bluuebunny/crossref_metadata_2025 huggingface dataset:
Establishment and Application of a duplex real-time qPCR method for detection ofSalmonellaspp. andSerratia fonticolain imported feedstuffs
Authors: Ruan Jing hua , Wang Wu jun , Bai Quan yang , Zhang Ti yin , zheng Teng , Yu Shi yu , Zhang Zhi deng , Lin Su jie , Zhong Bo xiong , Yu Dao jin
Published: May 2018

Salmonellaspp. is a high-risk bacterial pathogen that is monitored in imported animal-derived feedstuffs.Serratia fonticolais the bacterial species most frequently confused withSalmonellaspp. in traditional identification methods based on biochemical characteristics, which are time-consuming and labor-intensive, and thus unsuitable for daily inspection and quarantine work. In this study, we established a duplex real-time qPCR method withinvA-andgyrB-specific primers and probes corresponding toSalmonellaspp. andS. fonticola. The method could simultaneously detect both pathogens in imported feedstuffs, with a minimum limit of detection forSalmonellaspp. andS. fonticolaof 197 copies/μL and 145 copies/μL, respectively (correlation coefficient R2= 0.999 in both cases). The amplification efficiency forSalmonellaspp. andS. fonticolawas 98.346% and 96.49%, respectively. Detection of clinical samples was consistent with method GB/T 13091-2002, and all 20 artificially contaminated imported feed samples were positively identified. Thus, the developed duplex real-time qPCR assay displays high specificity and sensitivity, and can be used for the rapid and accurate detection of genomic DNA fromSalmonellaspp. andS. fonticolawithin hours. This represents a significant improvement in the efficiency of detection of both pathogens in imported feedstuffs.

Importance

Imported feedstuffs must be tested for pathogenicSalmonellaspecies that represent a biological hazard. Variousnon-Salmonellacolony-forming species belong toEnterobacteriaceae,andSerratia fonticolaforms colonies of similar color and morphology toSalmonellaspp., leading to confusion in daily quarantine tests. Traditional methods based on biochemical and serological characteristics are cumbersome and labor-intensive, and unable to fully support current quarantine testing demands. Thus, there is an urgent need to develop a rapid and accurate method for the effective identification of these pathogens. The duplex real-time qPCR method established herein can rapidly identifySalmonellaspp. andS. fonticola, and has great potential for application to feed safety and prevention of exterior pathogens.
RNA-antimicrobial peptide LL-37 complexes fuel a TLR- and NET-mediated inflammatory cycle of neutrophil activation in psoriasis
Authors: Herster Franziska , Bittner Zsofia , Dickhöfer Sabine , Eise David , Eigenbrod Tatjana , Knorpp Thomas , Schneiderhan-Marra Nicole , Löffler Markus W. , Kalbacher Hubert , Hartl Dominik , Freund Lukas , Schäkel Knut , Heister Martin , Ghoreschi Kamran , Weber Alexander N.R.
Published: May 2018

Psoriasis is an inflammatory autoimmune disease characterized by skin lesions showing strong neutrophil (PMN) infiltration and high levels of the antimicrobial peptide, LL37, but the role of PMNs in this context remains unclear. We here show that primary human PMNs, especially PMNs from psoriasis patients, not only respond via TLR8 to human and bacterial RNA in complexed with LL37 by cytokine-, chemokine- and neutrophil extracellular trap (NET)-release; they also actively release additional RNA and LL37 in response to stimulation by the same complex and both RNA and LL37 were found to be highly abundant in psoriatic skin. Moreover, RNA-LL37-induced NETs propagated PMN activation and could thus fuel a PMN-mediated and self-sustaining inflammatory loop that may represent an unexpected early initiator or amplifying event in psoriasis. Given that TLR inhibitory oligodeoxynucleotides prevented the cytokine production and NETosis of PMNs by RNA-LL37 complexes in vitro, our study also highlights TLR blockade as a potential therapeutic intervention strategy in psoriasis.

Human and bacterial RNA in complex with LL37 activates neutrophils via TLR8 to release cytokines, chemokines and neutrophil extracellular traps (NETs). NETs and neutrophil-rich areas in psoriatic skin contain RNA and LL37, suggesting RNA-LL37 may fuel a PMN-mediated and self-sustaining inflammatory cycle in psoriasis.
Hypertrophic cardiomyopathy disease results from disparate impairments of cardiac myosin function and auto-inhibition
Authors: Robert-Paganin Julien , Auguin Daniel , Houdusse Anne
Published: May 2018

Hypertrophic cardiomyopathies (HCM) result from distinct single-point mutations in sarcomeric proteins that lead to muscle hypercontractility. While different models account for a pathological increase in the power output, clear understanding of the molecular basis of dysfunction in HCM is the mandatory next step to improve current treatments. An optimized quasi-atomic model of the sequestered state of cardiac myosin coupled to X-ray crystallography and in silico analysis of the mechanical compliance of the lever arm allowed us to perform a systematic study for a large set of HCM mutations. We define different classes of mutations depending on their effects on lever arm compliance, sequestered state stability and motor functions. This work reconciles previous models and explains how distinct HCM mutations can have disparate effects on the motor mechano-chemical parameters and yet lead to the same disease. The framework presented here can guide future investigations aiming at finding HCM treatments.
Planning a future randomized clinical trial based on a network of relevant past trials
Authors: Salanti Georgia , Nikolakopoulou Adriani , Sutton Alex J , Reichenbach Stephan , Trelle Sven , Naci Huseyin , Egger Matthias
Published: May 2018

Background: The important role of network meta-analysis of randomized clinical trials in health technology assessment and guideline development is increasingly recognized. This approach has the potential to obtain conclusive results earlier than with new standalone trials or conventional, pairwise meta-analyses.

Methods: Network meta-analyses can also be used to plan future trials. We introduce a four-steps framework to plan a new trial that aims to identify the optimal new design that will update the existing evidence to best serve timely clinical and public health decision making. The new trial designed within this framework does not need to include all competing interventions and comparisons of interest and can contribute direct and indirect evidence to the updated network meta-analysis. We present the method by virtually planning a new trial to compare biologics in rheumatoid arthritis and a new trial to compare two drugs for relapsing-remitting multiple sclerosis.

Results: A trial design based on updating the evidence from a network meta-analysis of relevant previous trials may require a considerably smaller sample size to reach the same conclusion compared with a trial designed and analyzed in isolation. Challenges in the approach include the complexity of the methodology and the need for a coherent network meta-analysis of previous trials with little heterogeneity.

Conclusions: When used judiciously, conditional trial design could significantly reduce waste in clinical research.
Enhanced inhibition of influenza virus infection by peptide-noble metal nanoparticle conjugates
Authors: Alghrair Zaid K. , Fernig David G. , Ebrahimi Bahram
Published: May 2018

Influenza virus is a major medical and veterinary health concern and causes global pandemics. The peptide ‘FluPep’ is an established inhibitor of influenza virus infectivity in model systems. We have explored the potential for FluPep functionalised noble metal nanoparticle to enhance the antiviral activity of the peptide Flupep and determined their potential for the delivery of FluPep. The FluPep ligand designed here is FluPep extended at its N-terminus with the sequence CVVVTAAA-, to allow its incorporation into a mix matrix ligand shell of a peptidol and an alkanethiol ethyleneglycol comprising 70% H-CVVVTol and 30% HS(CH2)11(ethyleneglycol)4 (both mole/mole). Gold and silver nanoparticles (~10 nm diameter) prepared with up to 5% (mole/mole) FluPep ligand contained in the mixture of mix-matrix peptide ligands remained as stable as the control mix-matrix coated nanoparticles against ligand exchange with dithiothreitol. FluPep ligand was found to inhibit viral plaque formation in canine MDCK cells (IC50 2.1 nM), but was less potent than FluPep itself (IC50 140 pM). FluPep ligand functonalised nanoparticles retained antiviral activity in the plaque assay. Moreover, at low grafting densities (where nanoparticles incorporate ~1 FluPep ligand, the antiviral potency in terms of FluPep ligand concentration was enhanced significantly for gold and silver nanoparticles (IC50 ~8-fold and ~3-fold lower, respectively). At higher grafting density the potency relative to free FluPep ligand concentration decreased. The data demonstrate that conjugation of FluPep to gold and silver nanoparticles enhances its antiviral potency; the antimicrobial activity of silver ions may enable the design of even more potent anti-microbial inhibitors.
Tau monomer encodes strains
Authors: Sharma Apurwa M. , Thomas Talitha L. , Woodard DaNae R. , Kashmer Omar M. , Diamond Marc I.
Published: May 2018

Tauopathies have diverse presentation, progression, and neuropathology. They are linked to tau prion strains, self-replicating assemblies of unique quaternary conformation. Strains can be propagated indefinitely in cultured cells, and induce unique patterns of transmissible neuropathology upon inoculation into mice. Aggregates from a single strain reproduce only that strain upon re-inoculation into cells or mice. DS9 and DS10 cell lines propagate distinct synthetic strains. Surprisingly, DS9 monomer inoculated into naïve cells encoded an identical “sub-strain,” whereas DS10 monomer encoded multiple sub-strains. Sub-strains produced distinct pathology upon inoculation into a tauopathy mouse model (PS19). Brain-derived tau monomer from an Alzheimer’s brain encoded a single strain. Monomer from a corticobasal degeneration brain encoded three sub-strains in which monomer from each encoded all three upon re-inoculation into cells. Tau monomer thus adopts multiple, stable seed-competent conformations, each of which encodes a limited number of strains. This provides insights into the origins of distinct tauopathies.
Absolute pitch can be learned by some adults
Authors: Van Hedger Stephen C. , Heald Shannon L.M , Nusbaum Howard C.
Published: May 2018

Absolute pitch (AP), the rare ability to name any musical note without the aid of a reference note, is thought to develop in an early critical period of development. Although recent research has shown that adults can improve AP abilities in a single training session, the best learners still did not achieve note classification performance comparable to performance of a genuine AP possessor. Here, we demonstrate that genuine AP levels of performance can be trained in eight weeks for some adults, with the best learner passing all measures of AP ability after training and retaining this knowledge for at least four months after training. Alternative explanations of these positive results, such as improving accuracy through adopting a slower, relative pitch strategy, are not supported based on joint analyses of response time and accuracy. The post-training AP assessments were extensive, totaling 204 notes taken from eight different timbres and spanning over seven octaves. These results clearly demonstrate that explicit perceptual training in some adults can lead to AP performance that is behaviorally indistinguishable from AP that results from childhood development. Implications for theories of AP acquisition are discussed.
Illumina sequencing analysis of the ruminal microbiota in high-yield and low-yield lactating dairy cows
Authors: Tong Jinjin , Zhang Hua , Yang Delian , Xiong Benhai , Jiang Linshu
Published: May 2018

In this study, differences in the ruminal bacterial community between high-yield and low-yield lactating dairy cows fed the same diets were investigated. Sixteen lactating dairy cows with similar parity were divided into two groups based on their milk yield: high-yield (HY) and low-yield (LY) groups. On day 21, rumen content samples were collected, and the microbiota composition was determined using Illumina MiSeq sequencing of the 16S rRNA gene. During the study period, dry matter intake (DMI) and milk yield were measured daily, and milk composition was assessed 3 times per week. The results showed that the milk of the LY group tended to have higher fat (P=0.08), protein (P=0.01) and total solid (P=0.04) contents than that of the HY group, though the HY group had higher ruminal acetate (P=0.05), propionate (P=0.02) and volatile fatty acid (VFA) (P=0.02) concentrations. Principal coordinate analysis indicated significant differences in ruminal bacterial community composition and structure between the HY group and LY group. Overall, Bacteroidetes (HY group: 52.91±3.06%; LY group: 61.88±3.03%) was the predominant phylum, followed by Firmicutes (HY group: 41.10±2.74%; LY group: 32.11±2.97%). The abundances of Ruminococcus 2, Lachnospiraceae and Eubacterium coprostanoligenes were significantly higher in the HY group than in the LY group. In addition, 3 genera—Anaerostipes, Bacteroidales and Anaeroplasma—were identified as biomarker species with the greatest impacts on the ruminal community structure in the LY group. These findings facilitate the understanding of bacterial synthesis within the rumen and reveal an important mechanism underlying differences in milk production in dairy cows.
The Influence of PTH 1-34 on the Osteogenic Characteristics of Adipose and Bone Marrow Derived Stem Cells from Juvenile and Ovarectomized Rats
Authors: Osagie-Clouard Liza , Sanghani-Kerai Anita , Coathup Melanie , Pendegrass catherine , Briggs Timothy , Blunn Gordon
Published: May 2018

Background: Mesenchymal Stem Cells (MSCs) are of growing interest in terms of bone regeneration; the majority of preclinical trials utilise bone marrow derived stem cells (bMSCs), though this is not without isolation and expansion difficulties

Objective: We compare the characteristics of bone marrow and adipose derived cells from juvenile, adult and ovarectomized rats; also assessing the effect of hPTH 1-34, on their osteogenic potential.

Methods: cells were isolated from the adipose and bone marrow of juvenile, adult and previously ovarectomized wistar rats. Cells were characterised with flowcytometery, proliferation assays, osteogenic and adipogenic differentiation, and migration to SDF-1. Experiments were repeated with and without co-culturing with 50nMol of intermittent PTH 1-34.

Results: The juvenile and adult MSCs demonstrated significantly increased differentiation into bone and fat and superior migration towards SDF-1 than ovarectomized groups, this was the case for adipose and bone marrow derived cells equally. PTH increased parameters of osteogenic differentiation and migration to SDF-1, this was significant for all cell types, though had the most significant effect on cells derived from OVX animals. Bone marrow derived cells from all groups, showed increased mineralisation and migration to SDF-1 compared to adipose derived cells.

Conclusion: Juvenile MSCs showed significantly greater migration to SDF-1 and showed greater osteogenic and adipogenic differentiation compared to cells from osteopenic rats, this was true for bone marrow and adipose derived cells. The addition of PTH, increased the osteogenic characteristics and migration of all cells, and further illustrates the possible clinical utility of both PTH and MSCs from various sources in bone regenerative therapies
First natural crossover recombination of intact ORFs between two distinct species of the familyClosteroviridae
Authors: Ruiz Leticia , Simón Almudena , García Carmen , Velasco Leonardo , Janssen Dirk
Published: May 2018

Lettuce chlorosis virus-SP (LCV-SP) (familyClosteroviridae, genusCrinivirus), is a new strain of LCV which is able to infect green bean plants and incapable of infecting lettuce crops. In the present study, high throughput and Sanger sequencing of RNA was used to obtain the LCV-SP full-length sequence. The LCV-SP genome comprises 8825 nt and 8672 nt equivalent with RNA1 and RNA2 respectively. RNA1 of LCV-SP contains four ORFs, the proteins encoded by the ORF1a and ORF1b are closely related to LCV RNA1 from California (FJ380118) whereas the 3´ end encodes proteins which share high amino acid sequence identity with RNA1 of BnYDV (EU191904). The genomic sequence of RNA2 consists of 8 ORFs, instead of 10 ORFs contained in LCV-California isolate. The distribution of vsiRNA (virus-derived small interfering RNA) along the LCV-SP genome suggested the presence of subgenomic RNAs corresponding with HSP70, P6.4 and P60. Results of the analysis using RDP4 and Simplot programs are the proof of the evidence that LCV-SP is the first recombinant of the familyClosteroviridaeby crossover recombination of intact ORFs, being the LCV RNA1 (FJ380118) and BnYDV RNA1 (EU191904) the origin of the new LCV strain. Genetic diversity values of virus isolates in the recombinant region obtained after sampling LCV-SP infected green bean between 2011 and 2017 might suggest that the recombinant virus event occurred in the area before this period. The presence of LCV-SP shows the role of recombination as a driving force of evolution within the genusCrinivirus, a globally distributed, emergent genus.
EWSR1 affects PRDM9-dependent histone 3 methylation and provides a link between recombination hotspots and the chromosome axis
Authors: Tian Hui , Billings Timothy , Walker Michael , Petkova Pavlina M. , Baker Christopher L. , Petkov Petko M.
Published: May 2018

Meiotic recombination in most mammals requires recombination hotspot activation through the action of the histone 3 lysine-4 and lysine-36 methyltransferase PRDM9 to ensure successful double-strand break initiation and repair. Here we show that EWSR1, a protein whose role in meiosis was not previously clarified in detail, binds to both PRDM9 and pREC8, a phosphorylated meiosis-specific cohesin, in male meiotic cells. We created aEwsr1conditional knockout mouse models to deplete EWSR1 before the onset of meiosis, and found that absence of EWSR1 causes meiotic arrest with decreased histone trimethylation at meiotic hotspots, impaired DNA double-strand break repair, and reduced crossover number. Our results demonstrate that EWSR1 is essential for promoting PRDM9-dependent histone methylation and normal meiotic progress, possibly by facilitating the linking between PRDM9-bound hotspots and the nascent chromosome axis.

Author Summary

In most mammals, including humans and mice, genetic recombination initiates when the meiosis-specific protein PRDM9 binds specific DNA sequences, known as hotspots, at the beginning of the extended prophase I of meiosis, and activates them by trimethylating histone 3 at lysine-4 and lysine-36 on nearby nucleosomes. Although this activation of hotspots is believed to occur on the chromatin loops, the subsequent double-strand break formation and repair occur on a proteinaceous structure known as the chromosome axis. We now show that Ewing sarcoma RNA binding protein 1 (EWSR1) is a key player in early recombination events, binding to PRDM9, promoting PRDM9-dependent histone methylation, and facilitating the linking between PRDM9-bound hotspots and the nascent chromosome axis through the meiosis-specific cohesion REC8. As a result of these activities, EWSR1 assures sufficient numbers of properly positioned crossovers in each meiosis.
A novel PCR method directly quantifies sequence features that block primer extension
Authors: Cawthon Richard M.
Published: May 2018

Many quantitative polymerase chain reaction (qPCR) assays indirectly quantify a target of interest as a drop in amplification signal relative to a larger total signal. The targeted sequence features include: DNA strand breaks introduced by enzymes that cleave at specific sequences or modifications, or caused by ionizing radiation or other DNA-damaging agents; DNA damage that does not break the DNA but blocks the DNA polymerase; and deletions of various sizes that prevent one or both primers from annealing. All of these loss of signal (a.k.a. negative) assays share the drawback of low sensitivity, as compared to positive assays, which generate an amplification signal that directly reflects the copy numbers of the sequence feature. Here we present a novel qPCR strategy that converts all of the above negative assays into positive ones. A mixture of three primers is added to genomic DNA, one primer pair that targets a sequence for strand-specific PCR, and a third, longer primer that prevents initiation of that PCR, by annealing at high temperature and extending across the target sequence, rendering it doublestranded and inaccessible for priming. Any sequence feature that blocks the third primer’s annealing or extension, while leaving the target sequence intact, allows the PCR to proceed and quantify the copy number of the sequence feature. This Primer Extension Blockade Enabled qPCR (PEBE-qPCR) method will facilitate many high-throughput, low-cost qPCR-based investigations in biology and medicine. As a first example, we present direct qPCR of the unmethylated allele at a MspI/HpaII site in the promoter of the human 45S rDNA gene.
CellexalVR: A virtual reality platform to visualise and analyse single-cell data
Authors: Legetth Oscar , Rodhe Johan , Lang Stefan , Dhapola Parashar , Pålsson Joel , Wallergård Mattias , Soneji Shamit
Published: May 2018

Single-cell RNAseq is a routinely used technique to explore the composition of cell populations, and they are often visualised using dimension reduction methods where the cells are represented in two or three dimensional space. Many tools are available to do this but visualising and cross-comparing these representations can be challenging, especially when cells are projected onto three dimensions which can be more informative for complex datasets. Here we present CellexalVR (www.cellexalvr.med.lu.se), a feature-rich, fully interactive virtual reality environment for the visualisation and analysis of single-cell experiments that allows researchers to intuitively and collaboratively gain an understanding of their data.
Synchrony surfacing: epicortical recording of correlated action potentials
Authors: Bockhorst Tobias , Pieper Florian , Engler Gerhard , Stieglitz Thomas , Galindo-Leon Edgar , Engel Andreas K.
Published: May 2018

Synchronous spiking of multiple neurons is a key phenomenon in normal brain function and pathologies. Recently, approaches to record spikes from the intact cortical surface using small high-density arrays of microelectrodes have been reported. It remained unaddressed how epicortical spiking relates to intracortical unit activity. We introduce a mesoscale approach using an array of 64 electrodes with intermediate diameter (250 µm) and combined large-coverage epicortical recordings in ferrets with intracortical recordings via laminar probes. Empirical data and modeling strongly suggest that our epicortical electrodes selectively captured synchronized spiking of neurons in the subjacent cortex. As a result, responses to sensory stimulation were more robust and less noisy as compared to intracortical activity, and receptive field properties were well preserved in epicortical recordings. This should promote insights into assembly-coding beyond the informative value of subdural EEG or single-unit spiking, and be advantageous to real-time applications in brain-machine interfacing.

Significance statement

Electrocorticography allows chronic, low-noise recordings from the intact cortical surface - a prerequisite for investigations into brain network dynamics and brain-machine interfaces. Novel electrodes can capture spiking activity at the surface, which should boost precision in the spatial - and time domain, compared to conventional EEG-like measurements. To clarify how surface spiking relates to intracortically fired action potentials, we recorded both types of signal simultaneously from sensory cortices in anesthetized ferrets. Results suggest that mesoscale (250 µm) surface electrodes can selectively capture synchronized spiking from nearby cortical columns, which reduces contamination by non-representative, jittering spikes. Given the high relevance of neural synchrony for sensorimotor and cognitive processing, the novel methodology may improve signal decoding in brain-machine interface approaches.

Author contributions

E.G.L., T.B. and A.K.E. conceptualized the research; E.G.L. and F.P. performed experiments; T.B. and E.G.L. wrote Matlab routines for data analysis; T.B. and E.G.L. analyzed the data; T.S. provided technical resources; T.B., E.G.L. and A.K.E. wrote the manuscript; G.E. administrated the project; A.K.E. acquired funding.
Is there a problem with methods skills in cognitive neuroscience? Evidence from an online survey
Authors: Hauk Olaf
Published: May 2018

Cognitive neuroscience increasingly relies on complex data analysis methods. Researchers in this field come from highly diverse scientific backgrounds, such as psychology, engineering and medicine. This poses challenges with respect to acquisition of appropriate scientific computing and data analysis skills, as well as communication among researchers with different knowledge and skills sets. Are researchers in cognitive neuroscience adequately equipped to address these challenges? Here, we present evidence from an online survey of methods skills. Respondents (n=305) mainly comprised students and post-doctoral researchers working in the cognitive neurosciences. Multiple choice questions addressed a variety of basic and fundamental aspects of neuroimaging data analysis, such as signal analysis, linear algebra, and statistics. We analysed performance with respect to the following factors: undergraduate degree (grouped into Psychology, Methods, Biology), current researcher status (undergraduate student, PhD student, post-doctoral researcher), gender, and self-rated expertise levels. Overall accuracy was 72%. Not surprisingly, the Methods group performed best (87%), followed by Biology (73%) and Psychology (66%). Accuracy increased from undergraduate (59%) to PhD (74%) level, but not from PhD to post-doctoral (74%) level. The difference in performance for the Methods versus non-methods (Psychology/Biology) groups was particularly striking for questions related to signal analysis and linear algebra, two areas especially relevant to neuroimaging research. Self-rated methods expertise was not strongly predictive of performance. The majority of respondents (93%) indicated they would like to receive at least some additional training on the topics covered in this survey. In conclusion, methods skills among junior researchers in cognitive neuroscience can be improved, researchers are aware of this, and there is strong demand for more skills-oriented training opportunities. We hope that this survey will provide an empirical basis for the development of bespoke skills-oriented training programmes in cognitive neuroscience institutions.
Pre-existing Technological Core and Roots for the CRISPR Breakthrough
Authors: Magee Christopher L. , Kleyn Patrick W. , monks Brendan M. , Betz Ulrich , Basnet Subarna
Published: May 2018

This paper applies objective methods to explore the technological origins of the widely acclaimed CRISPR breakthrough in the technological domain of genome engineering. Previously developed patent search techniques are first used to recover a set of patents that well-represent the genome editing domain before CRISPR. Main paths are then determined from the citation network associated with this patent set allowing identification of the three major knowledge trajectories. The most significant of these trajectories for CRISPR involves the core of genome editing with less significant trajectories involving cloning and endonuclease specific developments. The major patents on the core trajectory are consistent with qualitative expert knowledge of the topical area. A second set of patents that we call the CRISPR roots are obtained by finding the patents directly cited by the recent CRISPR patents along with patents cited by that set of patents. We find that the CRISPR roots contain 8 key patents from the genome engineering main path associated with restriction endonucleases and the expected strong connection of CRISPR to prior genome editing technology such as Zn finger nucleases. Nonetheless, analysis of the full CRISPR roots shows that a very wide array of technological knowledge beyond genome engineering has contributed to achieving the CRISPR breakthrough. Such breadth in origins is not surprising since “spillover” is generally perceived as important and previous qualitative studies of CRISPR have shown not only technological breadth in origins but scientific breadth as well. In addition, we find that the estimated rate of functional performance improvement of the CRISPR roots set is about 9% per year compared to the genome engineering set (˜4 % per year). These estimates indicate below average rates of improvement and may indicate that CRISPR (and perhaps yet undiscovered) genome engineering developments could evolve in effectiveness over an upcoming long rather than short time period.
Unperturbed Expression Bias of Imprinted Genes in Schizophrenia
Authors: Gulyás-Kovács Attila , Keydar Ifat , Xia Eva , Fromer Menachem , Hoffman Gabriel , Ruderfer Douglas ,   CommonMind Consortium, Lipska Barbara K , Devlin Bernie , Hahn Chang-Gyu , Lewis David A , Domenici Enrico , Schadt Eric , Shah Hardik R , Johnson Jessica S , Buxbaum Joseph D , Klei Lambertus L , Peters Mette A , Roussos Panos , Gur Raquel E , Sieberts Solveig K , Perumal Thanneer M , Haroutunian Vahram , Sachidanandam Ravi , Chess Andrew
Published: May 2018

How gene expression correlates with schizophrenia across individuals is beginning to be examined through analyses of RNA-seq from post-mortem brains of individuals with disease and control brains. Here we focus on variation in allele-specific expression, following up on the Common Mind Consortium (CMC) RNA-seq experiments of nearly 600 human dorsolateral prefrontal cortex (DLPFC) samples. Analyzing the extent of allelic expression bias—a hallmark of imprinting—we find that the number of imprinted human genes is consistent with lower estimates (≈0.5% of all genes) and thus contradicts much higher estimates. Moreover, the handful of putatively imprinted genes are all in close genomic proximity to known imprinted genes. Joint analysis of the imprinted genes across hundreds of individuals allowed us to establish how allelic bias depends on various factors. We find that age and genetic ancestry have gene-specific, differential effect on allelic bias. In contrast, allelic bias appears to be independent of schizophrenia.
Size-by-environment interactions: a neglected dimension of species’ responses to environmental variation
Authors: Tredennick Andrew T. , Teller Brittany J. , Adler Peter B. , Hooker Giles , Ellner Stephen P.
Published: May 2018

In both plant and animal systems, size can determine whether an individual survives and grows under different environmental conditions. However, it is less clear whether and when size-dependent responses to the environment affect population dynamics. Size-by-environment interactions create pathways for environmental fluctuations to influence population dynamics by allowing for negative covariation between sizes within vital rates (e.g., small and large individuals have negatively covarying survival rates) and/or size-dependent variability in a vital rate (e.g., survival of large individuals varies less than small individuals through time). Whether these phenomena affect population dynamics depends on how they are mediated by elasticities (they must affect the sizes and vital rates that matter) and their projected impacts will depend on model functional form (the impact of reduced variance depends on the relationship between the environment and vital rate). We demonstrate these ideas with an analysis of fifteen species from five semiarid plant communities. We find that size-by-environment interactions are common but do not impact long-term population dynamics. Size-by-environment interactions may yet be important for other species. Our approach can be applied to species in other ecosystems to determine if and how size-by-environment interactions allow them to cope with, or exploit, fluctuating environments.
Co-exposure to multipleRanavirustypes enhances viral infectivity and replication in a larval amphibian system
Authors: Mihaljevic Joseph R. , Hoverman Jason T. , Johnson Pieter T.J.
Published: May 2018

Multiple pathogens commonly co-occur in animal populations, yet few studies demonstrate how co-exposure of individual hosts scales up to affect transmission. Although viruses in the genusRanavirusare globally widespread and multiple virus species or strains likely co-occur in nature, no studies have examined how co-exposure affects infection dynamics in larval amphibians. We exposed individualRana aurora(Northern red-legged frog) larvae toAmbystoma tigrinumvirus (ATV), frog virus 3 (FV3), or an FV3-like strain isolated from a frog-culturing facility in Georgia, USA (RCV-Z2). We compared single-virus to pairwise co-exposures, while experimentally accounting for dosage. Co-exposure to ATV and FV3-like strains resulted in almost twice as many infected individuals compared to single-virus exposures, suggesting an effect of co-exposure on viral infectivity. The viral load in infected individuals exposed to ATV and FV3 was also higher than the single-dose FV3 treatment, suggesting an effect of co-exposure on viral replication. In a follow-up experiment, we examined how the co-occurrence of ATV and FV3 affected epizootics in mesocosm populations of larvalPseudacris triseriata(Western chorus frog). Although ATV did not generally establish within host populations (<4% prevalence), when ATV and FV3 were both present, this co-exposure resulted in a larger epizootic of FV3. Our results emphasize the importance of multi-pathogen interactions in epizootic dynamics and have management implications for natural and commercial amphibian populations.
The African Bullfrog (Pyxicephalus adspersus) genome unites the two ancestral ingredients for making vertebrate sex chromosomes
Authors: Denton Robert D. , Kudra Randal S. , Malcom Jacob W. , Preez Louis Du , Malone John H.
Published: May 2018

Heteromorphic sex chromosomes have evolved repeatedly among vertebrate lineages despite largely deleterious reductions in gene dose. Understanding how this gene dose problem is overcome is hampered by the lack of genomic information at the base of tetrapods and comparisons across the evolutionary history of vertebrates. To address this problem, we produced a chromosome-level genome assembly for the African Bullfrog (Pyxicephalus adspersus)—an amphibian with heteromorphic ZW sex chromosomes—and discovered that the Bullfrog Z is surprisingly homologous to substantial portions of the human X. Using this new reference genome, we identified ancestral synteny among the sex chromosomes of major vertebrate lineages, showing that non-mammalian sex chromosomes are strongly associated with a single vertebrate ancestral chromosome, while mammals are associated with another that displays increased haploinsufficiency. The sex chromosomes of the African Bullfrog however, share genomic blocks with both humans and non-mammalian vertebrates, connecting the two ancestral chromosome sequences that repeatedly characterize vertebrate sex chromosomes. Our results highlight the consistency of sex-linked sequences despite sex determination system lability and reveal the repeated use of two major genomic sequence blocks during vertebrate sex chromosome evolution.
A heuristic method for fast and accurate phasing and imputation of single nucleotide polymorphism data in bi-parental plant populations
Authors: Gonen Serap , Wimmer Valentin , Gaynor R. Chris , Byrne Ed , Gorjanc Gregor , Hickey John M.
Published: May 2018

This paper presents a new heuristic method for phasing and imputation of genomic data in diploid plant species. Our method, called AlphaPlantImpute, explicitly leverages features of plant breeding programs to maximise the accuracy of imputation. The features are a small number of parents, which can be inbred and usually have high-density genomic data, and few recombinations separating parents and focal individuals genotyped at low-density (i.e. descendants that are the imputation targets). AlphaPlantImpute works roughly in three steps. First, it identifies informative low-density genotype markers in parents. Second, it tracks the inheritance of parental alleles and haplotypes to focal individuals at informative markers. Finally, it uses this low-density information as anchor points to impute focal individuals to high-density.

We tested the imputation accuracy of AlphaPlantImpute in simulated bi-parental populations across different scenarios. We also compared its accuracy to existing software called PlantImpute. In general, AlphaPlantImpute had better or equal imputation accuracy as PlantImpute. The computational time and memory requirements of AlphaPlantImpute were tiny compared to PlantImpute. For example, accuracy of imputation was 0.96 for a scenario where both parents were inbred and genotyped at 25,000 markers per chromosome and a focal F2 individual was genotyped with 50 markers per chromosome. The maximum memory requirement for this scenario was 0.08 GB and took 37 seconds to complete.
Chloroplast competition is controlled by lipid biosynthesis in evening primroses
Authors: Sobanski Johanna , Giavalisco Patrick , Fischer Axel , Kreiner Julia , Walther Dirk , Schöttler Mark Aurel , Pellizzer Tommaso , Golczyk Hieronim , Obata Toshihiro , Bock Ralph , Sears Barbara B. , Greiner Stephan
Published: May 2018

In most eukaryotes, organellar genomes are transmitted preferentially by the mother, but molecular mechanisms and evolutionary forces underlying this fundamental biological principle are far from understood. It is believed that biparental inheritance promotes competition between the cytoplasmic organelles and allows the spread of so-called selfish cytoplasmic elements. Those can be, for example, fast replicating or aggressive chloroplasts (plastids) that are incompatible with the hybrid nuclear genome and therefore maladaptive. Here we show that the ability of plastids to compete against each other is a metabolic phenotype determined by extremely rapidly evolving genes in the plastid genome of the evening primroseOenothera. Repeats in the regulatory region ofaccD(the plastid-encoded subunit of the acetyl-CoA carboxylase, which catalyzes the first and rate limiting step of lipid biosynthesis), as well as inycf2(a giant reading frame of still unknown function), are responsible for the differences in competitive behavior of plastid genotypes. Polymorphisms in these genes influence lipid synthesis and most likely profiles of the plastid envelope membrane. These in turn determine plastid division and/or turn-over rates and hence competitiveness. This work uncovers cytoplasmic drive loci controlling the outcome of biparental chloroplast transmission. Here, they define the mode of chloroplast inheritance, since plastid competitiveness can result in uniparental inheritance (through elimination of the “weak” plastid) or biparental inheritance (when two similarly “strong” plastids are transmitted).

Significance statement

Plastids and mitochondria are usually uniparentally inherited, typically maternally. When the DNA-containing organelles are transmitted to the progeny by both parents, evolutionary theory predicts that the maternal and paternal organelles will compete in the hybrid. As their genomes do not undergo sexual recombination, one organelle will “try” to outcompete the other, thus favoring the evolution and spread of aggressive cytoplasms. The investigations described here in the evening primrose, a model species for biparental plastid transmission, have discovered that chloroplast competition is a metabolic phenotype. It is conferred by rapidly evolving genes that are encoded on the chloroplast genome and control lipid biosynthesis. Due to their high mutation rate these loci can evolve and become fixed in a population very quickly.
Neural mechanisms underlying the precision of visual working memory
Authors: Zhao Yijie , Kuai Shuguang , Zanto Theodore P. , Ku Yixuan
Published: May 2018

The neural mechanisms associated with the limited capacity of working memory has long been studied, but it is still unclear how the brain maintains the fidelity of representations in working memory. Here, an orientation recall task for estimating the precision of visual working memory was performed both inside and outside an fMRI scanner. Results showed that the trial-by-trial recall error (in radians) was correlated with delay period activity in the lateral occipital complex (LOC) during working memory maintenance, regardless of the memory load. Moreover, delay activity in LOC also correlated with the individual participant’s precision of working memory from a separate behavioral experiment held two weeks prior. Furthermore, a region within the prefrontal cortex, the inferior frontal junction (IFJ), exhibited greater functional connectivity with LOC when the working memory load increased. Together, our findings provide unique evidence that the LOC supports visual working memory precision, while communication between the IFJ and LOC varys with visual working memory load.
Inhibition of classical and alternative modes of respiration in C. albicans leads to cell wall remodelling and increased macrophage recognition
Authors: Duvenage Lucian , Walker Louise A. , Bojarczuk Aleksandra , Johnston Simon A. , MacCallum Donna M. , Munro Carol A. , Gourlay Campbell W.
Published: May 2018

The human fungal pathogen C. albicans requires respiratory function for normal growth, morphogenesis and virulence. As such the mitochondria represent an enticing target for the development of new antifungal strategies. This possibility is further bolstered by the presence of fungal specific characteristics. However, respiration in C. albicans, as is the case in many fungal organisms, is facilitated by redundant electron transport mechanisms that makes direct inhibition a challenge. In addition, many chemicals known to target the electron transport chain are highly toxic. Here we make use of chemicals with low toxicity in mammals to efficiently inhibit respiration in C. albicans. We find that use of the Nitric Oxide donor, Sodium Nitroprusside (SNP), and the alternative oxidase inhibitor, SHAM, prevent respiration, lead to a loss in viability and to cell wall rearrangements that increase the rate of uptake by macrophages in vitro and in vivo. We propose that SNP+SHAM treatment leads to transcriptional changes that drive cell wall re-arrangement but which also prime cells to activate transition to hyphal growth. In line with this we find that pre-treatment of C. albicans with SNP+SHAM leads to an increase in virulence. Our data reveals strong links between respiration, cell wall remodelling and activation of virulence factors. Our findings also demonstrate that respiration in C. albicans can be efficiently inhibited with chemicals which are not damaging to the mammalian host, but that we need to develop a deeper understanding of the roles of mitochondria in cellular signalling if they are to be developed successfully as a target for new antifungals.

Author Summary

Current approaches to tackling fungal infections are limited and new targets must be identified to protect against the emergence of resistant strains. We investigate the potential of targeting mitochondria, organelles required for energy production, growth and virulence, in the yeast human fungal pathogen Candida albicans. Our findings suggest that mitochondria can be targeted using drugs that can be tolerated by humans and that this treatment enhances their recognition by immune cells. However release of C. albicans cells from mitochondrial inhibition appears to activate a stress response that increases traits associated with virulence. Our results make it clear that mitochondria are a valid target for the development of anti-fungal strategies but that we must determine the mechanisms by which they regulate stress signalling and virulence ahead of successful therapeutic advance.
Virus and CTL dynamics in the extra-follicular and follicular tissue compartments in SIV-infected macaques
Authors: Wodarz Dominik , Skinner Pamela J. , Levy David N. , Connick Elizabeth
Published: May 2018

Data from SIV-infected macaques indicate that virus-specific cytotoxic T lymphocytes (CTL) are mostly present in the extrafollicular (EF) compartment of the lymphoid tissue, with reduced homing to the follicular (F) site. This contributes to the majority of the virus being present in the follicle and represents a barrier to virus control. Using mathematical models, we investigate these dynamics. Two models are analyzed. The first assumes that CTL can only become stimulated and expand in the extra-follicular compartment, with migration accounting for the presence of CTL in the follicle. In the second model, follicular CTL can also undergo antigen-induced expansion. Consistent with experimental data, both models predict increased virus compartmentalization in the presence of stronger CTL responses and lower virus loads, and a more pronounced rise of extra-follicular compared to follicular virus during CD8 cell depletion experiments. The models, however, differ in other aspects. The follicular expansion model results in dynamics that promote the clearance of productive infection in the extrafollicular site, with any productively infected cells found being the result of immigration from the follicle. This is not observed in the model without follicular CTL expansion. The models further predict different consequences of introducing engineered, follicular-homing CTL, which has been proposed as a therapeutic means to improve virus control. Without follicular CTL expansion, this is predicted to result in a reduction of virus load in both compartments. The follicular CTL expansion model, however, makes the counter-intuitive prediction that addition of F-homing CTL not only results in a reduction of follicular virus load, but also in an increase in extrafollicular virus replication. These predictions remain to be experimentally tested, which will be relevant for distinguishing between models and for understanding how therapeutic introduction of F-homing CTL might impact the overall dynamics of the infection.
A new in vitro assay measuring direct interaction of nonsense suppressors with the eukaryotic protein synthesis machinery
Authors: Ng Martin Y. , Zhang Haibo , Weil Amy , Singh Vijay , Jamiolkowski Ryan , Baradaran-Heravi Alireza , Roberge Michel , Jacobson Allan , Friesen Westley , Welch Ellen , Goldman Yale E. , Cooperman Barry S.
Published: May 2018

Nonsense suppressors (NonSups) induce “readthrough”, i.e., the selection of near cognate tRNAs at premature termination codons and insertion of the corresponding amino acid into nascent polypeptide. Prior readthrough measurements utilized contexts in which NonSups can promote readthrough directly, by binding to one or more of the components of the protein synthesis machinery, or indirectly, by several other mechanisms. Here we utilize a new, highly-purified in vitro assay to measure exclusively direct nonsense suppressor-induced readthrough. Of 16 NonSups tested, 12 display direct readthrough, with results suggesting that such NonSups act by at least two different mechanisms. In preliminary work we demonstrate the potential of single molecule fluorescence energy transfer measurements to elucidate mechanisms of NonSup-induced direct readthrough, which will aid efforts to identify NonSups having improved clinical efficacy.

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