleri cells. We then study distribution of the Golgi marker NgCOPB by fluorescence, identifying membranous structures that can be disrupted by Brefeldin A treatment consistent with Golgi localisation. Confocal and immuno-electron microscopy revealed that NgCOPB is localized to membranous structures consistent with tubules. Our data not only identify the Golgi organelle for the first time in this major eukaryotic lineage, but also provide the rare example of a tubular form of the organelle representing an important sampling point for the comparative understanding of Golgi organellar diversity.
Transcription activator-coactivator specificity is mediated by a large and dynamic fuzzy protein-protein complex
Authors: Tuttle Lisa M. , Pacheco Derek , Warfield Linda , Luo Jie , Ranish Jeff , Hahn Steven , Klevit Rachel E.
Published: November 2017

Transcription activation domains (ADs) are inherently disordered proteins that often target multiple coactivator complexes, but the specificity of these interactions is not understood. Efficient activation by yeast Gcn4 requires tandem Gcn4 ADs and four activator-binding domains (ABDs) on its target, the Mediator subunit Med15. Multiple ABDs are a common feature of coactivator complexes. We find that the large Gcn4-Med15 complex is heterogeneous, containing nearly all possible AD-ABD interactions. This complex forms using a dynamic fuzzy protein-protein interface where ADs use hydrophobic residues to bind hydrophobic surfaces of the ABDs in multiple orientations. This combinatorial mechanism allows individual interactions of low affinity and specificity to generate a biologically functional, specific, and higher affinity complex despite lacking a defined protein-protein interface. This binding strategy is likely representative of many activators that target multiple coactivators and allows great flexibility in combinations of activators that synergize to regulate genes with variable coactivator requirements.
Biologically plausible mechanisms underlying motor response correction during reward-based decision-making
Authors: Lee Jung Hoon
Published: November 2017

Abstract

Our propensity to acclimate to new surroundings and choose a goal-directed behavior for a maximal reward (i.e., optimal outcome) is natural, for it affects our survival. A line of studies suggested that anterior cingulate cortex (ACC) could be a potential hub for adaptive behaviors. For instance, an experimental study noted ACC’s contribution to selecting motor responses for maximal rewards; it found 1) that ACC neurons were selectively activated when the reward was reduced and 2) that suppression of ACC activity impaired monkeys’ ability to change motor responses to obtain the maximal reward. To probe ACC functions in adaptive behaviors, we sought biologically-plausible mechanisms to account for the experimental findings mentioned above by utilizing a computational model. Our simulation results raise the possibility that ACC can correct behavioral responses by reading out and updating the motor plans (guiding future motor responses) stored in prefrontal cortex (PFC).
Time intervals in sequence sampling, not data modifications, have a major impact on estimates of HIV escape rates
Authors: Ganusov Vitaly V.
Published: November 2017

The ability of HIV to avoid recognition by humoral and cellular immunity (viral escape) is well documented but the strength of the immune response needed to cause such a viral escape remains poorly quantified. Several previous studies observed a more rapid escape of HIV from CD8 T cell responses in the acute phase of infection as compared to the chronic infection. With the help of simple mathematical models the rate of HIV escape was estimated and results were interpreted to suggest that CD8 T cell responses causing escape in acute HIV infection may be more efficient at killing virus-infected cells than responses that cause escape in chronic infection, or alternatively, early escapes occur in epitopes mutations in which there is minimal fitness cost to the virus. These conclusions, however, were challenged on several grounds, including linkage and interference of multiple escape mutations due to a low population size and because of potential issues associated with modifying the data to estimate escape rates. Here we use a parametric resampling method which does not require data modification to show that previous results on the decline of the viral escape rate with time since infection remain unchanged. However, using this method we also show that estimates of the escape rate are highly sensitive to the time interval between measurements with longer intervals biasing estimates of the escape rate downwards. Our results thus suggest that data modifications for early and late escapes were not the primary reason for the observed decline in the escape rate with time since infection. However, longer sampling periods for escapes in chronic infection strongly influence estimates of the escape rate. More frequent sampling of viral sequences in the chronic infection may improve our understanding of factors influencing the rate of HIV escape from CD8 T cell responses.