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: Direct and indirect effects of the El Niño Southern Oscillation on development and survival of young of a tropical passerine; The El Niño Southern Oscillation (ENSO) is a global phenomenon that influences climate variation and, in turn, the ecological processes affecting the abundance and distribution of populations across taxa. For example, the ENSO can profoundly influence the development and survival of pelagic species, but the extent to which the ENSO affects offspring of terrestrial species is less well known. We used piecewise structural equation modeling to investigate the direct and indirect relationship between the ENSO and offspring development and survival in a terrestrial tropical passerine, the lance-tailed manakin (Chiroxiphia lanceolata). The Oceanic Niño Index (ONI), a measure of the ENSO, was negatively related to individual growth rate, maximum number of lesion developed by nestlings, and hatching day-of-year; which in turn mediated indirect effects on fledging success and recruitment. Further the ONI was a better predictor of nestling development compared to local temperature and rainfall. Our study establishes a link between the ENSO and the development and survival of young of a terrestrial species and underscores the need to better understand how offspring cope with global climate variation., Lance-tailed manakin, Chiroxiphia lanceolata, Oceanic Niño Index, climate, El Niño, La Niña, Growth rate, Piecewise structural equation model, Data relevant to this project were collected with support from National Science Foundation (NSF) Grants 0843334 and 1453408 (CAREER) awarded to E.H.D., the Florida State University, and the Max Planck Institute for Ornithology

: Discovery of a Coregulatory Interaction between Kaposi's Sarcoma-Associated Herpesvirus ORF45 and the Viral Protein Kinase ORF36.; Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of three human malignancies. KSHV ORF36 encodes a serine/threonine viral protein kinase, which is conserved throughout all herpesviruses. Although several studies have identified the viral and cellular substrates of conserved herpesvirus protein kinases (CHPKs), the precise functions of KSHV ORF36 during lytic replication remain elusive. Here, we report that ORF36 interacts with another lytic protein, ORF45, in a manner dependent on ORF36 kinase activity. We mapped the regions of ORF36 and ORF45 involved in the binding. Their association appears to be mediated by electrostatic interactions, since deletion of either the highly basic N terminus of ORF36 or an acidic patch of ORF45 abolished the binding. In addition, the dephosphorylation of ORF45 protein dramatically reduced its association with ORF36. Importantly, ORF45 enhances both the stability and kinase activity of ORF36. Consistent with previous studies of CHPK homologs, we detected ORF36 protein in extracellular virions. To investigate the roles of ORF36 in the context of KSHV lytic replication, we used bacterial artificial chromosome mutagenesis to engineer both ORF36-null and kinase-dead mutants. We found that ORF36-null/mutant virions are moderately defective in viral particle production and are further deficient in primary infection. In summary, our results uncover a functionally important interaction between ORF36 and ORF45 and indicate a significant role of ORF36 in the production of infectious progeny virions. Kaposi's sarcoma-associated herpesvirus (KSHV) is a human tumor virus with a significant public health burden. KSHV ORF36 encodes a serine/threonine viral protein kinase, whose functions throughout the viral life cycle have not been elucidated. Here, we report that ORF36 interacts with another KSHV protein, ORF45. We mapped the regions of ORF36 and ORF45 involved in their association and further characterized the consequences of this interaction. We engineered ORF36 mutant viruses in order to investigate the functional roles of ORF36 in the context of KSHV lytic replication, and we confirmed that ORF36 is a component of KSHV virions. Moreover, we found that ORF36 mutants are defective in virion production and primary infection. In summary, we discovered and characterized a functionally important interaction between KSHV ORF36 and ORF45, and our results suggest a significant role of ORF36 in the production of infectious progeny virions, a process critical for KSHV pathogenesis., Grant Number: F31 CA183250, R01 DE016680, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907238.

: Distinct Tissue-specific Transcriptional Regulation Revealed By Gene Regulatory Networks In Maize; Background: Transcription factors (TFs) are proteins that can bind to DNA sequences and regulate gene expression. Many TFs are master regulators in cells that contribute to tissue-specific and cell-type-specific gene expression patterns in eukaryotes. Maize has been a model organism for over one hundred years, but little is known about its tissue-specific gene regulation through TFs. In this study, we used a network approach to elucidate gene regulatory networks (GRNs) in four tissues (leaf, root, SAM and seed) in maize. We utilized GENIE3, a machine-learning algorithm combined with large quantity of RNA-Seq expression data to construct four tissue-specific GRNs. Unlike some other techniques, this approach is not limited by high-quality Position Weighed Matrix (PWM), and can therefore predict GRNs for over 2000 TFs in maize. Results: Although many TFs were expressed across multiple tissues, a multi-tiered analysis predicted tissue-specific regulatory functions for many transcription factors. Some well-studied TFs emerged within the four tissue-specific GRNs, and the GRN predictions matched expectations based upon published results for many of these examples. Our GRNs were also validated by ChIP-Seq datasets (KN1, FEA4 and O2). Key TFs were identified for each tissue and matched expectations for key regulators in each tissue, including GO enrichment and identity with known regulatory factors for that tissue. We also found functional modules in each network by clustering analysis with the MCL algorithm. Conclusions: By combining publicly available genome-wide expression data and network analysis, we can uncover GRNs at tissue-level resolution in maize. Since ChIP-Seq and PWMs are still limited in several model organisms, our study provides a uniform platform that can be adapted to any species with genome-wide expression data to construct GRNs. We also present a publicly available database, maize tissue-specific GRN (mGRN, https://www.bio.fsu.edu/mcginnislab/mgrn/), for easy querying. All source code and data are available at Github (https://github.com/timedreamer/maize_tissue-specific_GRN)., Keywords: dynamics, Gene expression, protein, inference, genome, Network, dna, arabidopsis-thaliana, Bioinformatics, coexpression network, Database, duplicate genes, expression patterns, Machine learning, Maize, meristems, Systems biology, Transcription factor, Transcriptional regulation, Publication Note: The publisher’s version of record is available at https://doi.org/10.1186/s12870-018-1329-y

: Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize.; Transcription factors (TFs) are proteins that can bind to DNA sequences and regulate gene expression. Many TFs are master regulators in cells that contribute to tissue-specific and cell-type-specific gene expression patterns in eukaryotes. Maize has been a model organism for over one hundred years, but little is known about its tissue-specific gene regulation through TFs. In this study, we used a network approach to elucidate gene regulatory networks (GRNs) in four tissues (leaf, root, SAM and seed) in maize. We utilized GENIE3, a machine-learning algorithm combined with large quantity of RNA-Seq expression data to construct four tissue-specific GRNs. Unlike some other techniques, this approach is not limited by high-quality Position Weighed Matrix (PWM), and can therefore predict GRNs for over 2000 TFs in maize. Although many TFs were expressed across multiple tissues, a multi-tiered analysis predicted tissue-specific regulatory functions for many transcription factors. Some well-studied TFs emerged within the four tissue-specific GRNs, and the GRN predictions matched expectations based upon published results for many of these examples. Our GRNs were also validated by ChIP-Seq datasets (KN1, FEA4 and O2). Key TFs were identified for each tissue and matched expectations for key regulators in each tissue, including GO enrichment and identity with known regulatory factors for that tissue. We also found functional modules in each network by clustering analysis with the MCL algorithm. By combining publicly available genome-wide expression data and network analysis, we can uncover GRNs at tissue-level resolution in maize. Since ChIP-Seq and PWMs are still limited in several model organisms, our study provides a uniform platform that can be adapted to any species with genome-wide expression data to construct GRNs. We also present a publicly available database, maize tissue-specific GRN (mGRN, https://www.bio.fsu.edu/mcginnislab/mgrn/ ), for easy querying. All source code and data are available at Github ( https://github.com/timedreamer/maize_tissue-specific_GRN )., Keywords: Bioinformatics, Database, Gene expression, Machine learning, Maize, Network, Systems biology, Transcription factor, Transcriptional regulation, Grant Number: 035919, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6040155.

: Diversification in wild populations of the model organism Anolis carolinensis; The green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary history in association with morphological, physiological, or reproductive biology studies among sampling localities and necessitate increased effort to resolve evolutionary relationships among natural populations. Here, we used anchored hybrid enrichment of hundreds of genetic markers across the genome of A. carolinensis and identified five strongly supported phylogeographic groups. Using multiple analyses, we produced a fully resolved species tree, investigated relative support for each lineage across all gene trees, and identified mito-nuclear discordance when comparing our results to previous studies. We found fixed differences in only one clade-southern Florida restricted to the Everglades region-while most polymorphisms were shared between lineages. The southern Florida group likely diverged from other populations during the Pliocene, with all other diversification during the Pleistocene. Multiple lines of support, including phylogenetic relationships, a latitudinal gradient in genetic diversity, and relatively more stable long-term population sizes in southern phylogeographic groups, indicate that diversification in A. carolinensis occurred northward from southern Florida., Keywords: Anolis, bayesian-inference, coalescent model, divergence, fragmentation, geographical variation, lizard, Morphology, patterns, phylogeography, sequence data, snp data, Species tree, target capture, Publication Note: The publisher’s version of record is available at https://doi.org/10.1002/ece3.2547

: Do Florida Harvester Ant Colonies (pogonomyrmex Badius) Have A Nest Architecture "plan?"; Keywords: hymenoptera, formicidae, Publication Note: The publisher's version of record is available at https://doi.org/10.1002/ecy.1739/suppinfo

: Do Sperm Really Compete And Do Eggs Ever Have A Choice? Adult Distribution And Gamete Mixing Influence Sexual Selection, Sexual Conflict, And The Evolution Of Gamete Recognition Proteins In The Sea; The evolution of gametic compatibility and the effectiveness of compatibility, within and across species, depend on whether sperm from different males directly compete for an egg and whether eggs ever have a choice. Direct sperm competition and egg choice depend on whether sperm from different males arrive at an egg in the brief interval between first sperm contact and fertilization. Although this process may be relevant for all sexually reproducing organisms, it is most easily examined in aquatic external fertilizers. When sperm are released into the sea, packets of seawater at the spatial scale relevant to single eggs might contain sperm from only one male, eliminating the potential for direct sperm competition and egg choice. Field experiments and a simple heuristic model examining the degree of sperm mixing for the sea urchin Strongylocentrotus franciscanus indicate that degree of competitive fertilization depends on density and distribution of competing males and that the nature of this competition influences whether males with high- or low-affinity gamete recognition protein genotypes have higher reproductive success. These results provide a potential explanation for the generation and maintenance of variation in gamete recognition proteins and why effectiveness of conspecific sperm precedence can be density dependent., Keywords: consequences, sexual selection, kinetics, conspecific sperm, female choice, fertilization, fertilization success, gamete recognition protein, hybridization, male reproductive success, mating systems, precedence, reef corals, sea urchin, spawning marine-invertebrates, sperm competition, Publication Note: The publisher's version of record is available at https://doi.org/10.1086/694780

: Dopamine; Circadian rhythms are daily rhythms that regulate many biological processes - from gene transcription to behavior - and a disruption of these rhythms can lead to a myriad of health risks. Circadian rhythms are entrained by light, and their 24-h oscillation is maintained by a core molecular feedback loop composed of canonical circadian ("clock") genes and proteins. Different modulators help to maintain the proper rhythmicity of these genes and proteins, and one emerging modulator is dopamine. Dopamine has been shown to have circadian-like activities in the retina, olfactory bulb, striatum, midbrain, and hypothalamus, where it regulates, and is regulated by, clock genes in some of these areas. Thus, it is likely that dopamine is essential to mechanisms that maintain proper rhythmicity of these five brain areas. This review discusses studies that showcase different dopaminergic mechanisms that may be involved with the regulation of these brain areas' circadian rhythms. Mechanisms include how dopamine and dopamine receptor activity directly and indirectly influence clock genes and proteins, how dopamine's interactions with gap junctions influence daily neuronal excitability, and how dopamine's release and effects are gated by low- and high-pass filters. Because the dopamine neurons described in this review also release the inhibitory neurotransmitter GABA which influences clock protein expression in the retina, we discuss articles that explore how GABA may contribute to the actions of dopamine neurons on circadian rhythms. Finally, to understand how the loss of function of dopamine neurons could influence circadian rhythms, we review studies linking the neurodegenerative disease Parkinson's Disease to disruptions of circadian rhythms in these five brain areas. The purpose of this review is to summarize growing evidence that dopamine is involved in regulating circadian rhythms, either directly or indirectly, in the brain areas discussed here. An appreciation of the growing evidence of dopamine's influence on circadian rhythms may lead to new treatments including pharmacological agents directed at alleviating the various symptoms of circadian rhythm disruption., Keywords: dopamine, circadian rhythms, clock gene-expression, contrast sensitivity, hypothalamus, midbrain, mouse retina, nigra pars compacta, olfactory bulb, Parkinson's disease, parkinsons-disease, rat olfactory-bulb, retina, retinal ganglion-cells, striatum, suprachiasmatic nucleus, tyrosine-hydroxylase-immunoreactivity, ventral tegmental area, Publication Note: The publisher's version of record is available at https://doi.org/10.3389/fncel.2017.00091

: Dual-Color Reporter Assay of Cohesin-Mediated Gene Regulation in Budding Yeast Meiosis.; In this chapter, we describe a quantitative fluorescence-based assay of gene expression using the ratio of the reporter green fluorescence protein (GFP) to the internal red fluorescence protein (RFP) control. With this dual-color heterologous reporter assay, we have revealed cohesin-regulated genes and discovered a cis-acting DNA element, the Ty1-LTR, which interacts with cohesin and regulates gene expression during yeast meiosis. The method described here provides an effective cytological approach for quantitative analysis of global gene expression in budding yeast meiosis., Keywords: Cohesin, Fluorescence-based reporter assay, Green fluorescence protein, Meiosis, Red fluorescence protein, Ty1-LTR, Grant Number: R01 GM117102, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5551346.

: Early-life telomere length and dynamics of the lance-tailed manakin; telomere length, telomere dynamics, early-life

: Ecdysone and Notch Pathways Synergistically Regulate Cut at the Dorsal-Ventral Boundary in Drosophila Wing Discs.; Metazoan development requires coordination of signaling pathways to regulate patterns of gene expression. In Drosophila, the wing imaginal disc provides an excellent model for the study of how signaling pathways interact to regulate pattern formation. The determination of the dorsal-ventral (DV) boundary of the wing disc depends on the Notch pathway, which is activated along the DV boundary and induces the expression of the homeobox transcription factor, Cut. Here, we show that Broad (Br), a zinc-finger transcription factor, is also involved in regulating Cut expression in the DV boundary region. However, Br expression is not regulated by Notch signaling in wing discs, while ecdysone signaling is the upstream signal that induces Br for Cut upregulation. Also, we find that the ecdysone-Br cascade upregulates cut-lacZ expression, a reporter containing a 2.7 kb cut enhancer region, implying that ecdysone signaling, similar to Notch, regulates cut at the transcriptional level. Collectively, our findings reveal that the Notch and ecdysone signaling pathways synergistically regulate Cut expression for proper DV boundary formation in the wing disc. Additionally, we show br promotes Delta, a Notch ligand, near the DV boundary to suppress aberrant high Notch activity, indicating further interaction between the two pathways for DV patterning of the wing disc., Keywords: Broad, Cut, Dorsal–ventral boundary, Drosophila, Ecdysone, Notch, Wing disc, Grant Number: R01 GM072562, R01 GM084947, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5391978.

: Effects of intraspecific diversity on survivorship, growth, and recruitment of the eastern oyster across sites; Intraspecific diversity, particularly of foundation species, can significantly affect population, community, and ecosystem processes. Examining how genetic diversity relates to demographic traits provides a key mechanistic link from genotypic and phenotypic variation of taxa with complex life histories to their population dynamics. We conducted a field experiment to assess how two metrics of intraspecific diversity (cohort diversity, the number of independent juvenile cohorts created from different adult source populations, and genetic relatedness, genetic similarity among individuals within and across cohorts) affect the survivorship, growth, and recruitment of the foundation species Crassostrea virginica. To assess the effects of both cohort diversity and genetic relatedness on oyster demographic traits under different environmental conditions, we manipulated juvenile oyster diversity and predator exposure (presence/absence of a cage) at two sites differing in resource availability and predation intensity. Differences in predation pressure between sites over-whelmingly determined post-settlement survivorship of oysters. However, in the absence of predation (i.e., cage treatment), one or both metrics of intraspecific diversity, in addition to site, influenced long-term survivorship, growth, and recruitment. While both cohort diversity and genetic relatedness were negatively associated with long-term survivorship, genetic relatedness alone showed a positive association with growth and cohort diversity alone showed a positive association with recruitment. Thus, our results demonstrate that in the absence of predation, intraspecific diversity can affect multiple demographic traits of a foundation species, but the relative importance of these effects depends on the environmental context. Moreover, the magnitude and direction of these effects vary depending on the diversity metric, cohort diversity or genetic relatedness, suggesting that although they are inversely related in this system, each captures sufficiently different components of intraspecific diversity. Given the global loss of oyster reef habitat and rapid decline in oyster population size, our results are particularly relevant to management and restoration. In addition, aquaculture, which commonly excludes predators during early life history stages, may benefit from incorporation of oyster cohort diversity into standard practice., Keywords: colonization success, community, context dependent, crassostrea-virginica, demography, ecosystem genetics, eelgrass zostera-marina, genetic diversity, genetic relatedness, growth, oyster, plant genotypic diversity, population, predation, productivity, propagule pressure, recruitment, survivorship, trait, Publication Note: The publisher’s version of record is available at http://www.dx.doi.org/10.1890/15-1710.1

: Elevated Anxiety And Impaired Attention In Super-smeller, Kv1.3 Knockout Mice; It has long been recognized that olfaction and emotion are linked. While chemosensory research using both human and rodent models have indicated a change in emotion can contribute to olfactory dysfunction, there are few studies addressing the contribution of olfaction to a modulation in emotion. In mice, olfactory deficits have been linked with heightened anxiety levels, suggesting that there could be an inverse relationship between olfaction and anxiety. Furthermore, increased anxiety is often co-morbid with psychiatric conditions such as attention disorders. Our study aimed to investigate the roles of olfaction in modulating anxiety. Voltage-gated potassium ion channel Kv1.3 knockout mice (Kv1.3-/-), which have heightened olfaction, and wild-type (WT) mice were examined for anxiety-like behaviors using marble burying (MB), light-dark box (LDB) and elevated-plus maze (EPM) tests. Because Kv1.3-/- mice have increased locomotor activity, inattentive and hyperactive behaviors were quantified for both genotypes. Kv1.3-/- mice showed increased anxiety levels compared to their WT counterparts and administration of methylphenidate (MPH) via oral gavage alleviated their increased anxiety. Object-based attention testing indicated young and older Kv1.3-/- mice had attention deficits and treatment with MPH also ameliorated this condition. Locomotor testing through use of a metabolic chamber indicated that Kv1.3-/- mice were not significantly hyperactive and MPH treatment failed to modify this activity. Our data suggest that heightened olfaction does not necessarily lead to decreased anxiety levels, and that Kv1.3-/- mice may have behaviors associated with inattentiveness., Keywords: ion-channel, brain insulin, body-weight, deficit hyperactivity disorder, dopamine, anxiety, methylphenidate, oral methylphenidate, olfaction, animal-models, attention deficit, deficit/hyperactivity disorder, gated potassium channel, Kv1.3, olfactory bulbectomized rat, voltage-gated potassium ion channel, Publication Note: The publisher's version of record is available at https://doi.org/10.3389/fnbeh.2018.00049

: Elevated Anxiety and Impaired Attention in Super-Smeller, Kv1.3 Knockout Mice.; It has long been recognized that olfaction and emotion are linked. While chemosensory research using both human and rodent models have indicated a change in emotion can contribute to olfactory dysfunction, there are few studies addressing the contribution of olfaction to a modulation in emotion. In mice, olfactory deficits have been linked with heightened anxiety levels, suggesting that there could be an inverse relationship between olfaction and anxiety. Furthermore, increased anxiety is often co-morbid with psychiatric conditions such as attention disorders. Our study aimed to investigate the roles of olfaction in modulating anxiety. Voltage-gated potassium ion channel Kv1.3 knockout mice (Kv1.3-/-), which have heightened olfaction, and wild-type (WT) mice were examined for anxiety-like behaviors using marble burying (MB), light-dark box (LDB) and elevated-plus maze (EPM) tests. Because Kv1.3-/- mice have increased locomotor activity, inattentive and hyperactive behaviors were quantified for both genotypes. Kv1.3-/- mice showed increased anxiety levels compared to their WT counterparts and administration of methylphenidate (MPH) via oral gavage alleviated their increased anxiety. Object-based attention testing indicated young and older Kv1.3-/- mice had attention deficits and treatment with MPH also ameliorated this condition. Locomotor testing through use of a metabolic chamber indicated that Kv1.3-/- mice were not significantly hyperactive and MPH treatment failed to modify this activity. Our data suggest that heightened olfaction does not necessarily lead to decreased anxiety levels, and that Kv1.3-/- mice may have behaviors associated with inattentiveness., Keywords: Kv1.3, Anxiety, Attention deficit, Methylphenidate, Olfaction, Voltage-gated potassium ion channel, Grant Number: R01 DC013080, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5867313.

: Emergence and evolution of Zfp36l3.; In most mammals, the Zfp36 gene family consists of three conserved members, with a fourth member, Zfp36l3, present only in rodents. The ZFP36 proteins regulate post-transcriptional gene expression at the level of mRNA stability in organisms from humans to yeasts, and appear to be expressed in all major groups of eukaryotes. In Mus musculus, Zfp36l3 expression is limited to the placenta and yolk sac, and is important for overall fecundity. We sequenced the Zfp36l3 gene from more than 20 representative species, from members of the Muridae, Cricetidae and Nesomyidae families. Zfp36l3 was not present in Dipodidae, or any families that branched earlier, indicating that this gene is exclusive to the Muroidea superfamily. We provide evidence that Zfp36l3 arose by retrotransposition of an mRNA encoded by a related gene, Zfp36l2 into an ancestral rodent X chromosome. Zfp36l3 has evolved rapidly since its origin, and numerous modifications have developed, including variations in start codon utilization, de novo intron formation by mechanisms including a nested retrotransposition, and the insertion of distinct repetitive regions. One of these repeat regions, a long alanine rich-sequence, is responsible for the full-time cytoplasmic localization of Mus musculus ZFP36L3. In contrast, this repeat sequence is lacking in Peromyscus maniculatus ZFP36L3, and this protein contains a novel nuclear export sequence that controls shuttling between the nucleus and cytosol. Zfp36l3 is an example of a recently acquired, rapidly evolving gene, and its various orthologues illustrate several different mechanisms by which new genes emerge and evolve., Keywords: Gene evolution, Intronization, New gene formation, Repetitive element expansion, Retrotransposon, Subcellular localization, Grant Number: ZIA ES090080-18, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4663143.

: Emergent Properties Of Branching Morphologies Modulate The Sensitivity Of Coral Calcification To High P-co2; Experiments with coral fragments (i.e. nubbins) have shown that net calcification is depressed by elevated P-CO2. Evaluating the implications of this finding requires scaling of results from nubbins to colonies, yet the experiments to codify this process have not been carried out. Building from our previous research demonstrating that net calcification of Pocillopora verrucosa (2-13 cm diameter) was unaffected by P-CO2 (400 and 1000 mu atm) and temperature (26.5 and 29.7 degrees C), we sought generality to this outcome by testing how colony size modulates P-CO2 and temperature sensitivity in a branching acroporid. Together, these taxa represent two of the dominant lineages of branching corals on Indo-Pacific coral reefs. Two trials conducted over 2 years tested the hypothesis that the seasonal range in seawater temperature (26.5 and 29.2 degrees C) and a future P-CO2 (1062 mu atm versus an ambient level of 461 mu atm) affect net calcification of an ecologically relevant size range (5-20 cm diameter) of colonies of Acropora hyacinthus. As for P. verrucosa, the effects of temperature and P-CO2 on net calcification (mg day(-1)) of A. verrucosa were not statistically detectable. These results support the generality of a null outcome on net calcification of exposing intact colonies of branching corals to environmental conditions contrasting seasonal variation in temperature and predicted future variation in P-CO2. While there is a need to expand beyond an experimental culture relying on coral nubbins as tractable replicates, rigorously responding to this need poses substantial ethical and logistical challenges., growth, ecology, responses, climate-change, temperature, impacts, Allometry, ocean acidification, Ocean acidification, pocillopora-damicornis, Scleractinia, water-flow, zooxanthellae, The publisher's version of record is availible at https://doi.org/10.1242/jeb.217000

: Emetine Inhibits Zika And Ebola Virus Infections Through Two Molecular Mechanisms; The re-emergence of Zika virus (ZIKV) and Ebola virus (EBOV) poses serious and continued threats to the global public health. Effective therapeutics for these maladies is an unmet need. Here, we show that emetine, an anti-protozoal agent, potently inhibits ZIKV and EBOV infection with a low nanomolar half maximal inhibitory concentration (IC50) in vitro and potent activity in vivo. Two mechanisms of action for emetine are identified: the inhibition of ZIKV NS5 polymerase activity and disruption of lysosomal function. Emetine also inhibits EBOV entry. Cephaeline, a desmethyl analog of emetine, which may be better tolerated in patients than emetine, exhibits a similar efficacy against both ZIKV and EBOV infections. Hence, emetine and cephaeline offer pharmaceutical therapies against both ZIKV and EBOV infection., Keywords: system, identification, models, rna, assay, dengue, cardiotoxicity, niemann-pick c1, repurposing screen, Publication Note: The publisher’s version of record is available at https://doi.org/10.1038/s41421-018-0034-1

: Emetine inhibits Zika and Ebola virus infections through two molecular mechanisms; The re-emergence of Zika virus (ZIKV) and Ebola virus (EBOV) poses serious and continued threats to the global public health. Effective therapeutics for these maladies is an unmet need. Here, we show that emetine, an anti-protozoal agent, potently inhibits ZIKV and EBOV infection with a low nanomolar half maximal inhibitory concentration (IC) in vitro and potent activity in vivo. Two mechanisms of action for emetine are identified: the inhibition of ZIKV NS5 polymerase activity and disruption of lysosomal function. Emetine also inhibits EBOV entry. Cephaeline, a desmethyl analog of emetine, which may be better tolerated in patients than emetine, exhibits a similar efficacy against both ZIKV and EBOV infections. Hence, emetine and cephaeline offer pharmaceutical therapies against both ZIKV and EBOV infection., Grant Number: R21 NS100477, R35 NS097370, R01 AI089539, R37 NS047344, U19 AI109762, U19 AI131130, R01 AI079110, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5986771.

: Enhanced cellular uptake of size-separated lipophilic silicon nanoparticles.; Specific size, shape and surface chemistry influence the biological activity of nanoparticles. In the case of lipophilic nanoparticles, which are widely used in consumer products, there is evidence that particle size and formulation influences skin permeability and that lipophilic particles smaller than 6 nm can embed in lipid bilayers. Since most nanoparticle synthetic procedures result in mixtures of different particles, post-synthetic purification promises to provide insights into nanostructure-function relationships. Here we used size-selective precipitation to separate lipophilic allyl-benzyl-capped silicon nanoparticles into monodisperse fractions within the range of 1 nm to 5 nm. We measured liposomal encapsulation and cellular uptake of the monodisperse particles and found them to have generally low cytotoxicities in Hela cells. However, specific fractions showed reproducibly higher cytotoxicity than other fractions as well as the unseparated ensemble. Measurements indicate that the cytotoxicity mechanism involves oxidative stress and the differential cytotoxicity is due to enhanced cellular uptake by specific fractions. The results indicate that specific particles, with enhanced suitability for incorporation into lipophilic regions of liposomes and subsequent in vitro delivery to cells, are enriched in certain fractions., Grant Number: R01 GM107172, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5341124.

: Environmental Forcing And Predator Consumption Outweigh The Nonconsumptive Effects Of Multiple Predators On Oyster Reefs; The ability to predict how predators structure ecosystems has been shown to depend on identifying both consumptive effects (CEs) and nonconsumptive effects (NCEs) of predators on prey fitness. Prey populations may also be affected by interactions between multiple predators across life stages of the prey and by environmental factors such as disturbance. However, the intersection of these multiple drivers of prey dynamics has yet to be empirically evaluated. We addressed this knowledge gap using eastern oysters (Crassostrea virginica), a species known to suffer NCEs, as the focal prey. Over 4 months, we manipulated orthogonally the life stage (none, juvenile, adult, or both) at which oysters experienced simulated predation (CE) and exposure to olfactory cues of a juvenile oyster predator (crab), adult predator (conch), sequentially the crab and then the conch, or none. We replicated this experiment at three sites along an environmental gradient in a Florida (USA) estuary. For both juvenile and adult oysters, survival was reduced solely by CEs, and variation in growth was best explained by among-site variation in water flow, with a much smaller and negative effect of predator cue. Adults exposed to conch cue exhibited reduced growth (an NCE), but this effect was outweighed by a positive CE on growth: Surviving oysters grew faster at lower densities. Finally, conch cue reduced larval settlement (another NCE), but this was swamped by among-site variation in larval supply. This research highlights how strong environmental gradients and predator CEs may outweigh the influence of NCEs, even in prey known to respond to predator cues. These findings serve as a cautionary tale for the importance of evaluating NCE processes over temporal scales and across environmental gradients relevant to prey demography., impact, risk, predation, food, complexity, antipredator response, density-mediated effect, environmental gradient, intimidation, larval recruitment, ontogeny, predator cue, refuge, trait-mediated effect, trophic cascades, The publisher's version of record is availible at https://doi.org/10.1002/ecy.3041

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