bluuebunny/crossref_metadata_2025 huggingface dataset:
Chemoreception of Meloidogyne incognita and Caenorhabditis elegans on botanical nematicidals
Authors: Sobkowiak Robert , Bojarska Natalia , Krzyżaniak Emilia , Wągiel Karolina , Ntalli Nikoletta
Published: March 2018

Plant–parasitic nematodes cause serious damage to various agricultural crops worldwide, and their control necessitates environmentally safe measures. Plant secondary metabolites of botanical origin are tested here–in to study their effect in Meloidogyne incognita locomotion, being this an important factor affecting host inoculation inside the soil. We compare the effect to the respective behavioral responses of the model organism Caenorhabditis elegans. The tested botanical nematicidals, all reported of activity against Meloidogyne sp. in our previous works, belong to different chemical groups of small molecular weight molecules encompassing acids, alcohols, aldehydes and ketones. Specifically we report on the attractant or repellent properties of trans–anethole, (E,E)–2,4–decadienal, (E)–2–decenal, fostiazate, and 2–undecanone. The treatments for both nematode species were made at sublethal concentration levels, namely 1mM (<EC50), and the chemical control used for the experiment was the commercial nematicide fosthiazate and oxamyl. According to our results, trans–anethole, decenal, and oxamyl act as C. elegans attractants. 2–undecanone strongly attracts M. incognita. These findings can be of use in the development of nematicidal formulates, contributing to the disruption of nematode chemotaxis to root systems.
Interindividual variability in HRV reactivity: autonomic flexibility or regression to the mean?
Authors: Dimitriev Dimitriy A. , Saperova Elena V. , Indeykina Olga S. , Dimitriev Aleksey D.
Published: March 2018

Objective

There is now a substantial body of evidence linking the baseline level of heart rate variability (HRV) with the magnitude of stress-induced reduction in respiratory sinus arrhythmia. However, it remains to be proved to what extent these interindividual differences in stress responses may be attributed to the statistical phenomenon of regression to the mean (RTM). We sought to test the hypothesis that the statistical artifact RTM explains part of the baseline effect.

Approach

Heart rate recording was carried out in 1,156 volunteers. To obtain an estimate of the stress response, 148 persons were randomly selected. Participants were monitored on a rest day and just before an academic examination for state anxiety and HRV. Participants were divided into quartiles according to baseline HRV levels and were compared for response to academic stress.

Main results

We observed a significant reduction in HRV in subjects with a high baseline HRV (> 75th percentile), while a significant increase was found in the group with low baseline HRV. Regression analysis demonstrated that the value of baseline HRV correlated with the magnitude of stress reaction consistent with the RTM model. Baseline-adjusted ANCOVA does not reveal significant intergroup differences in the changes in heart rate (HR) and HRV from rest to exam. RTM-adjusted estimates confirmed an exam effect for HR and HRV.

Significance

The results of our study strongly support RTM as the source of variability of stress-related changes in HRV.
Dopamine is a double-edged sword: Enhancing memory retrieval performance at the expense of metacognition
Authors: Clos Mareike , Bunzeck Nico , Sommer Tobias
Published: March 2018

While memory encoding and consolidation processes have been linked with dopaminergic signaling for a long time, the role of dopamine in episodic memory retrieval remained mostly unexplored. Based on previous observations of striatal activity during memory retrieval, we used pharmacological fMRI to investigate the effects of dopamine on retrieval performance and metacognitive memory confidence in healthy humans. Dopaminergic modulation by the D2 antagonist haloperidol administered acutely during the retrieval phase improved recognition accuracy of previously learned pictures significantly and was associated with increased activity in the SN/VTA, locus coeruleus, hippocampus and amygdala during retrieval. In contrast, confidence for new-decisions was impaired by unsystematically increased activity of the striatum across confidence levels and restricted range of responsiveness in frontostriatal networks under haloperidol. These findings offer new insights into the mechanisms underlying memory retrieval and metacognition and provide a broader perspective on the presence of memory problems in dopamine-related diseases and the treatment of memory disorders.
Cryo-EM visualization of an active high open probability CFTR ion channel
Authors: Fay Jonathan F. , Aleksandrov Luba A. , Jensen Timothy J. , Cui Liying L. , Kousouros Joseph N. , He Lihua , Aleksandrov Andrei A. , Gingerich Drew S. , Riordan John R. , Chen James Z.
Published: March 2018

The Cystic fibrosis transmembrane conductance regulator (CFTR) anion channel, crucial to epithelial salt and water homeostasis, and defective due to mutations in its gene in patients with cystic fibrosis is a unique member of the large family of ATP-binding cassette transport proteins. Regulation of CFTR channel activity is stringently controlled by phosphorylation and nucleotide binding. Structural changes that underlie transitions between active and inactive functional states are not yet fully understood. Indeed the first 3D structures of dephosphorylated, ATP-free and phosphorylated ATP-bound states were only recently reported. Here we have determined the structure of inactive and active states of a thermally stabilized CFTR with very high channel open probability, confirmed after reconstitution into proteoliposomes. The unique repositioning of the TMHs and R domain density that we observe provide insights into the structural transition between active and inactive functional states of CFTR.

Highlights

Structures of thermostabilized avian CFTR in dephosphorylated or phosphorylated forms at 4.3 Å and 6.6 Å resolution, respectively.

Conformational differences of transmembrane helices 7 & 8 compared to zebra fish and human CFTR structures reveal an extracellular vestibule that may provide anion access to the pore.

R-domain density appears to “plug” the intercellular vestibule in the dephosphorylated avian CFTR cryo-EM map.
Comprehensive analysis of lung cancer pathology images to discover tumor shape features that predict survival outcome
Authors: Wang Shidan , Chen Alyssa , Yang Lin , Cai Ling , Xie Yang , Fujimoto Junya , Gazdar Adi , Xiao Guanghua
Published: March 2018

Pathology slide images capture tumor histomorphological details in high resolution. However, manual detection and characterization of tumor regions in pathology slides is labor intensive and subjective. Using a deep convolutional neural network (CNN), we developed an automated tumor region recognition system for lung cancer pathology slides. From the identified regions, we extracted 22 well-defined tumor shape features and found that 15 of them were significantly associated with patient survival outcome in lung adenocarcinoma patients from the National Lung Screening Trial. A tumor shape-based prognostic model was developed and validated in an independent patient cohort (n=389). The predicted high-risk group had significantly worse survival than the low-risk group (p value = 0.0029). Predicted risk group serves as an independent prognostic factor (high-risk vs. low-risk, hazard ratio = 2.25, 95% CI 1.34-3.77, p value = 0.0022) after adjusting for age, gender, smoking status, and stage. This study provides new insights into the relationship between tumor shape and patient prognosis.
Thermoneutrality induces skeletal muscle myopathy via brown adipose tissue in an IRF4- and myostatin-dependent manner
Authors: Kong Xingxing , Zhou Peng , Yao Ting , Kazak Lawrence , Tenen Danielle , Lyubetskaya Anna , Dawes Brian A. , Tsai Linus , Kahn Barbara B. , Spiegelman Bruce M. , Liu Tiemin , Rosen Evan D.
Published: March 2018

Skeletal muscle and brown adipose tissue (BAT) share a common lineage and have been functionally linked, as exercise increases browning through the actions of various myokines. It is unknown, however, whether BAT can affect skeletal muscle function. Our prior work has shown that loss of the transcription factor IRF4 in BAT (BATI4KO) reduces adaptive thermogenesis. Here, we note that these mice also have reduced exercise capacity relative to wild-type littermates, associated with diminished mitochondrial function, ribosomal protein synthesis, and mTOR signaling in muscle, in addition to the signature ultrastructural abnormalities of tubular aggregate myopathy. Within brown adipose tissue, loss of IRF4 caused the induction of a myogenic gene expression signature, which includes an increase in the secreted factor myostatin, a known inhibitor of muscle function. Reduction of myostatin activity by the injection of neutralizing antibodies or soluble ActRIIB receptor rescued the exercise capacity of BATI4KO mice. Additionally, overexpression of IRF4 in brown adipocytes reduced serum myostatin and increased mitochondrial function and exercise capacity in muscle. A physiological role for this system is suggested by the observation that mice housed at thermoneutrality show lower exercise capacity with increased serum myostatin; both of these abnormalities are corrected by surgical removal of BAT. Collectively, our data point to an unsuspected level of BAT-muscle cross-talk driven by IRF4 and myostatin.

Highlights

Mice lacking IRF4 in BAT have a decrease in exercise capacity, accompanied by histological, ultrastructural, signaling, gene expression, and bioenergetic evidence of myopathy in white vastus.

Loss of IRF4 promotes the expression of a myogenic signature in BAT, including the myokine myostatin.

Neutralization of serum myostatin rescues the ability of BATI4KO mice to exercise normally, while overexpression of IRF4 in BAT allows mice to run better than wild-type counterparts.

Thermoneutrality reduces the level of IRF4 in BAT of WT mice, resulting in a myopathic phenotype that can be reversed by surgical excision of BAT.
Both functional trait divergence and trait plasticity confer polyploid advantage in changing environments
Authors: Wei Na , Cronn Richard , Liston Aaron , Ashman Tia-Lynn
Published: March 2018

Polyploidy, or whole genome duplication, exists in all eukaryotes and is thought to drive ecological and evolutionary success especially in plants. The mechanisms of polyploid success in ecologically relevant contexts, however, remain largely unknown. Here we conducted an extensive test of functional trait divergence and trait plasticity in conferring polyploid fitness advantage in changing environments by growing clonal replicates of a worldwide genotype collection of six polyploid and five diploid wild strawberry (Fragaria) species in three climatically different common gardens. Among leaf functional traits, we detected divergence in means but not plasticities between polyploids and diploids, suggesting that increased genomic redundancy does not necessarily translate into broader phenotypic amplitude in polyploids. Across the heterogeneous garden environments, however, polyploids exhibited fitness advantage, which was conferred by both trait means and adaptive trait plasticities, supporting a ‘jack-and-master’ hypothesis for polyploids. Our findings provide unparalleled insight into the prevalence and persistence of polyploidization.
Machine learning as an effective method for identifying true SNPs in polyploid plants
Authors: Korani Walid , Clevenger Josh P. , Chu Ye , Ozias-Akins Peggy
Published: March 2018

Single Nucleotide Polymorphisms (SNPs) have many advantages as molecular markers since they are ubiquitous and co-dominant. However, the discovery of true SNPs especially in polyploid species is difficult. Peanut is an allopolyploid, which has a very low rate of true SNP calling. A large set of true and false SNPs identified from the Arachis 58k Affymetrix array was leveraged to train machine learning models to select true SNPs straight from sequence data. These models achieved accuracy rates of above 80% using real peanut RNA-seq and whole genome shotgun (WGS) re-sequencing data, which is higher than previously reported for polyploids. A 48K SNP array, Axiom Arachis2, was designed using the approach which revealed 75% accuracy of calling SNPs from different tetraploid peanut genotypes. Using the method to simulate SNP variation in peanut, cotton, wheat, and strawberry, we show that models built with our parameter sets achieve above 98% accuracy in selecting true SNPs. Additionally, models built with simulated genotypes were able to select true SNPs at above 80% accuracy using real peanut data, demonstrating that our model can be used even if real data are not available to train the models. This work demonstrates an effective approach for calling highly reliable SNPs from polyploids using machine learning. A novel tool was developed for predicting true SNPs from sequence data, designated as SNP-ML (SNP-Machine Learning, pronounced “snip mill”), using the described models. SNP-ML additionally provides functionality to train new models not included in this study for customized use, designated SNP-MLer (SNP-Machine Learner, pronounced “snip miller”). SNP-ML is freely available for public use.
Architecture of Marine Food Webs: to be or not be a ‘small-world’
Authors: Marina Tomás Ignacio , Saravia Leonardo A. , Cordone Georgina , Salinas Vanesa , Doyle Santiago R. , Momo Fernando R.
Published: March 2018

The search for general properties in network structure has been a central issue for food web studies in recent years. One such property is the small-world topology that combines a high clustering and a small distance between nodes of the network. This property may increase food web resilience but make them more sensitive to the extinction of connected species. Food web theory has been developed principally from freshwater and terrestrial ecosystems, largely omitting marine habitats. If theory needs to be modified to accommodate observations from marine ecosystems, based on major differences in several topological characteristics is still on debate. Here we investigated if the small-world topology is a common structural pattern in marine food webs. We developed a novel, simple and statistically rigorous method to examine the largest set of complex marine food webs to date. More than half of the analyzed marine networks exhibited a similar or lower characteristic path length than the random expectation, whereas 39% of the webs presented a significantly higher clustering than its random counterpart. Our method proved that 5 out of 28 networks fulfilled both features of the small-world topology: short path length and high clustering. This work represents the first rigorous analysis of the small-world topology and its associated features in high-quality marine networks. We conclude that such topology is a structural pattern that is not maximized in marine food webs; thus it is probably not an effective model to study robustness, stability and feasibility of marine ecosystems.
Quantifying the unquantifiable: why Hymenoptera – not Coleoptera – is the most speciose animal order
Authors: Forbes Andrew A. , Bagley Robin K. , Beer Marc A. , Hippee Alaine C. , Widmayer Heather A.
Published: March 2018

Background

We challenge the oft-repeated claim that the beetles (Coleoptera) are the most species-rich order of animals. Instead, we assert that another order of insects, the Hymenoptera, are more speciose, due in large part to the massively diverse but relatively poorly known parasitoid wasps. The idea that the beetles have more species than other orders is primarily based on their respective collection histories and the relative availability of taxonomic resources, which both disfavor parasitoid wasps. Though it is unreasonable to directly compare numbers of described species in each order, the ecology of parasitic wasps – specifically, their intimate interactions with their hosts – allows for estimation of relative richness. We present a simple logical model that shows how the specialization of many parasitic wasps on their hosts suggests few scenarios in which there would be more beetle species than parasitic wasp species. We couple this model with an accounting of what we call the “genus-specific parasitoid-host ratio” from four well-studied genera of insect hosts, a metric by which to generate extremely conservative estimates of the average number of parasitic wasp species attacking a given beetle or other insect host species. Synthesis of our model with data from real host systems suggests that the Hymenoptera may have 2.5 - 3.2× more species than the Coleoptera. While there are more described species of beetles than all other animals, the Hymenoptera are almost certainly the larger order.
How strong are correlations in strongly recurrent neuronal networks?
Authors: Darshan Ran , Vreeswijk Carl van , Hansel David
Published: March 2018

Cross-correlations in the activity in neural networks are commonly used to characterize their dynamical states and their anatomical and functional organizations. Yet, how these latter network features affect the spatiotemporal structure of the correlations in recurrent networks is not fully understood. Here, we develop a general theory for the emergence of correlated neuronal activity from the dynamics in strongly recurrent networks consisting of several populations of binary neurons. We apply this theory to the case in which the connectivity depends on the anatomical or functional distance between the neurons. We establish the architectural conditions under which the system settles into a dynamical state where correlations are strong, highly robust and spatially modulated. We show that such strong correlations arise if the network exhibits an effective feedforward structure. We establish how this feedforward structure determines the way correlations scale with the network size and the degree of the connectivity. In networks lacking an effective feedforward structure correlations are extremely small and only weakly depend on the number of connections per neuron. Our work shows how strong correlations can be consistent with highly irregular activity in recurrent networks, two key features of neuronal dynamics in the central nervous system.
Retronasal Habituation: Characterization and Impact on Flavor Perception using Time-Intensity
Authors: Pellegrino Robert , Atchley Addison , Ali Simrah , Shingleton Joel , Luckett Curtis R.
Published: March 2018

Olfactory habituation results from prolonged exposure to an odor, leading to perceptual changes defined by several characteristics. To date, human habituation research has focused on orthonasal olfaction which is perceived externally while ignoring internal routes of odor perception related to flavor. In our study, we conducted two experiments to characterize retronasal olfactory habituation and measured its impact on flavor perception. In Experiment 1, 22 participants rhythmically breathed a food odor (lime), non-food odor (lavender), and blank (propylene glycol) that was presented using an orally-adhered strip, while rating the odor intensity using the time-intensity procedure. After a 10-minute exposure, the participants ate a lime-flavored gummy and rated the lime flavor. In Experiment 2, the same procedure was performed for a low-level lime odor, a simple (lime oil) and complex (lime oil + sucrose + citric acid) beverage as the flavor stimuli. Our results demonstrated two known principles of habituation for retronasally presented odors: 1) prolonged exposure lead to decreased perception, 2) weaker stimuli lead to more rapid habituation. Additionally, we found that the non-food odor habituated slower than the food odor; however, the participants seemed to recover simultaneously upon food and beverage consumption leading to no change in flavor perception.
The homoeologous genes for the Rec8-like meiotic cohesin in wheat: structure, function, and evolutionary implication
Authors: Ma Guojia , Zhang Wei , Liu Liwang , Chao Wun S. , Gu Yong Qiang , Qi Lili , Xu Steven S. , Cai Xiwen
Published: March 2018

The Rec8-like cohesin is a cohesion protein essential for orderly chromosome segregation in meiosis. Here, we cloned twoRec8-like homoeologous genes (homoeoalleles) from tetraploid wheat (TtRec8-A1andTtRec8-B1) and one from hexaploid wheat (TaRec8-D1), and performed expression and functional analyses of the homoeoalleles. Also, we identified other twoRec8homoeoalleles in hexaploid wheat (TaRec8-A1andTaRec8-B1) and the one inAegilops tauschii(AetRec8-D1) by comparative analysis. The coding DNA sequences (CDS) of these sixRec8homoeoalleles are all 1,827 bp in length, encoding 608 amino acids. They differed from each other primarily in introns although single nucleotide polymorphisms were detected in CDS. Substantial difference was observed between the homoeoalleles from the subgenome B (TtRec8-B1andTaRec8-B1) and those from the subgenomes A and D (TtRec8-A1, TaRec8-A1, andTaRec8-D1).TtRec8-A1expressed dominantly overTtRec8-B1, but comparably toTaRec8-D1. Therefore, theRec8homoeoalleles from the subgenomes A and D may be functionally more active than the one from the subgenome B in wheat. The structural variation and differential expression of theRec8homoeoalleles indicate a unique cross-genome coordination of the homoeologous genes in the polyploid, and imply the distinction of the wheat subgenome B from other subgenomes in the origin and evolution.

HIGHLIGHT

This work revealed the structural and expression patterns of theRec8-like homoeologous genes in polyploid wheat, implying a unique origin and evolutionary route of the wheat B subgenome.
Comparative Analysis ofUL16Mutants Derived from Multiple Strains of HSV-2 and HSV-1 Reveals Species-Specific Requirements for the UL16 Protein
Authors: Gao Jie , Yan Xiaohu , Banfield Bruce W.
Published: March 2018

Orthologs of the herpes simplex virus (HSV)UL16gene are conserved throughout theHerpesviridae. Because of this conservation, one might expect that these proteins perform similar functions for all herpesviruses. Previous studies on aUL16null mutant derived from HSV-2 strain 186 revealed a roughly 100-fold replication defect and a critical role for UL16 in the nuclear egress of capsids. These findings were in stark contrast to what has been observed withUL16mutants of HSV-1 and pseudorabies virus where roughly 10-fold replication deficiencies were reported that were accompanied by defects in the secondary envelopment of cytoplasmic capsids. One possible explanation for this discrepancy is that the HSV-2 186 strain is not representative of the HSV-2 species. To address this possibility, multipleUL16null mutants were constructed in multiple HSV-2 and HSV-1 strains by CRISPR/Cas9 mutagenesis and their phenotypes characterized side-by-side. This analysis showed that all the HSV-2UL16mutants had 50 to 100-fold replication deficiencies that were accompanied by defects in the nuclear egress of capsids as well as defects in the secondary envelopment of cytoplasmic capsids. By contrast, most HSV-1UL16mutants had 10-fold replication deficiencies that were accompanied by defects in secondary envelopment of cytoplasmic capsids. These findings indicated that UL16 has HSV species-specific functions. Interestingly, HSV-1 UL16 could promote the nuclear egress of HSV-2UL16null strains, suggesting that, unlike HSV-1, HSV-2 lacks an activity that can compensate for nuclear egress in the absence of UL16.

Importance

HSV-2 and HSV-1 are important human pathogens that cause distinct diseases in their hosts. A complete understanding of the morphogenesis of these viruses is expected to reveal vulnerabilities that can be exploited in the treatment of HSV disease. UL16 is a virion structural component that is conserved throughout theHerpesviridaeand functions in virus morphogenesis, however, previous studies have suggested different roles for UL16 in the morphogenesis of HSV-2 and HSV-1. This study sought to resolve this apparent discrepancy by analyzing multiple UL16 mutant viruses derived from multiple strains of HSV-2 and HSV-1. The data indicate that UL16 has HSV species-specific functions insofar as HSV-2 has a requirement for UL16 in the escape of capsids from the nucleus whereas both HSV-2 and HSV-1 require UL16 for final envelopment of capsids at cytoplasmic membranes.
Differential splicing of ANP32A in birds alters its ability to stimulate RNA synthesis by restricted influenza polymerase
Authors: Baker Steven F. , Ledwith Mitchell P. , Mehle Andrew
Published: March 2018

Adaptation of viruses to their host can result in specialization and a restricted host range. Species-specific polymorphisms in the influenza virus polymerase restrict its host range during transmission from birds to mammals. ANP32A was recently been identified as a cellular co-factor impacting polymerase adaption and activity. Avian influenza polymerases require ANP32A containing an insertion resulting from an exon duplication uniquely encoded in birds. Here we find that natural splice variants surrounding this exon create avian ANP32A proteins with distinct effects on polymerase activity. We demonstrate species-independent direct interactions between all ANP32A variants and the PB2 polymerase subunit. This interaction is enhanced in the presence of viral genomic RNA. In contrast, only avian ANP32A restored ribonucleoprotein complex assembly for a restricted polymerase by enhancing RNA synthesis. Our data suggest that ANP32A splicing variation amongst birds differentially impacts viral replication, polymerase adaption, and the potential of avian hosts to be reservoirs.
Analysis ofEscherichia coliFlagellin Gene Expression in Simulated Spaceflight Growth Conditions
Authors: Hetrick Kyle M. , Juergensmeyer Elizabeth A. , Henderson Jeffrey O.
Published: March 2018

Population growth curves ofEscherichia coli(E. coli) cultures propagated in spaceflight environments demonstrate an extended log phase duration and an increased final cell concentration compared toE. colicultures grown on Earth. We suggest that during spaceflight, a lack of convective mixing in the growth medium alters a cell’s microenvironment such that the cell at first devotes its resources primarily to motility and later shifts most of its resources to reproduction. As flagellin is the major protein component of flagella, the motility structure ofE. coli, we propose that the expression of the flagellin gene (fliC) can be used as a diagnostic marker for determining if the bacterium is in fact altering its allocation of cellular resources to motility during specific growth phases. We have used semiquantitative RT-PCR to analyze the expression offliCin cultures grown in laboratory apparatus that simulate various aspects of the spaceflight environment. The data from this pilot study indicate thatfliCexpression increases initially under stationary, slow clinorotation, and fast clinorotation growth conditions, peaking at mid-exponential phase and decreasing dramatically in stationary phase. These data support the hypothesis that metabolic resources are being directed towards forming the flagellum, the bacteria motile structure, before shifting resources to growth, reproduction, and maintenance.
Molecular Genetic Analysis of Rbm45/Drbp1: Genomic Structure, Expression, and Evolution
Authors: Price Lauren E. , Loewen Faul Abigail B. , Vuchkovska Aleksandra , Lopez Kevin J. , Fast Katie M. , Eck Andrew G. , Hoferer David W. , Henderson Jeffrey O.
Published: March 2018

RNA recognition motif-type RNA-binding domain containing proteins (RBDPs) participate in RNA metabolism including regulating mRNA stability, nuclear-cytoplasmic shuttling, and splicing. Rbm45 is an RBDP first cloned from rat brain and expressed spatiotemporally during rat neural development. More recently, RBM45 has been associated with pathological aggregates in the human neurological disorders amyotrophic lateral sclerosis, frontotemporal lobar degeneration, and Alzheimer’s. Rbm45 and the neural developmental protein musashi-1 are in the same family of RDBPs and have similar expression patterns. In contrast to Musashi-1, which is upregulated during colorectal carcinogenesis, we found no association ofRBM45overexpression in human colon cancer tissue. In order to begin characterizing RNA-binding partners of Rbm45, we have successfully cloned and expressed human RBM45 in an Intein fusion-protein expression system. Furthermore, to gain a better understanding of the molecular genetics and evolution of Rbm45, we used anin silicoapproach to analyze the gene structure of the human and mouse Rbm45 homologues and explored the evolutionary conservation of Rbm45 in metazoans. HumanRBM45and mouseRbm45span ∽17 kb and 13 kb, respectively, and contain 10 exons, one of which is non-coding. Both genes have TATA-less promoters with an initiator and a GC-rich element. Downstream of exon 10, both homologues have canonical polyadenylation signals and an embryonic cytoplasmic polyadenylation element. Moreover, our data indicate Rbm45 is conserved across all metazoan taxa from sponges (phylum Porifera) to humans (phylum Chordata), portending a fundamental role in metazoan development.
Meta-analysis of genome-wide association studies for height and body mass index in ∼700,000 individuals of European ancestry
Authors: Yengo Loic , Sidorenko Julia , Kemper Kathryn E. , Zheng Zhili , Wood Andrew R. , Weedon Michael N. , Frayling Timothy M. , Hirschhorn Joel , Yang Jian , Visscher Peter M. ,   the GIANT Consortium
Published: March 2018

Genome-wide association studies (GWAS) stand as powerful experimental designs for identifying DNA variants associated with complex traits and diseases. In the past decade, both the number of such studies and their sample sizes have increased dramatically. Recent GWAS of height and body mass index (BMI) in ∼250,000 European participants have led to the discovery of ∼700 and ∼100 nearly independent SNPs associated with these traits, respectively. Here we combine summary statistics from those two studies with GWAS of height and BMI performed in ∼450,000 UK Biobank participants of European ancestry. Overall, our combined GWAS meta-analysis reaches N∼700,000 individuals and substantially increases the number of GWAS signals associated with these traits. We identified 3,290 and 716 near-independent SNPs associated with height and BMI, respectively (at a revised genome-wide significance threshold of p<1 × 10−8), including 1,185 height-associated SNPs and 554 BMI-associated SNPs located within loci not previously identified by these two GWAS. The genome-wide significant SNPs explain ∼24.6% of the variance of height and ∼5% of the variance of BMI in an independent sample from the Health and Retirement Study (HRS). Correlations between polygenic scores based upon these SNPs with actual height and BMI in HRS participants were 0.44 and 0.20, respectively. From analyses of integrating GWAS and eQTL data by Summary-data based Mendelian Randomization (SMR), we identified an enrichment of eQTLs amongst lead height and BMI signals, prioritisting 684 and 134 genes, respectively. Our study demonstrates that, as previously predicted, increasing GWAS sample sizes continues to deliver, by discovery of new loci, increasing prediction accuracy and providing additional data to achieve deeper insight into complex trait biology. All summary statistics are made available for follow up studies.
In Silico Processing of the Complete CRISPR-Cas Spacer Space for Identification of PAM Sequences
Authors: Mendoza Brian J , Trinh Cong T
Published: March 2018

Despite extensive exploration of the diversity of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems, biological applications have been mostly confined to Class 2 systems, specifically the Cas9 and Cas12 (formerly Cpf1) single effector proteins. A key limitation of exploring and utilizing other CRISPR-Cas systems with unique functionalities, particularly Class I types and their multi-protein effector complex, is the knowledge of the system’s protospacer adjacent motif (PAM) sequence identity. In this work, we developed a systematic pipeline, named CASPERpam, that enables us to comprehensively assess the PAM sequences of all the available CRISPR-Cas systems in the NCBI database of bacterial genomes. The CASPERpam analysis revealed that within the 30,389 assemblies previously screen for CRISPR arrays, there exists 26,364 spacers that match somewhere in the viral, bacterial, and plasmid databases of NCBI, using the constraints of 95% sequence identity and 95% sequence coverage for blast hits. When grouping these results by species, we were able to identify putative PAM sequences for 1,049 among 1,493 unique species. The remaining species either have insufficient data or an undetermined result from the analysis. Finally, we were able to infer certain design principles that are relevant for understanding PAM diversity and a baseline for further experimental studies including PAM assays. We envision CASPERpam is a useful bioinformatic tool for understanding and harnessing the diversity of CRISPR systems.
Proteome-wide Prediction of Lysine Methylation Reveals Novel Histone Marks and Outlines the Methyllysine Proteome
Authors: Biggar Kyle K , Charih Francois , Liu Huadong , Ruiz-Blanco Yasser B , Stalker Leanne , Chopra Anand , Connolly Justin , Adhikary Hemanta , Frensemier Kristin , Galka Marek , Fang Qi , Wynder Christopher , Standford William L , Green James R , Li Shawn S-C.
Published: March 2018

Protein Lys methylation plays a critical role in numerous cellular processes, yet it has been challenging to identify Lys methylation in a systematic manner. We present here an approach combining in silico prediction with targeted mass spectrometry (MS) to identify Lys methylation (Kme) sites at the proteome level. We have developed MethylSight, a program that predicts Kme events solely on physicochemical and biochemical properties of putative methylation sites, which can then be validated by targeted MS. Using this approach, we have identified 70 new histone Kme marks with a 90% validation rate. H2BK43me2, which undergoes dynamic changes during stem cell differentiation, is found to be a substrate of KDM5b. Furthermore, MethylSight predicts ~50,000 Kme sites in non-histone proteins with high confidence, suggesting that Lys methylation is a prevalent post-translational modification. Our work provides a useful resource for systematic exploration of the role of Lys methylation in human health and disease.
Crowding tunes 3D collagen fibrils and reveals matrix regulation of cancer cell morphogenesis
Authors: Han A. , Ranamukhaarachchi S. , Velez D. O. , Kumar A. , Engler A. J. , Fraley S. I.
Published: March 2018

It is well established that the collagenous extracellular matrix surrounding solid tumors significantly influences the dissemination of cancer cells. However, the underlying mechanisms remain poorly understood, in part because of a lack of methods to modulate collagen fibril topology in the presence of embedded cells. In this work, we develop a technique to tune the fibril architecture of cell-laden 3D collagen matrices using PEG as an inert molecular crowding agent. With this approach, we demonstrate that fibril length and pore size can be modulated independently of bulk collagen density and stiffness. Using live cell imaging and quantitative analysis, we show that matrices with long fibrils induce cell elongation and single cell migration, while shorter fibrils induce cell rounding, collective migration, and morphogenesis. We conclude that fibril architecture is an independent regulator of cancer cell phenotype and that cell shape and invasion strategy are functions of collagen fibril length.
Fractionated follow-up chemotherapy delays the onset of resistance in bone metastatic prostate cancer
Authors: Warman Pranav I. , Kaznatcheev Artem , Araujo Arturo , Lynch Conor C. , Basanta David
Published: March 2018

Prostate cancer to bone metastases are almost always lethal. This results from the ability of metastatic prostate cancer cells to co-opt bone remodeling leading to what is known as thevicious cycle. Understanding how tumor cells can disrupt bone homeostasis through their interactionswith the stroma and how metastatic tumors respond to treatment is key to the development of new treatments for what remains an incurable disease. Here we describe an evolutionary game theoretical model of both the homeostatic bone remodeling and its co-option by prostate cancer metastases. This model extends past the evolutionary aspects typically considered in game theoretical models by also including ecological factors such as the physical microenvironment of the bone. Our model recapitulates the current paradigm of the”vicious cycle”driving tumor growth and sheds light on the interactions of heterogeneous tumor cells with the bone microenvironment and treatment response. Our results show that resistant populations naturally become dominant in the metastases under conventional cytotoxic treatment and that novel schedules could be used to better control the tumor and the associated bone disease compared to the current standard of care. Specifically, we introduce fractionated follow up therapy – chemotherapy where dosage is administered initially in one solid block followed by alternating smaller doeses and holidays – and argue that it is better than either a continuous application or a periodic one. Furthermore, we also show that different regimens of chemotherapy can lead to different amounts of pathological bone that are known to correlate with poor quality of life for bone metastatic prostate cancer patients.
Construction of a Genetic Sexing Strain for Aedes albopictus: a promising tool for the development of sterilizing insect control strategies targeting the tiger mosquito
Authors: Lebon Cyrille , Benlali Aude , Atyame Célestine , Mavingui Patrick , Tortosa Pablo
Published: March 2018

Background

Aedes albopictus is an invasive mosquito species of global medical concern as its distribution has recently expanded to Africa, the Americas and Europe. In the absence of prophylaxis protecting human populations from emerging arboviruses transmitted by this mosquito species, the most straightforward control measures rely on the suppression or manipulation of vector natural populations. A number of environmental-friendly methods using innundative releases of sterilizing males are currently under development. However, these strategies are still lacking an efficient sexing method required for mass production of males.

Results

We present the first Genetic Sexing Strain (GSS) in Ae. albopictus, hereafter referred as TiCoq, obtained by sex linkage of rdl gene conferring dieldrin resistance. Hatching rate, larval survival and sex ratio were followed during twelve generations. The use of dieldrin at third larval stage allowed selecting 98% of males on average.

Conclusion

A good production rate of TiCoq males makes this GSS suitable for any control method based on mass production of Ae. albopictus sterilizing males. Despite limitations resulting from affected egg hatch as well as the nature of the used insecticide, the construction of this GSS paves the way for industrial sex separation of Ae. albopictus.
Neural Modulation of Social Distance on Third-Party Punishment
Authors: Qu Chen , Tang Zixuan , Zhang Huijun , Hu Yang , Dreher Jean Claude
Published: March 2018

As a crucial mechanism to enforce social norms, people as third parties tend to punish the norm violators even it costs their own pay-off. However, people do not usually treat everyone equally, e.g., it is shown that people are nice to close others. Here, we investigated how third party punishment (TPP) and its neural correlates is modulated by social distance (SD) by using fMRI. Behaviorally, participants punished more when the unfair perpetrator was more distant to them. Such SD-modulation effect was stronger when the punishment was free. Model-based results showed that SD-dependent computational signals were encoded in right dlPFC. More interestingly, SD modulated the relationship between punishment levels and neural activities in default network including vmPFC and bilateral hippocampus. The explorative functional connectivity analysis further showed that the vmPFC increased the association with left dlPFC when participants punished close others. Finally, punishment type (costly vs. free) also modulated the relationship between punishment levels and neural correlates in dACC and the ventral striatum. Taken together, our results revealed the neurocomputational underpinnings of how SD plays an important role in affecting TPP.
Deep mutational scanning by FACS-sorting of encapsulated E. coli micro-colonies
Authors: Behrendt Lars , Stein Amelie , Shah Shiraz Ali , Zengler Karsten , Sørensen Søren J. , Lindorff-Larsen Kresten , Winther Jakob R.
Published: March 2018

We present a method for high-throughput screening of protein variants where the signal is enhanced by micro-encapsulation of single cells into 20-30 μm agarose beads. Cells inside beads are propagated using standard agitation in liquid media and grow clonally into micro-colonies harboring several hundred bacteria. We have, as a proof-of-concept, analyzed random amino acid substitutions in the five C-terminal β-strands of the Green Fluorescent Protein (GFP). Starting from libraries of variants, each bead represents a clonal line of cells that can be separated by Fluorescence Activated Cell Sorting (FACS). Pools representing collections of individual variants with desired properties are subsequently analyzed by deep sequencing. Notably, the encapsulation approach described holds the potential for high-throughput analysis of systems where the fluorescence signal from a single cell is insufficient for detection. Fusion to GFP, or use of fluorogenic substrates, allows coupling protein levels or activity to sequence for a wide range of proteins. Here we analyzed more than 10,000 individual variants to gauge the effect of mutations on GFP-fluorescence. In the mutated region, we observed virtually all amino acid substitutions that are accessible by single nucleotide exchange. Lastly, we assessed the performance of biophysical protein stability predictors, FoldX and Rosetta, in predicting the outcome of the experiment. Both tools display good performance on average, suggesting that loss of thermodynamic stability is a key mechanism for the observed variation of the mutants. This, in turn, suggests that deep mutational scanning datasets may be used to more efficiently fine-tune such predictors, especially for mutations poorly covered by current biophysical data.
Cross-regulation between CDK and MAPK control cellular fate
Authors: Durandau Eric , Pelet Serge
Published: March 2018

Commitment to a new cell cycle is controlled by a number of cellular signals. Mitogen-Activated Protein Kinase pathways, which transduce multiple extracellular cues, have been shown to be interconnected with the cell cycle. Using budding yeast as a model system, we have quantified in hundreds of live single cells the interplay between the MAPK regulating the mating response and the Cyclin-Dependent Kinase controlling cell cycle progression. Different patterns of MAPK activity dynamics could be identified by clustering cells based on their CDK activity, denoting the tight relationship between these two cellular signals. In mating mixtures, we have verified that the interplay between CDK and MAPK activities allows cells to select their fate, preventing them from being blocked in an undesirable cellular program.
Spatial photosynthesis modelling sets guidelines to constructing a viable single-cell cytoplasm-to-stroma C4 cycle
Authors: Jurić Ivan , Hibberd Julian M. , Blatt Mike , Burroughs Nigel J.
Published: March 2018

It has been proposed that introducing C4 photosynthesis into C3 crops would increase yield. The simplest scheme in- volves concentrating carbon originating from the cytosol in the chloroplast stroma of mesophyll cells without altering leaf or cell anatomy. Photosynthetic efficiency would then strongly depend on the chloroplast envelope permeability to CO2. We examine the performance of this C4 cycle with a spatial model of carbon assimilation in C3 mesophyll cell geometry, conducting a thorough exploration of parameter space relevant to C4 photosynthesis. For envelope perme- abilities below 300 µm/s C4 photosynthesis has a higher quantum efficiency than C3. However, even when envelope permeability is above this threshold, the C4 pathway can provide a substantial boost to carbon assimilation with only a moderate decrease in efficiency. Depending on the available light-harvesting capacity of plastids, C4 photosynthesis could boost carbon assimilation anywhere from 20% to 100%. Gains are even more prominent under CO2 deprivation, and can be achieved in conjunction with lower investment in plastids if chloroplast surface coverage is also altered. A C4 pathway operating within individual mesophyll cells of C3 plants could hence lead to higher growth rates and better drought resistance in dry, high-sunlight climates.
PACAP neurons in the ventral premammillary nucleus regulate reproductive function in the female mouse
Authors: Ross Rachel A. , León Silvia , Madara Joseph C. , Schafer Danielle , Fergani Chrysanthi , Maguire Caroline A. , Verstegen Anne M. J. , Brengle Emily , Kong Dong , Herbison Allan E , Kaiser Ursula B. , Lowell Bradford B. , Navarro Victor M.
Published: March 2018

Pituitary adenylate cyclase activating polypeptide (PACAP) is a neuromodulator implicated in anxiety, metabolism and reproductive behavior. PACAP global knockout mice have decreased fertility and PACAP modulates LH release. However, its source and role at the hypothalamic level remain unknown. We demonstrate that PACAP-expressing neurons of the ventral premamillary nucleus of the hypothalamus (PMVPACAP) project to, and make direct contact with, kisspeptin neurons in the arcuate and AVPV/PeN nuclei and a subset of these neurons respond to PACAP exposure. Targeted deletion of PACAP from the PMV through stereotaxic virally mediated cre- injection or genetic cross to LepR-i-cre mice with PACAPfl/flmice led to delayed puberty onset and impaired reproductive function in female, but not male, mice. We propose a new, sex-specific role for PACAP-expressing neurons in the PMV in the relay of nutritional state information to regulate GnRH release by modulating the activity of kisspeptin neurons, thereby regulating reproduction.

Disclosure statement

The authors have nothing to disclose.
Perforin-2 Permeabilizes the Envelope of Phagocytosed Bacteria
Authors: Bai Fangfang , McCormack Ryan M. , Hower Suzanne , Plano Gregory V. , Lichtenheld Mathias G. , Munson George P.
Published: March 2018

Perforin-2, the product of theMPEG1gene, limits the spread and dissemination of bacterial pathogens in vivo. It is highly expressed in murine and human phagocytes, and macrophages lacking Perforin-2 are compromised in their ability to kill phagocytosed bacteria. In this study we usedSalmonella typhimuriumas a model intracellular pathogen to elucidate the mechanism of Perforin-2‘s bactericidal activity. In vitro Perforin-2 was found to facilitate the degradation of antigens contained within the envelope of phagocytosed bacteria. In contrast, degradation of a representative surface antigen was found to be independent of Perforin-2. Consistent with our in vitro results a protease sensitive, periplasmic superoxide disumutase (SodCII) contributed to the virulence ofS. typhimuriumin Perforin-2 knockout but not wild-type mice. In aggregate our studies indicate that Perforin-2 breaches the envelope of phagocytosed bacteria facilitating the delivery of proteases and other antimicrobial effectors to sites within the bacterial envelope.