bluuebunny/crossref_metadata_2025 huggingface dataset:
Reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates
Authors: Marjanović David , Laurin Michel
Published: January 2018

The largest data matrix for phylogeny of early limbed vertebrates (Ruta M, Coates MI. 2007. J. Syst. Palaeont. 5:69–122) has supported controversial hypotheses; e.g., it has recovered Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl hypothesis” on the origin of Lissamphibia (TH) to be one step more parsimonious than the “lepospondyl hypothesis” (LH). Scrutiny of the matrix reveals thousands of suboptimal scores (many clearly due to typographic and similar errors) as well as logically linked (redundant) characters, characters with only one described state, and even cases where taxa were scored after presumed relatives. Moreover, all characters – even obviously continuous ones – were unordered, effects of ontogeny were not sufficiently taken into account, and the authors mostly excluded data published after 2001, even their own. Our revised version – we document and justify all changes – yields much longer trees with a different topology, e.g. monophyletic Caudata, Diadectomorpha and (sometimes) Seymouriamorpha, Ichthyostega more rootward than Acanthostega, Anthracosauria more rootward than Temnospondyli, and the LH, which is 10 steps more parsimonious than the TH and 15 more than the “polyphyly hypothesis” (PH). Bootstrap values, though, are low, and few of the topologies are statistically distinguishable. For another set of analyses, we added 48 OTUs to the original 102. This destabilizes parts of the tree, e.g. the relationships of Anthracosauria and Temnospondyli. However, many of the added taxa have a fully resolved position or nearly so; this concerns the well-known Chroniosaurus (sister to a clade containing Solenodonsaurus, Seymouriamorpha, Diadectomorpha, Amniota and Amphibia), but also isolated lower-jaw material from the Devonian and Carboniferous. Despite the addition of Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton, the difference between LH and TH only shrinks to 9 steps, that between LH and PH to 13 steps. The “lepospondyl” Brachydectes is neither found as sister to Lissamphibia nor in the “microsaur” grade. Bootstrap values plummet, though, and all three hypotheses become statistically indistinguishable at p = 0.05. We then duplicated all analyses after coding all losses of bones as irreversible. Anthracosauria is then consistently placed more rootward than Temnospondyli; given the original taxon sample, the LH is 12 steps shorter than the “temnospondyl hypothesis” and 17 steps shorter than the PH, while the expanded taxon sample makes the LH 10 steps shorter than the TH and only 12 steps shorter than the PH. More robust results could likely be obtained by adding the many characters used in other analyses or discussed in the literature. We discuss phylogeny, approaches to coding, and certain character complexes, in particular the supposed middle ear of temnospondyls.
The acceptability of TV-based game platforms as an instrument to support cognitive evaluation of senior adults at home
Authors: Rivas Costa Carlos , Fernández Iglesias Manuel José , Anido Rifón Luis Eulogio , Gómez Carballa Miguel , Valladares Rodríguez Sonia
Published: January 2018

Introduction: The recent advances in consumer electronics paved the way for new approaches to neurophysiological evaluation at home. More specifically, the computing capabilities of state-of-the-art television sets and media centres may facilitate the introduction of computer-assisted evaluation at home. This approach would help to overcome the drawbacks of traditional pen-and-paper evaluations administered in clinical facilities, as they could be performed in a more comfortable environment, the subject’s home, and they would be more flexible to design complex environments for the evaluation of neuropsychological constructs that are difficult to evaluate through traditional testing. The objective of this work was to obtain some initial evidence about the technical acceptance by senior adults of serious games played at home on the TV set for their cognitive evaluation, and therefore about the convenience of further investigating such approach to cognitive evaluation.

Materials and methods: We developed a collection of games to be deployed on a smart TV environment. These games were tried by a group of senior adults at their homes. Surveys were performed to study the perceived usefulness and perceived ease of use of such technical setting as an instrument for their cognitive evaluation, that is, its technical acceptance. An additional survey was performed 36 months after pilot testing to have an indication about the long-term perceptions about perceived usefulness and perceived ease of use.

Results: More than 90% of participating subjects perceive cognitive games on TV as useful or very useful, and this result correlates with the number of participants perceiving them as easily usable or very easy to use. Besides, these perceptions are fairly stable in time.

Limitations: Although participating users were carefully selected to obtain a representative sample of the Galician population, which in turn is comparable to the population of most rural areas in Europe, a larger and more diverse user sample may be needed to obtain significant results for a wider population profile.

Conclusion: The study confirmed the technical acceptance, that is, the perceived usefulness and perceived ease of use, of the home technical setting introduced as a means of cognitive evaluation. Nevertheless, more research is needed in order to implement serious games in a way that medical community accepts them as a valid, reliable way to perform cognitive evaluations at home.
Potential problems of removing one invasive species at a time: Interactions between invasive vertebrates and unexpected effects of removal programs
Authors: Ballari Sebastián A , Kuebbing Sara E , Nuñez Martin A
Published: January 2018

Although the co-occurrence of nonnative vertebrates is a ubiquitous global phenomenon, the study of interactions between invaders is poorly represented in the literature. Limited understanding of the interactions between co-occurring vertebrates can be problematic for predicting how the removal of only one invasive—a common management scenario—will affect native communities. We suggest a trophic food web framework for predicting the effects of single-species management on native biodiversity. We used a literature search and meta-analysis to assess current understanding of how the removal of one invasive vertebrate affects native biodiversity relative to when two invasives are present. The majority of studies focused on the removal of carnivores, mainly within aquatic systems, which highlights a critical knowledge gap in our understanding of co-occurring invasive vertebrates. We found that removal of one invasive vertebrate caused a significant negative effect on native species compared to when two invasive vertebrates were present. These unexpected results could arise because of the positioning and hierarchy of the co-occurring invasives in food web (e.g. carnivore-carnivore or carnivore-herbivore). We consider that there are important knowledge gaps to determinate the effects of multiple co-existing invaders on native ecosystems, and this information could be precious for management.
Acoustic monitoring indicates a positive relationship between calling frequency and spawning in captive spotted seatrout (Cynoscion nebulosus)
Authors: Montie Eric W , Hoover Matt , Kehrer Chris , Yost Justin , Brenkert Karl , O'Donnell Timothy , Denson Mike R
Published: January 2018

Background: Fish sound production is widespread throughout many families. Agonistic and courtship behaviors are the most common reasons for fish sound production. Yet, there is still some debate on how sound production and spawning are correlated in many soniferous fish species. In the present study, our aim was to determine if a quantitative relationship exists between calling and egg deposition in captive spotted seatrout (Cynoscion nebulosus). This type of data is essential if scientists and managers plan to use acoustic metrics to identify spawning aggregations over large spatial scales and monitor reproductive activity over annual and decadal timeframes.Methods: Wild caught spotted seatrout were held in three laboratory tanks equipped with long-term acoustic loggers (i.e., DSG-Oceans) to record underwater sound throughout an entire, simulated reproductive season. Acoustic monitoring occurred from April 13 to December 19, 2012 for Tank 1 and from April 13 to November 21, 2012 for Tanks 2 and 3. DSG-Oceans were scheduled to record sound for 2 min every 20 min. We enumerated the number of calls, calculated the received sound pressure level (SPL in dB re 1 µPa; between 50 and 2000 Hz) of each 2 min ‘wav file’, and counted the number of eggs every morning in each tank.Results: Spotted seatrout produced three distinct call types characterized as “drums”, “grunts”, and “staccatos”. Spotted seatrout calling increased as the light cycle shifted from 13.5 to 14.5 h of light, and the temperature increased to 27.7oC. Calling began to decrease once the temperature fell below 27.7 oC, and the light cycle shifted to 12 h of light. These captive settings are similar to the amount of daylight and water temperatures observed during the summer, which is the primary spawning period of spotted seatrout. Spotted seatrout exhibited daily patterns of calling. Sound production began once the lights turned off, and calling reached maximum activity approximately 3 h later. Spawning occurred only on evenings in which spotted seatrout were calling. Significantly more calling and higher mean SPLs occurred on evenings in which spawning occurred as compared to evenings in which spawning did not occur. Spawning was more productive when spotted seatrout produced more calls. For all tanks, more calling and higher SPLs were associated with more eggs released by females.Discussion: The fact that more calling and higher SPLs were associated with spawns that were more productive indicates that acoustic metrics can provide quantitative information on spotted seatrout spawning in the wild. These findings will help us to identify spawning aggregations over large spatial scales and monitor the effects of noise pollution, water quality, and climatic changes on reproductive activity using acoustic technology.
Nest site selection and nutritional provision through excreta: a form of parental care in a tropical endogeic earthworm
Authors: Ortiz-Ceballos Angel I. , Pérez-Staples Diana , Pérez-Rodríguez Paulino
Published: January 2018

Nest construction is a common form of parental care in soil organisms. However, it is unknown whether the tropical earthworm Pontoscolex corethrurus selects sites for nest construction when the nutritional quality of the soil is irregular. Here we studied the reproductive behaviour and nest site selection of P. corethrurus. In tridimensional terrariums we evaluated the combined effect of the food quality (soil only = S, soil+grass = G, soil+legume = L) and soil depth (0-9 cm = Shallow, 10-18 cm = Intermediate, 19-27 cm = Deep) in a factorial 32 design. The number and biomass of cocoons, progeny and the production of internal and external excreta were evaluated. The nutritional quality and depth of soil and their interaction had a significant effect on nest site construction and the deposition of internal excreta. P. corethrurus built a higher amount of nests in the S-Intermediate and G-Intermediate treatments while more internal excreta were found in the L-Intermediate treatment. Offspring biomass was positively associated with internal excreta in the S (soil only) and G (soil + grass) treatments. We conclude that P. corethrurus shows parental care when selecting sites for its offspring in the form of nest construction and excreta deposition. Further research is needed on the ecological conditions that favour the evolution of parental care in earthworms according to their ecological category (anecic, endogeic and anecic).
Meta-analysis of published frequencies of the first decade of field-based mortality and seropositivity in avian species affected by West Nile virus in the United States
Authors: Verdugo Claudio , Fuentes Claudio , Long Maureen T
Published: January 2018

A meta-analysis approach was used to extract the frequency of avian seropositivity to West Nile Virus (WNV) (fS) and mortality from WNV (fM) from the literature published between the years 2001-2010. The indices, fS and fM, were used to represent states of resistance (seropositivity with no or limited mortality) and susceptibility in birds (detection of WNV with mortality), respectively. The indices fS and fM were calculated for each species across publications into different taxonomic strata, year, combined time intervals, and geographic location. The data were analyzed by logistic regression to assess the status of WNV infection amongst different avian taxonomic strata and infer changes of WNV infection status over time. Using level of peak viremia as a proxy for host competence among the avian species, the value of the phylogenetic signal was tested by Blomberg´s K after transformation of the branch lengths. Sixty-three publications were used for the final dataset representing studies performed from 1999 to 2008 and published between 2001-2010. Analysis of both fS and fM demonstrated variability in avian responses to WNV across order, family, and species. When the data were analyzed for fS, the families and species of the orders Ciconiiformes, Galliformes, and Columbiformes had significantly higher fS than that of the Passeriformes (P < 0.0001). Within the Passeriformes, the Corvidae and Cardinalidae families had higher fS than any other family. When the data were analyzed for fM, dead Corvidae and Paridae were most likely to test positive for virus. Temporally, a positive trend of increasing fS was detected in several avian species while the American crow (Corvus brachyrhynchos) was the only species with a significant negative trend in fM (P = 0.042). Little to no interaction of geographic location with time was detected within species of birds. A weak but significant phylogenetic signal corresponded to host range, suggesting that the rate of spread of WNV through the avian community was partially dependent of the relatedness of hosts. The meta-data predicted that species within families, and even order, were heterogeneous in their disease susceptibility traits to WNV. The Passeriformes contributed most to this variation. Several trends in various families and orders of birds were observed from which new studies could be pursued. The pooling of data was key in detecting areas where data was lacking and identified aspects of avian responses to WNV could be expanded.
Sequencing and characterization of mitochondrial DNA genome for Brama japonica (Perciformes: Bramidae) with phylogenetic consideration
Authors: Chen Fenfang , Ma Hongyu , Ma Chunyan , Zhang Heng , Zhao Mengdi , Meng Yongyong , Wei Hongqing , Ma Lingbo
Published: January 2018

In the present study, we isolated and characterized the complete mitochondrial genome sequence of Brama japonica by polymerase chain reaction (PCR) amplification and primer-walking sequencing. The complete DNA was 17,009 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a long putative control region. The gene organization and nucleotide composition of complete mitogenome were identical to those of other Bramidae fishes. In contrast, the 12S rRNA gene contained a big poly C structure which was larger than those from other Bramidae species. Of 37 genes, twenty-eight were encoded by heavy strand, while nine were encoded by light strand. Among the 13 protein-coding genes, twelve employed ATG as start codon, while only COI utilized GTG as start codon. In the control region, the terminal associated sequence (TAS), the central and conserved sequence block (CSB-E and CSB-D) and a variable domain (CSB-1, CSB-2 and CSB-3) were identified, while the typical central conserved CSB-F could not be detected in B. japonica. The putative OL region can fold into a conserved secondary structure and the conserved motif (5’-GCCGG-3’) was found at the base of the stem in tRNACys. The overall nucleotide composition of this genome was 26.43% for A, 16.71% for G, 31.35% for C, and 25.50% for T, with a high A+T content of 51.93%. From the NJ phylogenetic tree, we can find that B. japonica was together with other five Bramidae species formed a monophyletic group among 24 species. This work provided a set of useful data for studying on population genetic diversity and molecular evolution in Bramidae and related fish species.
Indolo[2,3-b]quinoline derivatives as novel promising antitumor agents
Authors: Kaczmarek Lukasz , Badowska-Rosłonek Katarzyna , Jaromin Anna , Łuniewski Wojciech , Peczyńska-Czoch Wanda , Sidoryk Katarzyna , Szczepek Wojciech , Wietrzyk Joanna , Zagrodzki Bogdan
Published: January 2018

In the search for novel antineoplastic compounds we have found that four-membered, linear 5,11-dimethyl -5H- indolo[2,3-b]quinoline (DIMIQ) reveals cytostatic activity in vitro and moderate antitumor activity in vivo in mice melanoma B16 as well as leukemias L1210 and P388. Preliminary studies showed that DIMIQ stabilizes DNA-topoisomerase II complex. Some years later indolo[2,3-b]quinoline was found as an alkaloid neocryptolepine in the West African shrub Cryptolepis sanguinolenta. Unfortunately, DIMIQ’s high toxicity, lack of selectivity and very low solubility in aqueous media seriously limit the practical use of this compound as an anticancer drug. Extensive research on the structure-activity relationships of different indolo[2,3-b]quinoline derivatives showed that the position and type of the substituent is conclusive both to the antitumor activity and general toxicity of the compound. These studies led us to discover derivatives of DIMIQ which exhibit very low toxicity against normal cells and are highly toxic against selected human tumors. These derivatives are soluble in water and some of them are able to overcome multidrug resistance in human tumors cells.
Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets
Authors: Rideout Jai Ram , Chase John H , Bolyen Evan , Ackermann Gail , Gonzalez Antonio , Knight Rob , Caporaso J Gregory
Published: January 2018

Bioinformatics software often requires human-generated tabular text files as input and have specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, which is convenient for researchers who are compiling the requisite information because the spreadsheet programs can easily be used on different platforms including laptops and tablets, and because they provide a familiar interface. It is increasingly common for many different researchers to be involved in compiling these data, including study coordinators, clinicians, lab technicians, and bioinformaticians. As a result, many research groups are shifting toward using cloud-based spreadsheet programs, such as Google Sheets, which support concurrent editing of a single spreadsheet by different users working on different platforms. Often most of the researchers who are entering data will not be familiar with the formatting requirements of the bioinformatics programs that will be used, so validating and correcting file formats is often a bottleneck prior to beginning bioinformatics analysis. We present Keemei, a Google Sheets Add-on for validating tabular files used in bioinformatics analyses. Keemei is available free of charge from Google’s Chrome Web Store. Keemei can be installed and run on any web browser supported by Google Sheets. Keemei currently supports validation of two widely used tabular bioinformatics formats, the QIIME sample metadata mapping file format, and the Spatially Referenced Genetic Data (SRGD) format, but is designed to easily support the addition of others. Keemei will save researchers time and frustration by providing a convenient interface for tabular bioinformatics file format validation. By allowing everyone involved with data entry for a project to easily validate their data, it will reduce the validation and formatting bottlenecks that are commonly encountered when human-generated data files are first used with a bioinformatics system. Simplifying the validation of essential tabular data files, such as sample metadata, will reduce common errors and thereby improve the quality and reliability of research outcomes.
The wings before the bird: an evaluation of flapping-based locomotory hypotheses in bird antecedents
Authors: Dececchi T. Alexander , Larsson Hans CE , Habib Michael B
Published: January 2018

Background. Powered flight is implicated as a major driver for the success of birds. Here we examine the effectiveness of three hypothesized pathways for the evolution of the flight stroke, the forelimb motion that powers aerial locomotion, in a terrestrial setting across a range of stem and basal avians: flap running, Wing Assisted Incline Running (WAIR), and wing-assisted leaping. Methods. Using biomechanical mathematical models based on known aerodynamic principals and in vivo experiments and ground trothed using extant avians we seek to test if an incipient flight stroke may have contributed sufficient force to permit flap running, WAIR, or leaping takeoff along the phylogenetic lineage from Coelurosauria to birds. Results. None of these behaviours were found to meet the biomechancial threshold requirements before Paraves. Neither was there a continuous trend of refinement for any of these biomechanical performances across phylogeny nor a signal of universal applicability near the origin of birds. None of these flap-based locomotory models appear to have been a major influence on pre-flight character acquisition such as pennaceous feathers, suggesting non-locomotory behaviours, and less stringent locomotory behaviours such as balancing and braking, played a role in the evolution of the maniraptoran wing and nascent flight stroke. We find no support for widespread prevalence of WAIR in non-avian theropods, but can’t reject its presence in large winged, small-bodied taxa like Microraptor and Archaeopteryx. Discussion. Using our first principles approach we find that “near flight” locomotor behaviors are most sensitive to wing area, and that non-locomotory related selection regimes likely expanded wing area well before WAIR and other such behaviors were possible in derived avians. These results suggest that investigations of the drivers for wing expansion and feather elongation in theropods need not be intrinsically linked to locomotory adaptations, and this separation is critical for our understanding of the origin of powered flight and avian evolution.
Temporal regulation of proteome profile in the fruit fly, Drosophila melanogaster
Authors: Subramanian Perumal , Jayapalan Jaime J , Abdul-Rahman Puteri , Arumugam Manjula , Hashim Onn
Published: January 2018

Background. Diurnal rhythms of protein synthesis controlled by the biological clock underlie rhythmic physiology in the fruit fly, Drosophila melanogaster. Self-sustained autonomous circadian oscillations were documented all over the organs of the fly. In this study, we conducted a proteome-wide investigation of rhythmic protein accumulation in D. melanogaster. Materials and Methods. We have used the whole fly for the proteomic study as performed in typical proteotypic peptide (PTP) studies and followed the same protocol with trypsin digestion. Total protein collected from fly samples harvested at 4h intervals over the 24-h period were subjected to two dimensional (2-D) gel electrophoresis, trypsin digestion and MS/MS analysis. Protein spots/clusters were identified with MASCOT search engine and Swiss-Prot database. Expression of proteins was documented as percentage of volume contribution using the Image Master 2D Platinum software. Results. A total of 124 protein spots/clusters were identified using MS/MS analysis. A significant variation in the expression of 88 proteins over the 24-h period was observed. Our present results suggested that the synthesis/regulation of numerous proteins is regulated by the biological clock in D. melanogaster. Relatively higher number of proteins was upregulated during nighttime as compared to daytime. Conclusion. As these rhythmically varying proteins/enzymes involve in metabolism, muscle activities, ion channels, protein synthesis, redox homeostasis and apoptosis our results indicate that these cellular processes could be regulated at the level of temporal expression of protein profile.
The 2013-2016 West African Ebola virus outbreak: Local contexts and future issues
Authors: Cecon Francesco , McGrath Peter F
Published: January 2018

Ebola is just one example of the many emerging and re-emerging diseases that continue to affect mainly the developing world. We argue that the unprecedented high level of infections and deaths in the 2013-2016 West African Ebola epidemic, together with the more general impact of Ebola and other emerging diseases on societies, is reflective of the unpreparedness of affected countries prior to an outbreak. Typically, the healthcare systems of most low-income countries are inadequately prepared to be able to deal with such large and unexpected outbreaks. In this paper, we attempt to analyse the emergence and spread of the West African Ebola epidemic, reviewing the situation in Guinea, Liberia and Sierra Leone prior to the 2013-2016 outbreak. We also highlight some of the additional societal burdens that the outbreak has placed on these countries. By drawing lessons from this epidemic, as well as case studies of other (re-)emerging epidemic infections through a combination of literature searches and news reports, combined with the views of 10 international experts, we develop eight actions that might help potentially susceptible countries and the international community to prevent, contain or better respond to possible future outbreaks.
High incidence of plasmid-mediated quinolone resistance genes among ciprofloxacin-resistant clinical isolates of Enterobacteriaceae at a tertiary care hospital in Puducherry, India
Authors: Yugendran Thiyagarajan , Harish Belgode Narasimha
Published: January 2018

Background: Plasmid-mediated quinolone resistance (PMQR) has received considerable attention recently. Data analysis in JIPMER revealed 75% of the Enterobacteriaceae isolates to be ciprofloxacin-resistant in 2012. Few reports regarding the prevalence of PMQR are available from India. Hence, the present study was carried out to ascertain the prevalence of PMQR genes among clinical isolates of ciprofloxacin-resistant Enterobacteriaceae in JIPMER. Methods: The study included 642 ciprofloxacin-resistant clinical Enterobacteriaceae isolates. JIPMER hospital’s annual consumption data for fluoroquinolones were retrieved from the Department of Pharmacy. The test isolates were screened for the presence of qnr A, B, D, S and aac(6’)-Ib-cr genes. PMQR-positive isolates alone were tested for the presence of class I (intI1) and class II (intI2) integrons. Randomly selected PCR amplicons were sequenced and analysed using MEGA software. A total of 30 PMQR strains chosen at random were assessed for the transferability of the PMQR genes. Results: Majority of the strains exhibited high MIC values with 106 strains exhibiting MIC value ˃256µg/mL. The aac(6’)-Ib-cr gene had the highest prevalence at 64% (414) while, qnrB and qnrS genes were present in 15% (97) and 10% (64) of the isolates respectively. None of the strains were positive for qnrA and qnrD. All PMQR-positive isolates were screened for class I (intI1) and class II (intI2) integrons. Class I integron was found to be predominant among the test isolates with a few of them carrying both the classes of integrons. Transferability of PMQR genes to transconjugants was identified. Discussion: PMQR genes were found to exhibit an increasing trend of prevalence among the clinical isolates in this study. Thus, the need for rational usage of fluoroquinolones and reconsideration of their clinical breakpoints has arisen.
Multiple dimensions of bacterial diversity unrelated to functioning, stability and multifunctionality
Authors: Roger Fabian , Bertilsson Stefan , Langenheder Silke , Ahmed Omneya , Gamfeldt Lars
Published: January 2018

Bacteria are essential for many ecosystem services but our understanding of factors controlling their functioning is incomplete. While biodiversity has been identified as an important driver of ecosystem processes in macrobiotic communities, we know much less about bacterial communities. Due to the high diversity of bacterial communities, high functional redundancy is commonly proposed as an explanation for a lack of clear effects of diversity. The generality of this claim has, however, been questioned. We present the results of an outdoor dilution-to-extinction experiment with four lake bacterial communities. We found no general effects of bacterial diversity in terms of effective number of species, phylogenetic diversity or functional diversity on (i) bacterial abundance, (ii) temporal stability of abundance, (iii) nitrogen concentration, or (iv) multifunctionality. A literature review of 21 peer-reviewed studies that used dilution-to-extinction to manipulate bacterial diversity corroborated our findings: only about 25% found positive relationships. Combined, these results suggest that bacterial communities are able to uphold multifunctional ecosystems even at extensive reductions in diversity.
Integration of multi-omics data from public resources for the functional analysis of biological networks: molecular-genetic pathways involving aryl hydrocarbon receptor
Authors: Dotolo Serena , Facchiano Angelo
Published: January 2018

Omics approaches are widely applied to investigate physiological processes and pathological conditions. Many public data repositories make it possible to extract data for their analyses, comparisons and integrations, provided the availability of suitable tools. Our interest is oriented to the integration of data from different experimental approaches and fields of investigation, covering transcriptomics, proteomics, interactomics, variation data, and drug discovery, in order to highlight hiddens information and to mine new knowledge from available experimental data. Therefore, we look at specific gene and protein functions, for which specific interest has been evidenced, and search for a complete view of their relationships in physiological processes. Moreover, focusing on specific pathologies, we extract from public databases the largest amount of experimental results and analyze them with meta-analysis approaches, to find novel insights on molecular aspects, useful for defining diagnostics or therapy. In this work, our attention is focused on integrative-functional analysis of molecular pathways that involve AHR (Aryl hydrocarbon receptor), a cytosolic transcription factor consisting of several protein domains with distinct functions, including hydrocarbon binding as well as DNA-protein and protein-protein interactions. Previous studies from our lab on this protein give us some specific interest and knowledge about its involvement in many pathologies. Therefore, we investigate it from the physiological point of view, as well as for its role in specific pathologies, also in the view of the molecular network that includes other proteins of interest for the pathology. The functional analysis is executed by means of different open-source bioinformatics platforms, including GeneCards, DSYSMAP, and in particular, Cytoscape platform for realizing and visualizing molecular networks at different levels, in order to improve the knowledge of molecular mechanisms. Furthermore, as an example on a specific pathology, we use the BioGPS platform to extrapolate by Gene Atlas the gene expression profile of our biological targets involved in melanoma, and MelGene DB (a database for melanoma genetic studies and for analysis some important melanoma biomarkers). The poster presents the molecular networks and discusses the potential roles of specifc nodes evidenced by the analysis, also in consideration of the role of disease-related mutations.
Evolution of Philodendron (Araceae) species along Neotropical biomes
Authors: Loss-Oliveira Leticia , Sakuragui Cassia CMS , Soares Maria de Lourdes , Schrago Carlos G
Published: January 2018

Philodendron is the second most diverse genus of the Araceae, a tropical monocot family with significant morphological diversity along its wide geographic distribution in the Neotropics. Although evolutionary studies of Philodendron were conducted in recent years, the phylogenetic relationship among its species remains unclear. Additionally, analyses conducted to date suggested the inclusion of all American representatives of a closely related genus, Homalomena, within the Philodendron clade. A thorough evaluation of the phylogeny and timescale of these lineages is thus necessary to elucidate the tempo and mode of evolution of this large Neotropical genus and to unveil the biogeographic history of Philodendron evolution along the Amazonian and Atlantic Rain Forests, as well as open dry forests of South America. To this end, we have estimated the molecular phylogeny for 68 Philodendron species, which consists of the largest sampling assembled to date aiming the study of the evolutionary affinities. We have also performed ancestral reconstruction of species distribution along biomes. Finally, we contrasted these results with the inferred timescale of Philodendron and Homalomena lineage diversification. Our estimates indicate that American Homalomena is the sister clade to Philodendron. The early diversification of Philodendron took place in the Amazon Forest from Early to Middle Miocene, followed by colonization of the Atlantic Forest and the savanna-like landscapes, respectively. Based on the age of the last common ancestor of Philodendron, the species of this genus diversified by rapid radiations, leading to its wide extant distribution in the Neotropical region.
A systematic review of natural processes in creating pierced shells: implications for the archaeological record
Authors: Kubicka Anna Maria , Rosin Zuzanna M , Tryjanowski Piotr , Nelson Emma
Published: January 2018

Background. The shells of molluscs survive well in most sedimentary contexts and yield information about the diet of prehistoric humans. They also yield evidence of symbolic behaviours, through their use as beads for body adornments. Researchers often analyse the location of perforations in shells to make judgements about their use as symbolic objects (i.e., beads), the assumption being, that holes attributable to deliberate human behaviour are more likely to exhibit low variability in their anatomical locations, while holes attributable to natural processes yield more random perforations. However, there are non-anthropogenic factors that can cause perforations in shells and these may not be random. The aim of the study is to look at the association between variation of holes in shell beads from archaeological sites and shells pierced by natural (non-human) processes. Methods. Two hundred and sixty scientific papers retrieved from online databases by using keywords, (e.g., ‘shell beads’; ‘pierced shells’); 77 of these publications enabled us to conduct a systematic review and assess the location of the hole in the shell beads in the published articles. Results. Almost all archaeological sites described shells beads with holes in a variety of anatomical locations. High variation of hole-placement was also found within the same species from the same site, as well as among sites. In contrast, predators were more specific in where they attacked molluscs; birds often select the thinnest part of the shell, while molluscs and cephalopods target thicker parts. Discussion. These results indicate that variation in hole-location on shells pierced by humans is greater than variation in the placement of holes created by natural processes. Consequently, these patterns are opposite to those expected. We also found that Gastropod and Bivalve predators choose similar hole locations to humans. Research into human shell-beads recovered from archaeological contexts should take into account non-anthropogenic factors, which can lead to more realistic scenarios of the cultural behaviours of prehistoric people.
Microsatellite loci discovery from next-generation sequencing data and marker characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1798)
Authors: Ewers-Saucedo Christine , Zardus John D , Wares John P
Published: January 2018

Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758). Chelonibia testudinaria appears to be a host generalist, and has a unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers. In the present study, we discovered thousands of new microsatellite loci from next-generation sequencing data, and characterized 12 loci thoroughly. We conclude that 11 of these loci will be useful markers in future ecological and evolutionary studies on C. testudinaria.
In vitro evaluation of antimicrobial activity of 1-lauroyl-rac-glycerol on Candidaalbicans biofilms
Authors: Chen Emily , Seleem Dalia , Benso Bruna , Pardi Vanessa , Murata Ramiro M
Published: January 2018

Monolaurin (also known as glycerol monolaurate) is a natural compound found in coconut oil and is known for its protective biological activities as an antimicrobial agent. The nature of oral candidiasis and the increased antifungal resistance, culminate the need for investigating novel antifungal therapeutic agents. In this study, we examine the antifungal activity of monolaurin against Candida albicans biofilms (strain ATCC: SC5314/MYA2876) in vitro and how monolaurin may alter specific host inflammatory markers, such as gene expression of inflammatory cytokines IL-1α and IL-1β, as illustrated in co-culture models. The results from three groups were compared: 1- monolaurin (in the range of 3.9-2500 μM), positive control fluconazole (322 μM), and vehicle control group 1% Ethanol (v/v) The MIC and MFC of monolaurin were in the range 62.5-125 µM and 125-250 µM, respectively. The results show significant reduction in Log (CFU/ ml) of biofilms treated with 1250 and 2500 µM of 1- monolaurin when compared to the control groups. There was also a significant down-regulation of IL-1α and IL-1β in the biofilms treated with monolaurin. It can be concluded that monolaurin has a potential antifungal activity against C. albicans and can modulate the host’s pro-inflammatory response.
Anxiolytic effects of fluoxetine and nicotine exposure on exploratory behavior in zebrafish
Authors: Singer Matthew L , Oreschak Kris , Rhinehart Zachariah , Robison Barrie D
Published: January 2018

Zebrafish (Danio rerio) have emerged as a popular model for studying pharmacological effects on behavior and anxiety. While there have been numerous studies documenting the anxiolytic and anxiogenic effects of common drugs in zebrafish, many do not report or test for behavioral differences between the sexes. Previous studies of zebrafish have indicated that males and females differ in their behavioral responses to anxiety. In this study, we test for sex-dependent effects of fluoxetine and nicotine. We exposed fish to system water (control), 10 mg/L fluoxetine, or 1 mg/L nicotine for three minutes prior to being subjected to four minutes in an open-field drop test. Video recordings were tracked using ProAnalyst. Fish from both drug treatments reduced swimming speed, increased vertical position, and increased use of the top half of the open field when compared with the control, though fluoxetine had a larger effect on depth related behaviors while nicotine mostly affected swimming speed. A significant sex effect was observed where females swam at a slower and more constant speed than males in all treatments. No interactions between sex and the drugs were observed across the entire study.
DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies
Authors: Chabbert Christophe D , Steinmetz Lars M , Klaus Bernd
Published: January 2018

The genome–wide study of epigenetic states requires the integrative analysis of histone modification ChIP–seq data. Here, we introduce an easy–to–use analytic framework to compare profiles of enrichment in histone modifications around classes of genomic elements, e.g. transcription start sites (TSS). Our framework is available via the user–friendly R/Bioconductor package DChIPRep. DChIPRep uses biological replicate information as well as chromatin Input data to allow for a rigorous assessment of differential enrichment. DChIPRep is available for download through the Bioconductor project at http://bioconductor.org/packages/DChIPRep. Contact DChIPRep@gmail.com
Mobula kuhlii cleaning station identified at an inshore reef in southern Mozambique
Authors: Murie Calum JG , Marshall Andrea D
Published: January 2018

Cleaning interactions between the short fin devil ray, Mobula kuhlii, and the blue streaked cleaner wrasse, Labroides dimidiatus, were observed at two sites on a single reef in southern Mozambique. Cleaning interactions were filmed and described, with the number and location of interactions recorded and subsequently binned into six distinct body patches. Cleaners preferentially foraged within certain ray body patches, and this was found to vary between the two sites, possibly signifying that variations in a habitats composition can influence cleaning. Mobula kuhlii were not found to clean sympatrically with their close relatives in the Manta genus, implying their cleaning requires a distinct habitat or that niche partitioning is required to stem competition for host cleaner fishes attention. In total, 15 individuals were observed interacting with cleaners, and they never arrived alone, suggesting they may travel to cleaning areas in an aggregative manner.
Evolutionary relationships within the lamioid tribe Synandreae (Lamiaceae) based on multiple low-copy nuclear loci
Authors: Roy Tilottama , Catlin Nathan S , Garner Drake M.G. , Cantino Philip D , Scheen Anne-Cathrine , Lindqvist Charlotte
Published: January 2018

The subfamily Lamioideae (Lamiaceae) comprises ten tribes, of which only Stachydeae and Synandreae include New World members. Previous studies have investigated the phylogenetic relationships among the members of Synandreae based on plastid and nuclear ribosomal DNA loci. In an effort to re-examine the phylogenetic relationships within Synandreae, the current study incorporates data from four low-copy nuclear loci, PHOT1, PHOT2, COR, and PPR. Our results confirm previous studies based on chloroplast and nuclear ribosomal markers in supporting monophyly of tribe Synandreae, as well as sister relationships between Brazoria and Warnockia, and between that pair of genera and a monophyletic Physostegia. However, we observe incongruence in the relationships of Macbridea and Synandra. The placement of Synandreae within Lamioideae is poorly resolved and incongruent among different analyses, and the sister group of Synandreae remains enigmatic. Comparison of the colonization and migration patterns corroborates a single colonization of the New World by Synandreae during the mid-Miocene. This is in contrast to the only other lamioid tribe that includes New World members, Stachydeae, which colonized the New World at least twice—during the mid-Miocene and Pliocene. Edaphic conditions and intolerance of soil acidity may be factors that restricted the distribution of most genera of Synandreae to southeastern and south-central North America, whereas polyploidy could have increased the colonizing capability of the more wide-ranging genus, Physostegia.
Mitonucleons formed during differentiation of Ishikawa endometrial cells generate vacuoles that elevate monolayer syncytia: Differentiation of Ishikawa domes, Part 1
Authors: Fleming Honoree
Published: January 2018

In 1998, we published a paper (Fleming et.al, 1998) describing some aspects of Ishikawa endometrial epithelial cell differentiation from monolayer cells into cells forming fluid-filled hemispheres called domes. The process begins with the dissolution of membranes within discrete regions of the monolayer. Nuclei from fused cells aggregate and endogenous biotin in particulate structures assumed to be mitochondria increase throughout the resulting syncytium. Endogenous biotin is also the distinguishing feature of a membrane that surrounds aggregates of multiple nuclei in a structure called a mitonucleon. The current paper includes additional observations on structural changes accompanying Ishikawa differentiation. Vacuoles form in the heterochromatin of the mitonucleon and within the biotin-containing double membrane surrounding heterochromatin. With the formation of vacuoles, the mitonucleon can be seen to rise along with the apical membrane of the syncytium in which it formed. The small vacuoles that form within the heterochromatin result in structures similar to “cells with optically clear nuclei” found in some cancers. The second larger vacuole that forms within the membrane surrounding the heterochromatin transforms the cell profile to one that resembles “signet ring” cells also observed in some cancers. Eventually the membrane surrounding the massed heterochromatin, generated three to four hours earlier, is breached and previously aggregated nuclei disaggregate. During this process heterochromatin in the mitonucleons undergoes changes usually ascribed to cells undergoing programmed cell death such as pyknosis and DNA fragmentation (Fleming, 2016b). The cells do not die, instead chromatin filaments appear to coalesce into a chromatin mass that gives rise to dome-filling nuclei by amitosis during the final three to four hours of the 20 hour differentiation (Fleming, 2016c).
Chomatin mass from previously aggregated, pyknotic, and fragmented monolayer nuclei is a source for dome cell nuclei generated by amitosis: Differentiation of Ishikawa Domes, Part 3
Authors: Fleming Honoree
Published: January 2018

Ishikawa endometrial epithelial cells are capable of differentiation from monolayer cells into fluid-enclosing hemispheres through a surprisingly complex series of structural changes as discussed in this and in two accompanying papers (Fleming, 2016a; Fleming 2016b). The process starts with the dissolution of cell membranes in defined regions throughout a monolayer that has been stimulated to differentiate (Fleming, 1995). Aggregated nuclei become wrapped in membranes containing mitochondrial carboxylases, and apparently generated by contiguous mitochondria. These mitonucleons are involved in vacuole formation that elevates the syncytium into a predome (Fleming, 2015a). The mitonucleons begin to fall apart several hours after formation as the enveloping membranes are breached and the pyknotic chromatin undergoes profound changes (Fleming, 2015b). Chromatin deconstruction, with attendant disappearance of the typical ovoid nuclear structure, results in chromatin fibers that fill the envelope formed by the apical and basal membranes of the syncytium, now stretching over a cavity filling with fluid. In the next several hours, hematoxylin staining, greatly diminished when nuclei were fragmented, reappears in an irregular mass of chromatin out of which nuclei form amitotically and increase in numbers until they fill the envelope. Subsequently cell membranes form around the nuclei. Domes can enlarge and even extend into tubules by becoming vacuolized and undergoing the same amitotic process that created the dome initially.