bluuebunny/crossref_metadata_2025 huggingface dataset:
Phosphotyrosine signalling and the origin of animal multicellularity
Authors: Tong Kai , Wang Yuyu , Su Zhixi
Published: August 2017

The evolution of multicellular animals (i.e. metazoans) from a unicellular ancestor is one of the most important yet least understood evolutionary transitions. Historically, given its indispensable functions in intercellular communication and exclusive presence in metazoans, phosphotyrosine (pTyr) signalling was considered a metazoan-specific evolutionary innovation that might have contributed to the origin of metazoan multicellularity. However, recent studies have led to a new understanding of pTyr signalling evolution and its role in the metazoan origin. Sequence analyses have unravelled a much earlier emergence of pTyr signalling in eukaryotic evolution. Even so, several distinct properties of holozoan pTyr signalling may have paved the way for a hypothesized functional transition of pTyr signalling at the multicellular origin, from environmental sensing to intercellular communication, and for it to evolve as a powerful intercellular signalling system for multicellularity. Biochemical analyses of premetazoan pTyr signalling components have further revealed the premetazoan origin of many key features of metazoan pTyr signalling, and the metazoan establishment of others, including the Csk-mediated negative regulation of the activity of Src, a conserved tyrosine kinase in the Holozoa. Finally, potential future directions are discussed, with a stress on the biological functions of premetazoan pTyr signalling via newly developed gene manipulation tools in non-animal holozoans.
Dynamical state transitions into addictive behaviour and their early-warning signals
Authors: Foo Jerome Clifford , Noori Hamid Reza , Yamaguchi Ikuhiro , Vengeliene Valentina , Cosa-Linan Alejandro , Nakamura Toru , Morita Kenji , Spanagel Rainer , Yamamoto Yoshiharu
Published: August 2017

The theory of critical transitions in complex systems (ecosystems, climate, etc.), and especially its ability to predict abrupt changes by early-warning signals based on analysis of fluctuations close to tipping points, is seen as a promising avenue to study disease dynamics. However, the biomedical field still lacks a clear demonstration of this concept. Here, we used a well-established animal model in which initial alcohol exposure followed by deprivation and subsequent reintroduction of alcohol induces excessive alcohol drinking as an example of disease onset. Intensive longitudinal data (ILD) of rat drinking behaviour and locomotor activity were acquired by a fully automated drinkometer device over 14 weeks. Dynamical characteristics of ILD were extracted using a multi-scale computational approach. Our analysis shows a transition into addictive behaviour preceded by early-warning signals such as instability of drinking patterns and locomotor circadian rhythms, and a resultant increase in low frequency, ultradian rhythms during the first week of deprivation. We find evidence that during prolonged deprivation, a critical transition takes place pushing the system to excessive alcohol consumption. This study provides an adaptable framework for processing ILD from clinical studies and for examining disease dynamics and early-warning signals in the biomedical field.
The evolution of dual meat and milk cattle husbandry in Linearbandkeramik societies
Authors: Gillis Rosalind E. , Kovačiková Lenka , Bréhard Stéphanie , Guthmann Emilie , Vostrovská Ivana , Nohálová Hana , Arbogast Rose-Marie , Domboróczki László , Pechtl Joachim , Anders Alexander , Marciniak Arkadiusz , Tresset Anne , Vigne Jean-Denis
Published: August 2017

Cattle dominate archaeozoological assemblages from the north-central Europe between the sixth and fifth millennium BC and are frequently considered as exclusively used for their meat. Dairy products may have played a greater role than previously believed. Selective pressure on the lactase persistence mutation has been modelled to have begun between 6000 and 4000 years ago in central Europe. The discovery of milk lipids in late sixth millennium ceramic sieves in Poland may reflect an isolated regional peculiarity for cheese making or may signify more generalized milk exploitation in north-central Europe during the Early Neolithic. To investigate these issues, we analysed the mortality profiles based on age-at-death analysis of cattle tooth eruption, wear and replacement from 19 archaeological sites of the Linearbandkeramik (LBK) culture (sixth to fifth millennium BC). The results indicate that cattle husbandry was similar across time and space in the LBK culture with a degree of specialization for meat exploitation in some areas. Statistical comparison with reference age-at-death profiles indicate that mixed husbandry (milk and meat) was practised, with mature animals being kept. The analysis provides a unique insight into LBK cattle husbandry and how it evolved in later cultures in central and western Europe. It also opens a new perspective on how and why the Neolithic way of life developed through continental Europe and how dairy products became a part of the human diet.
Is meiosis a fundamental cause of inviability among sexual and asexual plants and animals?
Authors: Levitis Daniel A. , Zimmerman Kolea , Pringle Anne
Published: August 2017

Differences in viability between asexually and sexually generated offspring strongly influence the selective advantage and therefore the prevalence of sexual reproduction (sex). However, no general principle predicts when sexual offspring will be more viable than asexual offspring. We hypothesize that when any kind of reproduction is based on a more complex cellular process, it will encompass more potential failure points, and therefore lower offspring viability. Asexual reproduction (asex) can be simpler than sex, when offspring are generated using only mitosis. However, when asex includes meiosis and meiotic restitution, gamete production is more complex than in sex. We test our hypothesis by comparing the viability of asexual and closely related sexual offspring across a wide range of plants and animals, and demonstrate that meiotic asex does result in lower viability than sex; without meiosis, asex is mechanistically simple and provides higher viability than sex. This phylogenetically robust pattern is supported in 42 of 44 comparisons drawn from diverse plants and animals, and is not explained by the other variables included in our model. Other mechanisms may impact viability, such as effects of reproductive mode on heterozygosity and subsequent viability, but we propose the complexity of cellular processes of reproduction, particularly meiosis, as a fundamental cause of early developmental failure and mortality. Meiosis, the leading cause of inviability in humans, emerges as a likely explanation of offspring inviability among diverse eukaryotes.
Baby fish working out: an epigenetic source of adaptive variation in the cichlid jaw
Authors: Hu Yinan , Albertson R. Craig
Published: August 2017

Understanding the developmental processes that underlie the production of adaptive variation (i.e. the ‘arrival of the fittest’) is a major goal of evolutionary biology. While most evo-devo studies focus on the genetic underpinnings of adaptive phenotypic variation, factors beyond changes in nucleotide sequence can also play a major role in shaping developmental outcomes. Here, we document a vigorous but enigmatic gaping behaviour during the early development of Lake Malawi cichlid larvae. The onset of the behaviour precedes the formation of bone, and we predicted that it might influence craniofacial shape by affecting the mechanical environment in which bone develops. Consistent with this, we found that both natural variation and experimental manipulation of this behaviour induced differential skeletal development that foreshadows adaptive variation in adult trophic morphology. In fact, the magnitude of difference in skeletal morphology induced by these simple shifts in behaviour was similar to those predicted to be caused by genetic factors. Finally, we demonstrate that this mechanical-load-induced shift in skeletal development is associated with differences inptch1expression, a gene previously implicated in mediating between-species differences in skeletal shape. Our results underscore the complexity of development, and the importance of epigenetic (sensuWaddington) mechanisms in determining adaptive phenotypic variation.
Phenotypic plasticity in reproductive effort: malaria parasites respond to resource availability
Authors: Birget Philip L. G. , Repton Charlotte , O'Donnell Aidan J. , Schneider Petra , Reece Sarah E.
Published: August 2017

The trade-off between survival and reproduction is fundamental in the life history of all sexually reproducing organisms. This includes malaria parasites, which rely on asexually replicating stages for within-host survival and on sexually reproducing stages (gametocytes) for between-host transmission. The proportion of asexual stages that form gametocytes (reproductive effort) varies during infections—i.e. is phenotypically plastic—in response to changes in a number of within-host factors, including anaemia. However, how the density and age structure of red blood cell (RBC) resources shape plasticity in reproductive effort and impacts upon parasite fitness is controversial. Here, we examine how and why the rodent malaria parasitePlasmodium chabaudialters its reproductive effort in response to experimental perturbations of the density and age structure of RBCs. We show that all four of the genotypes studied increase reproductive effort when the proportion of RBCs that are immature is elevated during host anaemia, and that the responses of the genotypes differ. We propose that anaemia (counterintuitively) generates a resource-rich environment in which parasites can afford to allocate more energy to reproduction (i.e. transmission) and that anaemia also exposes genetic variation to selection. From an applied perspective, adaptive plasticity in parasite reproductive effort could explain the maintenance of genetic variation for virulence and why anaemia is often observed as a risk factor for transmission in human infections.
Live imaging of heart tube development in mouse reveals alternating phases of cardiac differentiation and morphogenesis
Authors: Ivanovitch Kenzo , Temiño Susana , Torres Miguel
Published: August 2017

During vertebrate heart development two progenitor populations, first and second heart fields (FHF, SHF), sequentially contribute to longitudinal subdivisions of the heart tube (HT), with the FHF contributing the left ventricle and part of the atria, and the SHF the rest of the heart. Here we study the dynamics of cardiac differentiation and morphogenesis by tracking individual cells in live analysis of mouse embryos. We report that during an initial phase, FHF precursors differentiate rapidly to form a cardiac crescent, while limited morphogenesis takes place. In a second phase, no differentiation occurs while extensive morphogenesis, including splanchnic mesoderm sliding over the endoderm, results in HT formation. In a third phase, cardiac precursor differentiation resumes and contributes to SHF-derived regions and the dorsal closure of the HT. These results reveal tissue-level coordination between morphogenesis and differentiation during HT formation and provide a new framework to understand heart development.
ASPEN: A methodology for reconstructing protein evolution with improved accuracy using ensemble models
Authors: Sloutsky Roman , Naegle Kristen M.
Published: August 2017

Evolutionary reconstruction algorithms produce models of the evolutionary history of proteins: the order of duplications and speciations that led to extant homologous proteins observed across species. Although they are regularly used to gain insight into protein function, these models are estimates of an unknowable truth according to the underlying assumptions inherent in each algorithm, its objective function, and the input sequences supplied for reconstruction. In practice, the generated models are highly sensitive to the sequence inputs. In this work, we asked whether we could identify stronger phylogenetic signal by capitalizing on the variance introduced by perturbing the input to evolutionary reconstruction to explore a rich space of possible models that could explain protein evolution. We subsampled from available protein orthologs, “same” proteins across multiple extant species, and produced an ensemble of topologies representing the duplication history which produced related proteins (paralogs) for simulated protein families and in a real protein family – the LacI transcription factor family. We found that two very important phenomena arise from this approach. First, the reproducibility of an all-sequence, single-alignment reconstruction, measured by comparing topologies inferred from 90% subsamples, directly correlates with the accuracy of that single-alignment reconstruction, producing a measurable value for something that has been traditionally unknowable. Second, if we take a large ensemble of trees inferred from 50% subsamples and cast the ensemble into a form that represents the distribution of pairwise leaf distances observed across the ensemble, then trees that capture the most frequently observed relationships are also the most accurate. We propose a new methodology, ASPEN, a meta-algorithm that finds and ranks the trees that are most consistent with observations across the ensemble. Top-ranked ASPEN trees are significantly more accurate than the single-alignment tree produced from all available sequences. Importantly, our findings suggest that the true tree is currently inaccessible for most real protein families. Instead, applications that rely on evolutionary models should integrate across many trees that are equally likely to represent the true evolutionary history of a protein family.
Both DNA Polymerases δ and ε Contact Active and Stalled Replication Forks differently
Authors: Yu Chuanhe , Gan Haiyun , Zhang Zhiguo
Published: August 2017

Three DNA polymerases (Pol α, Pol δ, and Pol ε) are responsible for eukaryotic genome duplication. When DNA replication stress is encountered, DNA synthesis stalls until the stress is ameliorated. However, it is not known whether there is a difference in the association of each polymerase with active and stalled replication forks. Here, we show that each DNA polymerase has distinct patterns of association with active and stalled replication forks. Pol α is enriched at extending Okazaki fragments of active and stalled forks. In contrast, although Pol δ contacts the nascent lagging strands of active and stalled forks, it binds to only the matured (and not elongating) Okazaki fragments of stalled forks. Pol ε has a greater contact with the nascent ssDNA of leading strand on active forks compared with stalled forks. We propose that the configuration of DNA polymerases at stalled forks facilitate resumption of DNA synthesis after stress removal.
Heterosis is a systemic property emerging from nonlinear genotype-phenotype relationships: evidence fromin vitrogenetics and computer simulations
Authors: Fiévet Julie B. , Nidelet Thibault , Dillmann Christine , de Vienne Dominique
Published: August 2017

Heterosis, the superiority of hybrids over their parents for quantitative traits, represents a crucial issue in plant and animal breeding. Heterosis has given rise to countless genetic, genomic and molecular studies, but has rarely been investigated from the point of view of systems biology. We hypothesized that heterosis is an emergent property of living systems resulting from frequent concave relationships between genotypic variables and phenotypes, or between different phenotypic levels. We chose the enzyme-flux relationship as a model of the concave genotype-phenotype (GP) relationship, and showed that heterosis can be easily created in the laboratory. First, we reconstitutedin vitrothe upper part of glycolysis. We simulated genetic variability of enzyme activity by varying enzyme concentrations in test tubes. Mixing the content of “parental” tubes resulted in “hybrids”, whose fluxes were compared to the parental fluxes. Frequent heterotic fluxes were observed, under conditions that were determined analytically and confirmed by computer simulation. Second, to test this model in a more realistic situation, we modeled the glycolysis/fermentation network in yeast by considering one input flux, glucose, and two output fluxes, glycerol and acetaldehyde. We simulated genetic variability by randomly drawing parental enzyme concentrations under various conditions, and computed the parental and hybrid fluxes using a system of differential equations. Again we found that a majority of hybrids exhibited positive heterosis for metabolic fluxes. Cases of negative heterosis were due to local convexity between certain enzyme concentrations and fluxes. In both approaches, heterosis was maximized when the parents were phenotypically closeandwhen the distributions of parental enzyme concentrations were contrasted and constrained. These conclusions are not restricted to metabolic systems: they only depend on the concavity of the GP relationship, which is commonly observed at various levels of the phenotypic hierarchy, and could account for the pervasiveness of heterosis.
The Validity of the Coalescent Approximation for Large Samples
Authors: Melfi Andrew , Viswanath Divakar
Published: August 2017

The Kingman coalescent, widely used in genetics, is known to be a good approximation when the sample size is small relative to the population size. In this article, we investigate how large the sample size can get without violating the coalescent approximation. If the haploid population size is 2N, we prove that for samples of sizeN1/3−ϵ,ϵ> 0, coalescence under the Wright-Fisher (WF) model converges in probability to the Kingman coalescent in the limit of largeN. For samples of sizeN2/5−ϵor smaller, the WF coalescent converges to a mixture of the Kingman coalescent and what we call the mod-2 coalescent. For samples of sizeN1/2or larger, triple collisions in the WF genealogy of the sample become important. The sample size for which the probability of conformance with the Kingman coalescent is 95% is found to be 1.47 ×N0.31forN∈ [103, 105], showing the pertinence of the asymptotic theory. The probability of no triple collisions is found to be 95% for sample sizes equal to 0.92 ×N0.49, which too is in accord with the asymptotic theory.

Varying population sizes are handled using algorithms that calculate the probability of WF coalescence agreeing with the Kingman model or taking place without triple collisions. For a sample of size 100, the probabilities of coalescence according to the Kingman model are 2%, 0%, 1%, and 0% in four models of human population with constantN, constantNexcept for two bottlenecks, recent exponential growth, and increasing recent exponential growth, respectively. For the same four demographic models and the same sample size, the probabilities of coalescence with no triple collision are 92%, 73%, 88%, and 87%, respectively. Visualizations of the algorithm show that even distant bottlenecks can impede agreement between the coalescent and the WF model.

Finally, we prove that the WF sample frequency spectrum for samples of sizeN1/3−ϵor smaller converges to the classical answer for the coalescent.
Human placental syncytiotrophoblasts restrictToxoplasma gondiivertical transmission at two distinct stages and induce CCL22 in response to infection
Authors: Ander Stephanie E. , Rudzki Elizabeth N. , Arora Nitin , Sadovsky Yoel , Coyne Carolyn B. , Boyle Jon P.
Published: August 2017

Toxoplasma gondiiis a major source of congenital disease worldwide, but the cellular and molecular factors associated with its vertical transmission are largely unknown. In humans, the placenta forms the key interface between the maternal and fetal compartments and forms the primary barrier that restricts the hematogenous spread of microorganisms. Here, we utilized primary human trophoblast (PHT) cells isolated from full-term placentas and human mid-gestation chorionic villous explants to determine the mechanisms by which human trophoblasts restrict and respond toT. gondiiinfection. We show that placental syncytiotrophoblasts, multinucleated cells that are in direct contact with maternal blood, restrictT. gondiiinfection at distinct stages of the parasite lytic cycle—at the time of attachment and also during intracellular replication. Utilizing comparative RNAseq transcriptional profiling, we also show that human placental trophoblasts at both mid- and late-stages of gestation induce the chemokine CCL22 in response toT. gondiiinfection, which relies on the secretion of parasite effector(s). Collectively, our findings provide new insights into the mechanisms by which the human placenta restricts the vertical transmission ofT. gondiiat early and late stages of human pregnancy, and demonstrate the existence of at least two interferon-independent pathways that restrictT. gondiiaccess to the fetal compartment.

Significance statement

Toxoplasma gondiiis a major source of congenital disease worldwide and must breach the placental barrier to be transmitted from maternal blood to the developing fetus. The events associated with the vertical transmission of T. gondii are largely unknown. Here, we show that primary human syncytiotrophoblasts, the fetal-derived cells that comprise the primary placental barrier, restrictT. gondiiinfection at two distinct stages of the parasite life cycle and respond to infection through the induction of the chemokine CCL22. Collectively, our findings provide important insights into the mechanisms by which human syncytiotrophoblasts restrictT. gondiiinfection at early and late stages of human pregnancy and identify the placental-enriched signaling pathways induced in response to infection.
A synthetic integral feedback controller for robust tunable regulation in bacteria
Authors: Lillacci Gabriele , Aoki Stephanie , Schweingruber David , Khammash Mustafa
Published: August 2017

We report on the first engineered integral feedback control system in a living cell. The controller is based on the recently published antithetic integral feedback motif [1] which has been analytically shown to have favorable regulation properties. It is implemented along with test circuitry inEscherichia coliusing seven genes and three small-molecule inducers. The closed-loop system is highly tunable, allowing a regulated protein of interest to be driven to a desired level and maintained there with precision. Realized using a sigma/anti-sigma protein pair, the integral controller ensures that regulation is maintained in the face of perturbations that lead to the regulated protein’s degradation, thus serving as a proof-of-concept prototype of integral feedback implementation in living cells. When suitably optimized, this integral controller may be utilized as a general-purpose robust regulator for genetic circuits with unknown or partially-known topologies and parameters.
Transferring and Generalizing Deep-Learning-based Neural Encoding Models across Subjects
Authors: Wen Haiguang , Shi Junxing , Chen Wei , Liu Zhongming
Published: August 2017

Recent studies have shown the value of using deep learning models for mapping and characterizing how the brain represents and organizes information for natural vision. However, modeling the relationship between deep learning models and the brain (or encoding models), requires measuring cortical responses to large and diverse sets of natural visual stimuli from single subjects. This requirement limits prior studies to few subjects, making it difficult to generalize findings across subjects or for a population. In this study, we developed new methods to transfer and generalize encoding models across subjects. To train encoding models specific to a subject, the models trained for other subjects were used as the prior models and were refined efficiently using Bayesian inference with a limited amount of data from the specific subject. To train encoding models for a population, the models were progressively trained and updated with incremental data from different subjects. For the proof of principle, we applied these methods to functional magnetic resonance imaging (fMRI) data from three subjects watching tens of hours of naturalistic videos, while deep residual neural network driven by image recognition was used to model the visual cortical processing. Results demonstrate that the methods developed herein provide an efficient and effective strategy to establish subject-specific or populationwide predictive models of cortical representations of high-dimensional and hierarchical visual features.
Cool Enough for School: Second Version of Google Glass Rated by Children Facing Challenges to Social Integration as Desirable to Wear at School
Authors: Sahin Ned T. , Keshav Neha U. , Salisbury Joseph P. , Vahabzadeh Arshya
Published: August 2017

Background

On July 18th, 2017, X, a subsidiary of Alphabet Inc. announced the successor to Google Glass. Glass Enterprise Edition could function as an assistive technology for autism spectrum disorder (ASD), yet its acceptability, desirability, and the willingness of children with ASD to wear it, are not known. The authors review key issues surrounding smartglasses and social communication, child development, and the school environment.

Methods

The smartglasses were evaluated by eight children with ASD, who ranged from moderately non-verbal to verbal, in the context of whether they would desire to wear it and use it as an assistive device each day at their respective schools. Children represented the full range of school ages (6 – 17yrs).

Results

All eight children responded that they would want to wear and use Glass Enterprise Edition at school. Additionally, all eight parents said their child had fun during the testing session, and six of eight parents said the experience went better than they had thought.

Conclusion

The results show that children with ASD are willing to use Glass Enterprise Edition in a school setting, highlighting its desirability and social acceptability in this population, as well as its future potential as an assistive technology.
Targeting posttranslational modifications of RioK1 inhibits the progression of colorectal and gastric cancers
Authors: Hong Xuehui , Huang He , Ding Zhijie , Feng Xing , Zhu Yuekun , Zhuo Huiqin , Hou Jingjing , Cai Wangyu , Hong Xinya , Song Hongjiang , Zhang Zhiyong
Published: August 2017

RioK1 has recently been shown to play important roles in cancers, but its posttranslational regulation is largely unknown. Here we report that RioK1 is methylated at K411 by SETD7 methyltransferase, and that lysine-specific demethylase 1 (LSD1) reverses its methylation. The mutated RioK1 (K411R) that cannot be methylated exhibits a longer half-life than does the methylated RioK1. FBXO6 specifically interacts with K411-methylated RioK1 through its FBA domain to induce RioK1 ubiquitination. Casein kinase 2 (CK2) phosphorylates RioK1 at T410, which stabilizes RioK1 by antagonizing K411 methylation and impeding the recruitment of FBXO6 to RioK1. Functional experiments demonstrate the RioK1 methylation reduces the tumor growth and metastasis in CRC and GC. Importantly, the protein levels of CK2 and LSD1 show an inverse correlation with FBXO6 and SETD7 expression in human CRC tissues. Therefore, this study highlights the importance of a RioK1 methylation-phosphorylation switch in determining CRC and GC development.
Role of duplicate genes in determining the tissue-selectivity of hereditary diseases
Authors: Barshir Ruth , Hekselman Idan , Shemesh Netta , Sharon Moran , Novack Lena , Yeger-Lotem Esti
Published: August 2017

A longstanding puzzle in human genetics is what limits the clinical manifestation of hundreds of hereditary diseases to certain tissues or cell types, while their causal genes are present and expressed throughout the human body. Here we considered a possible role for paralogs of causal genes in affecting this tissue selectivity. It has been shown across organisms that paralogs can compensate for the loss of each other. We hypothesized that specifically in the disease tissue causal genes and their paralogs are imbalanced, leading to insufficient compensation and to the emergence of disease phenotypes. While demonstrated previously in the context of few specific diseases, this hypothesis was never assessed quantitatively at large-scale. For this, we analyzed functional relationships between causal genes and their paralogs associated with 112 tissue-selective hereditary diseases. To test our hypothesis we used several large-scale omics datasets, including RNA sequencing profiles of over 30 different human tissues. Indeed, the expression of causal genes and their paralogs was significantly imbalanced in their disease tissues compared to unaffected tissues. Imbalanced expression was evident across different disease tissues, and was common to causal genes with single or multiple paralogs. This imbalance was driven by significant upregulation of the causal gene in its disease tissue, often combined with significant down-regulation of a paralog. Nevertheless, in additional 20% of the causal genes, a paralog alone was significantly down-regulated in the disease tissue. Our results suggest that dosage relationships between paralogs affect the phenotypic outcome of germline aberrations, adding paralogs as important modifiers of disease manifestation.
An algorithm for template-based prediction of secondary structures of individual RNA sequences
Authors: Pánek Josef , Černý Martin
Published: August 2017

While understanding the structure of RNA molecules is vital for deciphering their functions, determining RNA structures experimentally is exceptionally hard. At the same time, extant approaches to computational RNA structure prediction have limited applicability and reliability. In this paper we provide a method to solve a simpler yet still biologically relevant problem: prediction of secondary RNA structure using structure of different molecules as a template.

Our method identifies conserved and unconserved subsequences within an RNA molecule. For conserved subsequences, the template structure is directly transferred into the generated structure and combined with de-novo predicted structure for the unconserved subsequences with low evolutionary conservation. The method also determines, when the generated structure is unreliable.

The method is validated using experimentally identified structures. The accuracy of the method exceeds that of classical prediction algorithms and constrained prediction methods. This is demonstrated by comparison using large number of heterogeneous RNAs. The presented method is fast and robust, and useful for various applications requiring knowledge of secondary structures of individual RNA sequences.
A ticket to ride - Allele delivery by rail in secondary ruderal colonization byArabidopsis arenosa
Authors: Baduel Pierre , Hunter Ben , Yeola Sarang , Bomblies Kirsten
Published: August 2017

Human-generated ruderal habitats are abundant, but challenging for plants. Some ruderal habitats, however, provide networked corridors (e.g. roadsides and railways) that can facilitate rapid long-distance spread of successfully adapted variants. Here we use transcriptomic and genomic analyses, coupled with genetic mapping and transgenics to understand adaptation to railways inArabidopsis arenosa. We show normally perennialA.arenosaswitched to rapid cycling, a common adaptation for ruderal plants, at least twice upon railway colonization. We further show substantial gene flow from a widely distributed railway colonist likely contributed to secondary colonization by a non-ruderal type, highlighting how connectivity can affect adaptability. We find loss of expression of the reproductive repressorFLOWERING LOCUS C(FLC) is likely primarily responsible for rapid cycling in the widely distributed railway variant. However, a second railway colonist in the Alps also cycles rapidly, but retains highFLC. Some alleles in this population encode non-functional proteins, suggestingFLChas started to decay, but most are functional. Instead, this population likely circumvents FLC via a derived allele ofCONSTANS (CO), which shows strong evidence of selection in this population. Importantly, we find this CO allele arrived via gene flow from the widespread ruderal, where it was also previously under selection. This suggests ruderal adaptation may have been progressive, perhaps in both cases, with FLC-circumvention arising first, and FLC loss arising later but ultimately obscuring its earlier circumvention. These snapshots of railway adaptation highlight that gene flow from widespread ruderals can provide opportunities for subsequent adaptation by local genotypes.
Triple dissociation of attention and decision computations across prefrontal cortex
Authors: Hunt Laurence T. , Malalasekera W. M. Nishantha , de Berker Archy O. , Miranda Bruno , Farmer Simon F. , Behrens Timothy E. J. , Kennerley Steven W.
Published: August 2017

Anatomical, neuroimaging and lesion studies indicate that prefrontal cortex (PFC) can be subdivided into different subregions supporting distinct aspects of decision making. However, explanations of neuronal computations within these subregions varies widely across studies. An integrated and mechanistic account of PFC function therefore remains elusive. Resolving these debates demands a rich dataset that directly contrasts neuronal activity across multiple PFC subregions within a single paradigm, whilst experimentally controlling factors such as the order, duration and frequency in which choice options are attended and compared. Here, we contrast neuronal population responses between macaque orbitofrontal (OFC), anterior cingulate (ACC) and dorsolateral prefrontal cortices (DLPFC) during sequential value-guided information search and choice. From the first fixation of choice-related stimuli, a strong triple dissociation of information encoding emerges in parallel across these PFC subregions. As further information is gathered, population responses in OFC reflect an attention-guided value comparison process. Meanwhile, parallel signals in ACC reflect belief updating in light of new evidence, integration of that evidence to a decision bound, and an emerging action plan for which option should be chosen. Our findings demonstrate the co-existence of multiple, distributed decision-related computations across PFC subregions during value-guided choice. They provide a synthesis of several competing accounts of PFC function.
Endosymbiont diversity and evolution across weevil tree of life
Authors: Zhang Guanyang , Browne Patrick , Zhen Geng , Johnston Andrew , Cadillo-Quiroz Hinsby , Franz Nico
Published: August 2017

As early as the time of Paul Buchner, a pioneer of endosymbionts research, it was shown that weevils host diverse bacterial endosymbionts, probably only second to the hemipteran insects. To date, there is no taxonomically broad survey of endosymbionts in weevils, which preclude any systematic understanding of the diversity and evolution of endosymbionts in this large group of insects, which comprise nearly 7% of described diversity of all insects. We gathered the largest known taxonomic sample of weevils representing four families and 17 subfamilies to perform a study of weevil endosymbionts. We found that the diversity of endosymbionts is exceedingly high, with as many as 44 distinct kinds of endosymbionts detected. We recovered an ancient origin of association ofNardonellawith weevils, dating back to 124 MYA. We found repeated losses of this endosymbionts, but also cophylogeny with weevils. We also investigated patterns of coexistence and coexclusion.
Male-driven reinforcement and cascade reinforcement in darters
Authors: Moran R. L. , Fuller R. C.
Published: August 2017

Reinforcement can act in response to maladaptive hybridization by selecting for increased discrimination against heterospecifics mates in sympatry compared to allopatry (i.e., reproductive character displacement - RCD). Additionally, reinforcement can select for increased discrimination against heterospecifics in a fighting context in sympatry compared to allopatry (i.e., agonistic character displacement - ACD). Because it directly affects conspecific recognition traits (signals and/or preferences), reinforcement between two species in sympatry can incidentally cause behavioral isolation among populations within a species, termed cascade reinforcement. Here we demonstrate that a pattern consistent with male-driven RCD and ACD is present between two groups of darters (orangethroat darter cladeCeasiaand rainbow darterEtheostoma caeruleum). Increased male discrimination against heterospecific females as mates and increased male discrimination against heterospecific males as competitors is present in sympatry. Furthermore, there is a pattern consistent with male-driven cascade RCD and cascade ACD withinCeasia. We found low levels of discrimination between two species ofCeasiathat occur in allopatry from one another and in allopatry withE. caeruleum. This result contrasts that of a recent study which observed high levels of behavioral isolation betweenCeasiaspecies that occurred in sympatry withE. caeruleum. We suggest reinforcement betweenCeasiaandE. caeruleumin sympatry has led to the evolution of behavioral isolation between lineages withinCeasiathat occur in sympatry withE. caeruleumbut in allopatry with respect to one another (i.e., cascade reinforcement). This study demonstrates the ability of male behavior to simultaneously drive sympatric and allopatric speciation via reinforcement.
A Tetratricopeptide Repeat Protein Regulates Carotenoid Biosynthesis and Chromoplast Development in Monkeyflowers (Mimulus)
Authors: Stanley Lauren E. , Ding Baoqing , Sun Wei , Mou Fengjuan , Hill Connor , Chen Shilin , Yuan Yao-Wu
Published: August 2017

The incredible diversity of floral color and pattern in nature is largely determined by the transcriptional regulation of anthocyanin and carotenoid biosynthetic genes. While the transcriptional control of anthocyanin biosynthesis is well understood, little is known about the factors regulating the carotenoid biosynthetic pathway in flowers. Here, we characterize theReduced Carotenoid Pigmentation 2(RCP2) locus from two monkeyflower (Mimulus) species, the bumblebee-pollinatedM. lewisiiand hummingbird-pollinatedM. verbenaceus. We show that loss-of-function mutations ofRCP2cause drastic down-regulation of the entire carotenoid biosynthetic pathway in these species. Through bulk segregant analysis and transgenic experiments, we have identified the causal gene underlyingRCP2, encoding a tetratricopeptide repeat (TPR) protein that is closely related to theArabidopsisReduced Chloroplast Coverage (REC) proteins. RCP2 appears to regulate carotenoid biosynthesis independently of RCP1, a previously identified R2R3-MYB master regulator of carotenoid biosynthesis. We show that RCP2 is required for chromoplast development and suggest that it most likely regulates the expression of carotenoid biosynthetic genes through chromoplast-to-nucleus retrograde signaling. Furthermore, we demonstrate thatM. verbenaceusis just as amenable to chemical mutagenesis andin plantatransformation as the more extensively studiedM. lewisii, making these two species an excellent platform for comparative developmental genetics studies of two closely related species with dramatic phenotypic divergence.
Weak interactions between groups and physical drivers of community dynamics in coastal phytoplankton
Authors: Barraquand F. , Picoche C. , Maurer D. , Carassou L. , Auby I.
Published: August 2017

Phytoplanktonic communities maintain a high diversity in a seemingly homogeneous environment, competing for the same set of resources. Many theories have been proposed to explain this coexistence despite likely competition, such as contrasted responses to temporal environmental variation. However, theory has developed at a faster pace than its empirical evaluation using field data, that requires to infer biotic and abiotic drivers of community dynamics from observational time series. Here, we combine autoregressive models with a data set spanning more than 20 years of biweekly plankton counts and abiotic variables, including nutrients and physical variables. By comparing models dominated by nutrients or physical variables (hydrodynamics and climate), we first explore which abiotic factors contribute more to phytoplankton growth and decline. We find that physical drivers - such as irradiance, wind, and salinity - explain some of the variability in abundances unexplained by biotic interactions. In contrast, responses to nutrients explain less of phytoplankton variability. Concerning biotic drivers of community dynamics, multivariate autoregressive models reveal that competition between different groups (at the genus level for most) has a much weaker effect on population growth rates than competition within a group. In fact, the few biotic interactions between genera that are detected are frequently positive. Hence, our system is unlikely to be best represented as a set of competitors whose differing responses to fluctuating environments allow coexistence, as in “paradox of the plankton” models with a storage effect or a relative nonlinearity of competition. Coexistence is more likely to result from stabilizing niche differences, manifested through high intragroup density-dependence. Competition between planktonic groups and nutrients are often invoked as drivers of phytoplankton dynamics; our findings suggest instead that more attention should be given to the physical structure of the environment and natural enemies, for coastal phytoplankton at least.
How Many Females Are There? Cheating and Female Dispersion Can Explain Mating Behavior Evolution
Authors: Gomes B. V. , Guimarães D. M. , Szczupak D. , Neves K.
Published: August 2017

Only around 3% of all mammalian species are socially monogamous and the conditions that favor the evolution of this mating system in mammals are not well understood. With several approaches, studies have proposed different hypotheses relating female dispersion and infanticide as drivers for the evolution of social monogamy. Here, we used an agent-based model, that allowed us to examine how different mating behaviors affect populations in a controlled computational environment. We found that the evolution of social monogamy does not rely on a single factor. Rather, our experimental results support an interplay of different factors in the evolution of social monogamy – female dispersion and availability and breeding season duration – and suggests that polygamy will only evolve in populations with a female-biased operational sex ratio or one where cheating is common. These results can explain why social monogamy is so uncommon in mammals and points to new lines for ethological investigation of mammalian behavior.
Approaches to crystal structure landscape exploration
Authors: Desiraju Gautam R.
Published: August 2017

Three approaches to the exploration of the crystal structure landscape are outlined. These are crystal structure prediction, non-ambient crystallography and charge density analysis.
Wind climate parameters, performance and reliability assessment of wind energy farm
Authors: Hulio Zahid Hussain , Jiang Wei
Published: August 2017

Purpose

The purpose of this paper is to analyze wind climate parameters and performance functions, on the basis of two years of data, and reliability of Pakistan’s first wind farm located at Jhimpir, Sindh.

Design/methodology/approach

The methodology covers assessment of wind climate parameters including wind variation at different hub heights, wind shear and diurnal wind shear. In addition, a performance assessment of a wind farm on the basis of technical and real availability, capacity factor and failure rate of mechanical and electrical components has been conducted. The Weibull method has been used for reliability analysis. The maintenance model is proposed for improving the performance. Last is about annual energy volume lost and of financial constraints’ assessment.

Findings

The monthly mean wind variation at heights of 80, 60 and 30 m was found to be 8, 6.9 and 5.9 m/s, respectively. The monthly mean wind shear coefficient was found to be 0.2419. The performance assessment of the wind farm includes technical and real availability, and the capacity factor was found to be 97, 90 and 35.5 per cent, respectively. The failure rate found in the first and second year was 8 and 14 per cent, respectively. Reliability decreased from the first year to the second year, i.e. 0.89 to 0.71 per cent. The components’ failure frequency rose to 57.2 per cent in the second year. The lost energy production due to electrical and mechanical failures was 27.241 GWh in two years that cost Pakistani Rs. 329.8m.

Originality/value

The results of the assessment show that a wind farm needs drastic maintenance strategies to maximize the its performance.
Contextual determinants in disclosing one’s stigmatized identity during expatriation
Authors: Kim Kowoon , Von Glinow Mary Ann
Published: August 2017

Purpose

The purpose of this paper is to add to the understanding of the international work experiences of lesbian and gay self-initiated expatriates (SIEs) with a particular focus on the effects of different contexts on their disclosure decisions. In doing so, this study responds to the call for more empirical and extensive studies of lesbian, gay, bisexual, and transgender (LGBT) expatriates.

Design/methodology/approach

This paper is based on in-depth analysis of four interviews of lesbian and gay SIEs.

Findings

The findings presented in this paper support three contextual determinants – personal, organizational, and country-level context. These contextual determinants significantly influence lesbian and gay SIEs’ disclosure decisions and their overall international work experience.

Originality/value

Given the rapid globalization and dynamic business environment, workforce diversity has become a business imperative over the past few decades. Diversity in today’s workforce includes not simply gender and racial diversity, but also age, culture, sexual orientation, religion, education, and disabilities as primary categories of diversity. Moreover, new technologies require highly skilled labor the world over, exacerbating existing global talent shortages. These advancements in technology, accompanied by massive shortfalls in skilled labor, have expanded the pool of potential expatriates to include those non-traditional ones who have been excluded from international assignments. Particularly, as LGBT rights to equal employment opportunity and their potential contributions to international assignments have been increasingly recognized worldwide in recent years, attention to LGBT expatriates has grown exponentially. Nevertheless, neither their experiences as lesbian and gay SIEs in international assignments nor the effects of contexts on those experiences, including disclosure decisions, have yet to be fully explored. In this sense, this paper provides a contribution to the deeper understanding of lesbian and gay SIEs in multidimensional contexts of an international assignment. Although the study examined lesbian and gay expatriates, results suggest insights into the entire LGBT expatriate community.