bluuebunny/crossref_metadata_2025_split huggingface dataset:
Origin of animal multicellularity: precursors, causes, consequences—the choanoflagellate/sponge transition, neurogenesis and the Cambrian explosion
Authors: Cavalier-Smith Thomas 
Published: December 2016

Evolving multicellularity is easy, especially in phototrophs and osmotrophs whose multicells feed like unicells. Evolving animals was much harder and unique; probably only one pathway via benthic ‘zoophytes’ with pelagic ciliated larvae allowed trophic continuity from phagocytic protozoa to gut-endowed animals. Choanoflagellate protozoa produced sponges. Converting sponge flask cells mediating larval settling to synaptically controlled nematocysts arguably made Cnidaria. I replace Haeckel's gastraea theory by a sponge/coelenterate/bilaterian pathway: Placozoa, hydrozoan diploblasty and ctenophores were secondary; stem anthozoan developmental mutations arguably independently generated coelomate bilateria and ctenophores. I emphasize animal origin's conceptual aspects (selective, developmental) related to feeding modes, cell structure, phylogeny of related protozoa, sequence evidence, ecology and palaeontology. Epithelia and connective tissue could evolve only by compensating for dramatically lower feeding efficiency that differentiation into non-choanocytes entails. Consequentially, larger bodies enabled filtering more water for bacterial food and harbouring photosynthetic bacteria, together adding more food than cell differentiation sacrificed. A hypothetical presponge of sessile triploblastic sheets (connective tissue sandwiched between two choanocyte epithelia) evolved oogamy through selection for larger dispersive ciliated larvae to accelerate benthic trophic competence and overgrowing protozoan competitors. Extinct Vendozoa might be elaborations of this organismal grade with choanocyte-bearing epithelia, before poriferan water channels and cnidarian gut/nematocysts/synapses evolved.This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
Cranial shape evolution in adaptive radiations of birds: comparative morphometrics of Darwin's finches and Hawaiian honeycreepers
Authors: Tokita Masayoshi , Yano Wataru , James Helen F. , Abzhanov Arhat 
Published: December 2016

Adaptive radiation is the rapid evolution of morphologically and ecologically diverse species from a single ancestor. The two classic examples of adaptive radiation are Darwin's finches and the Hawaiian honeycreepers, which evolved remarkable levels of adaptive cranial morphological variation. To gain new insights into the nature of their diversification, we performed comparative three-dimensional geometric morphometric analyses based on X-ray microcomputed tomography (µCT) scanning of dried cranial skeletons. We show that cranial shapes in both Hawaiian honeycreepers and Coerebinae (Darwin's finches and their close relatives) are much more diverse than in their respective outgroups, but Hawaiian honeycreepers as a group display the highest diversity and disparity of all other bird groups studied. We also report a significant contribution of allometry to skull shape variation, and distinct patterns of evolutionary change in skull morphology in the two lineages of songbirds that underwent adaptive radiation on oceanic islands. These findings help to better understand the nature of adaptive radiations in general and provide a foundation for future investigations on the developmental and molecular mechanisms underlying diversification of these morphologically distinguished groups of birds.This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
Major evolutionary transitions and innovations: the tympanic middle ear
Authors: Tucker Abigail S. 
Published: December 2016

One of the most amazing transitions and innovations during the evolution of mammals was the formation of a novel jaw joint and the incorporation of the original jaw joint into the middle ear to create the unique mammalian three bone/ossicle ear. In this review, we look at the key steps that led to this change and other unusual features of the middle ear and how developmental biology has been providing an understanding of the mechanisms involved. This starts with an overview of the tympanic (air-filled) middle ear, and how the ear drum (tympanic membrane) and the cavity itself form during development in amniotes. This is followed by an investigation of how the ear is connected to the pharynx and the relationship of the ear to the bony bulla in which it sits. Finally, the novel mammalian jaw joint and versatile dentary bone will be discussed with respect to evolution of the mammalian middle ear.This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
Human evolution: a tale from ancient genomes
Authors: Llamas Bastien , Willerslev Eske , Orlando Ludovic 
Published: December 2016

The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history.
This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
Waiting in the wings: what can we learn about gene co-option from the diversification of butterfly wing patterns?
Authors: Jiggins Chris D. , Wallbank Richard W. R. , Hanly Joseph J. 
Published: December 2016

A major challenge is to understand how conserved gene regulatory networks control the wonderful diversity of form that we see among animals and plants. Butterfly wing patterns are an excellent example of this diversity. Butterfly wings form as imaginal discs in the caterpillar and are constructed by a gene regulatory network, much of which is conserved across the holometabolous insects. Recent work inHeliconiusbutterflies takes advantage of genomic approaches and offers insights into how the diversification of wing patterns is overlaid onto this conserved network. WntA is a patterning morphogen that alters spatial information in the wing. Optix is a transcription factor that acts later in development to paint specific wing regions red. Both of these loci fit the paradigm of conserved protein-coding loci with diverse regulatory elements and developmental roles that have taken on novel derived functions in patterning wings. These discoveries offer insights into the ‘Nymphalid Ground Plan’, which offers a unifying hypothesis for pattern formation across nymphalid butterflies. These loci also represent ‘hotspots’ for morphological change that have been targeted repeatedly during evolution. Both convergent and divergent evolution of a great diversity of patterns is controlled by complex alleles at just a few genes. We suggest that evolutionary change has become focused on one or a few genetic loci for two reasons. First, pre-existing complexcis-regulatory loci that already interact with potentially relevant transcription factors are more likely to acquire novel functions in wing patterning. Second, the shape of wing regulatory networks may constrain evolutionary change to one or a few loci. Overall, genomic approaches that have identified wing patterning loci in these butterflies offer broad insight into how gene regulatory networks evolve to produce diversity.This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
The genetic and molecular architecture of phenotypic diversity in sticklebacks
Authors: Peichel Catherine L. , Marques David A. 
Published: December 2016

A major goal of evolutionary biology is to identify the genotypes and phenotypes that underlie adaptation to divergent environments. Stickleback fish, including the threespine stickleback (Gasterosteus aculeatus) and the ninespine stickleback (Pungitius pungitius), have been at the forefront of research to uncover the genetic and molecular architecture that underlies phenotypic diversity and adaptation. A wealth of quantitative trait locus (QTL) mapping studies in sticklebacks have provided insight into long-standing questions about the distribution of effect sizes during adaptation as well as the role of genetic linkage in facilitating adaptation. These QTL mapping studies have also provided a basis for the identification of the genes that underlie phenotypic diversity. These data have revealed that mutations in regulatory elements play an important role in the evolution of phenotypic diversity in sticklebacks. Genetic and molecular studies in sticklebacks have also led to new insights on the genetic basis of repeated evolution and suggest that the same loci are involved about half of the time when the same phenotypes evolve independently. When the same locus is involved, selection on standing variation and repeated mutation of the same genes have both contributed to the evolution of similar phenotypes in independent populations.This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
Diatom Centromeres Suggest a Novel Mechanism for Nuclear Gene Acquisition
Authors: Diner Rachel E. , Noddings Chari M. , Lian Nathan C. , Kang Anthony K. , McQuaid Jeffrey B. , Jablanovic Jelena , Espinoza Josh L. , Nguyen Ngocquynh A. , Anzelmatti Miguel A. , Jansson Jakob , Bielinski Vincent A. , Karas Bogumil J. , Dupont Christopher L. , Allen Andrew E. , Weyman Philip D. 
Published: December 2016

AbstractCentromeres are essential for cell division and growth in all eukaryotes, and knowledge of their sequence and structure guides the development of artificial chromosomes for functional cellular biology studies. Centromeric proteins are conserved among eukaryotes; however, centromeric DNA sequences are highly variable. We combined forward and reverse genetic approaches with chromatin immunoprecipitation to identify centromeres of the model diatom Phaeodactylum tricornutum. Diatom centromere sequences contain low GC content regions and an abundance of long contiguous AT windows, but lack repeats or other conserved sequence features. Native and foreign sequences of similar GC content can maintain episomes and recruit the diatom centromeric histone protein CENP-A, suggesting non-native sequences can also function as diatom centromeres. Thus, simple sequence requirements enable DNA from foreign sources to incorporate into the nuclear genome repertoire as stable extra-chromosomal episomes, revealing a potential mechanism for bacterial and foreign eukaryotic DNA acquisition.
Control of Lipid Domain Organization by a Biomimetic Contractile Actomyosin Cortex
Authors: Vogel Sven K. , Greiss Ferdinand , Khmelinskaia Alena , Schwille Petra 
Published: December 2016

AbstractThe cell membrane is a heterogeneously organized composite with lipid-protein micro-domains. The contractile actin cortex may govern the lateral organization of these domains in the cell membrane, yet the underlying mechanisms are not known. We recently reconstituted minimal actin cortices (MACs) (Vogel et al, 2013b) and here advanced our assay to investigate effects of rearranging actin filaments on the lateral membrane organization by introducing various phase-separated lipid mono-and bilayers to the MACs. The addition of actin filaments reorganized membrane domains. We found that the process reached a steady state where line tension and lateral crowding balanced. Moreover, the phase boundary allowed myosin driven actin filament rearrangements to actively move individual lipid domains, often accompanied by their shape change, fusion or splitting. Our findings illustrate how actin cortex remodeling in cells may control dynamic rearrangements of lipids and other molecules inside domains without directly binding to actin filaments.
The correlation between central and peripheral oxytocin concentrations: a systematic review and meta-analysis
Authors: Valstad Mathias , Alvares Gail A. , Egknud Maiken , Matziorinis Anna Maria , Andreassen Ole A. , Westlye Lars T. , Quintana Daniel S. 
Published: December 2016

AbstractThere is growing interest in the role of the oxytocin system in social cognition and behavior. Peripheral oxytocin concentrations are regularly used to approximate central concentrations in psychiatric research. This methodological approach has obvious appeal given the invasiveness of cerebrospinal fluid collection. However, the validity of this approach and potential moderators of the association between central and peripheral levels are unclear. Thus, we conducted a pre-registered systematic search and meta-analysis of correlations between central and peripheral oxytocin concentrations. A search of databases yielded 17 eligible studies for effect size synthesis and moderator analysis, resulting in a total sample size of 516 participants and subjects. Overall, a positive association between central and peripheral oxytocin concentrations was revealed [r=0.29, 95% CI (0.15, 0.42), p<0.0001], along with a moderate-to-high level of heterogeneity across effect sizes [Q=88.14, p<0.0001], and no evidence of publication bias (p=0.45). This association was significantly moderated by experimental context [Qb(4), p=0.0016]. The strongest association was observed after intranasal oxytocin administration (r=0.67,p<.0001), a correlation that was significantly greater (p=.0002) than the equivalent association under baseline conditions (r=0.08,p=.31). These results support the use of peripheral levels of oxytocin as a marker of central levels, but only after exogenous oxytocin administration. Despite the popularity of using peripheral OT levels to approximate central levels during baseline conditions, this approach is not supported by the present results.
Regulation of eIF4F complex by the peptidyl prolyl isomerase FKBP7 in taxane-resistant prostate cancer
Authors: Garrido Marine F. , Martin Nicolas J-P. , Gaudin Catherine , Commo Frédéric , AL Nakouzi Nader , Fazli Ladan , Del Nery Elaine , Camonis Jacques , Perez Franck , Lerondel Stéphanie , LE Pape Alain , Abou-Hamdan Hussein , Gleave Martin , Loriot Yohann , Désaubry Laurent , Vagner Stephan , Fizazi Karim , Chauchereau Anne 
Published: December 2016

ABSTRACTTargeted therapies that exploit the signaling pathways involved in prostate cancer are required to overcome chemoresistance and improve treatment outcomes for men. Molecular chaperones play a key role in the regulation of protein homeostasis and are potential targets to alleviate chemoresistance. Using image-based high content siRNA functional screening based on a gene expression signature, we identified FKBP7, a molecular chaperone overexpressed in docetaxel-resistant and in cabazitaxel-resistant prostate cancer cells. FKBP7 was upregulated in human prostate cancers and correlated with the recurrence in patients receiving Docetaxel.FKBP7silencing showed that FKBP7 is required to maintain the growth of chemoresistant cell lines and of chemoresistant tumors in mice. Mass spectrometry analysis revealed that FKBP7 interacts with the eIF4G component of the eIF4F translation initiation complex to mediate survival of chemoresistant cells. Using small molecule inhibitors of eIF4A, the RNA helicase component of eIF4F, we were able to overcome docetaxel and cabazitaxel resistance.
Magnetic resonance imaging findings of central nervous system in lysosomal storage diseases: A pictorial review
Authors: Fagan Nathan , Alexander Allen , Irani Neville , Saade Charbel , Naffaa Lena 
Published: December 2016

SummaryLysosomal storage diseases (LSD) are a complex group of genetic disorders that are a result of inborn errors of metabolism. These errors result in a variety of metabolic dysfunction and build‐up certain molecules within the tissues of the central nervous system (CNS). Although, they have discrete enzymatic deficiencies, symptomology and CNS imaging findings can overlap with each other, which can become challenging to radiologists. The purpose of this paper is to review the most common CNS imaging findings in LSD in order to familiarize the radiologist with their imaging findings and help narrow down the differential diagnosis.
Quantifying spatial variation in the size and structure of ecologically stratified communities
Authors: Tenan Simone , Brambilla Mattia , Pedrini Paolo , Sutherland Chris 
Published: December 2016

Summary

Including ecological specialization (e.g. functional guild) in analyses performed across regions can help to study how size and structure of communities vary across environmental gradients. Multi‐species occupancy models, and their extension to a multi‐region framework, represent useful tools for such gradient analysis based on functional traits. However, in these models species richness is only a derived parameter and therefore explicit relationships cannot be inferred.

We provide a novel hierarchical multi‐region community model that allows for direct modelling of trait‐based patterns of species richness along environmental gradients by partitioning communities into ecologically relevant strata (e.g. guilds). We illustrate the flexibility of the model by simulations, where we estimate guild richness and community composition using both categorical and continuous species traits. In addition, we apply our model to data from eight avian communities to explore how guild richness varies across elevational gradients.

Simulations indicate that the model is able to estimate relationships between guild richness and environmental gradients even when the number of regions is low. Applying the model to the bird community data set, we show how the number of species in four feeding guilds varies in different ways across an elevational gradient.

Understanding large scale variation in species richness and how it relates to environmental gradients requires an explicit treatment of community structure. Our modelling approach allows the testing of hypotheses directly and simultaneously on strata‐ and community‐specific species richness while accounting for the issues of rarity and detectability, and can be used to investigate the mechanisms which shape large scale spatial variation in species richness.
Developmental Trends in Flexibility and Automaticity of Social Cognition
Authors: Hayward Elizabeth O. , Homer Bruce D. , Sprung Manuel 
Published: December 2016

Age‐related changes in flexibility and automaticity of reasoning about social situations were investigated. Children (N = 101; age range = 7;8–17;7) were presented with the flexibility and automaticity of social cognition (FASC), a new measure of social cognition in which cartoon vignettes of social situations are presented and participants explain what is happening and why. Scenarios vary on whether the scenario is socially ambiguous and whether or not language is used. Flexibility is determined by the number of unique, plausible explanations, and automaticity is indicated by speed of response. Overall, both flexibility and automaticity increased significantly with age. Language and social ambiguity influenced performance. Future work should investigate differences in FASC in older populations and clinical groups.
Interaction of primary human trabecular meshwork cells with metal alloy candidates for microinvasive glaucoma surgery
Authors: Wang Wan Wendy , Watson Kelsey A , Dixon S Jeffrey , Liu Hong , Rizkalla Amin S , Hutnik Cindy ML 
Published: December 2016

AbstractBackgroundMicroinvasive glaucoma surgery (MIGS) is a relatively new addition to the glaucoma treatment paradigm. Small metallic stents are inserted into the trabecular meshwork in order to increase aqueous humour drainage. MIGS procedures are rapidly being adopted owing to a more favourable side effect profile when compared with traditional surgery. Remarkably, this rapid rate of utilization has occurred without any published studies on the effect of metal alloys used in these stents on human trabecular meshwork cells (HTMCs). Therefore, this study aimed to determine the effect of candidate metal alloys for MIGS on HTMC morphology, viability and function.MethodsHuman trabecular meshwork cells were cultured on the surfaces of titanium (polished and sandblasted), a titanium–nickel (nitinol) alloy and glass (as control substratum). Fluorescence imaging was used to assess cell morphology and spreading. A lactate dehydrogenase cytotoxicity assay, cell death detection ELISA, MTT cell viability assay, BrdU cell proliferation assay and fibronectin ELISA were also conducted.ResultsCells cultured on sandblasted titanium exhibited significantly greater spreading than cells cultured on other substrata. In comparison, HTMCs cultured on nitinol displayed poor spreading. Significantly more cell death, by both necrosis and apoptosis, occurred on nitinol than on titanium and glass. Also, cell viability and proliferation were suppressed on nitinol compared with titanium or glass. Finally, HTMCs on both titanium and nitinol produced greater amounts of fibronectin than cells grown on glass.ConclusionsSubstratum topography and metal alloy composition were found to impact morphology, viability and function of primary HTMC cultures.
The influence of collagen membrane and autogenous bone chips on bone augmentation in the anterior maxilla: a preclinical study
Authors: Janner Simone F. M. , Bosshardt Dieter D. , Cochran David L. , Chappuis Vivianne , Huynh‐Ba Guy , Jones Archie A. , Buser Daniel 
Published: December 2016

AbstractObjectivesTo evaluate the effect of a resorbable collagen membrane and autogenous bone chips combined with deproteinized bovine bone mineral (DBBM) on the healing of buccal dehiscence‐type defects.Material and methodsThe second incisors and the first premolars were extracted in the maxilla of eight mongrels. Reduced diameter, bone‐level implants were placed 5 weeks later. Standardized buccal dehiscence‐type defects were created and grafted at implant surgery. According to an allocation algorithm, the graft composition of each of the four maxillary sites was DBBM + membrane (group D + M), autogenous bone chips + DBBM + membrane (group A + D + M), DBBM alone (group D) or autogenous bone chips + DBBM (group A + D). Four animals were sacrificed after 3 weeks of healing and four animals after 12 weeks. Histological and histomorphometric analyses were performed on oro‐facial sections.ResultsThe pattern of bone formation and resorption within the grafted area showed high variability among the same group and healing time. The histomorphometric analysis of the 3‐week specimens showed a positive effect of autogenous bone chips on both implant osseointegration and bone formation into the grafted region (P < 0.05). The presence of the collagen membrane correlated with greater bone formation around the DBBM particles and greater bone formation in the grafted region after 12 weeks of healing (P < 0.05). The oro‐facial width of the augmented region at the level of the implant shoulder was significantly reduced in cases where damage of the protection splints occurred in the first week of healing (P < 0.05).ConclusionsThe addition of autogenous bone chips and the presence of the collagen membrane increased bone formation around DBBM particles. Wound protection from mechanical noxa during early healing may be critical for bone formation within the grafted area.