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: Epithelial Tumors Originate in Tumor Hotspots, a Tissue-Intrinsic Microenvironment; Malignant tumors are caused by uncontrolled proliferation of transformed mutant cells that have lost the ability to maintain tissue integrity. Although a number of causative genetic backgrounds for tumor development have been discovered, the initial steps mutant cells take to escape tissue integrity and trigger tumorigenesis remain elusive. Here, we show through analysis of conserved neoplastic tumor-suppressor genes (nTSGs) in Drosophila wing imaginal disc epithelia that tumor initiation depends on tissue-intrinsic local cytoarchitectures, causing tumors to consistently originate in a specific region of the tissue. In this "tumor hotspot" where cells constitute a network of robust structures on their basal side, nTSG-deficient cells delaminate from the apical side of the epithelium and begin tumorigenic overgrowth by exploiting endogenous Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling activity. Conversely, in other regions, the "tumor coldspot" nTSG-deficient cells are extruded toward the basal side and undergo apoptosis. When the direction of delamination is reversed through suppression of RhoGEF2, an activator of the Rho family small GTPases, and JAK/STAT is activated ectopically in these coldspot nTSG-deficient cells, tumorigenesis is induced. These data indicate that two independent processes, apical delamination and JAK/STAT activation, are concurrently required for the initiation of nTSG-deficient-induced tumorigenesis. Given the conservation of the epithelial cytoarchitecture, tumorigenesis may be generally initiated from tumor hotspots by a similar mechanism., Keywords: activation, cancer, cell-shape changes, drhogef2, drosophila gastrulation, planar spindle orientation, polarity, protein, rhogef2, signaling pathway, Publication Note: The publisher’s version of record is available at https://doi.org/10.1371/journal.pbio.1002537

: Epithelial Tumors Originate in Tumor Hotspots, a Tissue-Intrinsic Microenvironment.; Malignant tumors are caused by uncontrolled proliferation of transformed mutant cells that have lost the ability to maintain tissue integrity. Although a number of causative genetic backgrounds for tumor development have been discovered, the initial steps mutant cells take to escape tissue integrity and trigger tumorigenesis remain elusive. Here, we show through analysis of conserved neoplastic tumor-suppressor genes (nTSGs) in Drosophila wing imaginal disc epithelia that tumor initiation depends on tissue-intrinsic local cytoarchitectures, causing tumors to consistently originate in a specific region of the tissue. In this "tumor hotspot" where cells constitute a network of robust structures on their basal side, nTSG-deficient cells delaminate from the apical side of the epithelium and begin tumorigenic overgrowth by exploiting endogenous Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling activity. Conversely, in other regions, the "tumor coldspot" nTSG-deficient cells are extruded toward the basal side and undergo apoptosis. When the direction of delamination is reversed through suppression of RhoGEF2, an activator of the Rho family small GTPases, and JAK/STAT is activated ectopically in these coldspot nTSG-deficient cells, tumorigenesis is induced. These data indicate that two independent processes, apical delamination and JAK/STAT activation, are concurrently required for the initiation of nTSG-deficient-induced tumorigenesis. Given the conservation of the epithelial cytoarchitecture, tumorigenesis may be generally initiated from tumor hotspots by a similar mechanism., Grant Number: R01 GM072562, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5008749.

: Esco1 And Ctcf Enable Formation Of Long Chromatin Loops By Protecting Cohesin(stag1) From Wapl; Eukaryotic genomes are folded into loops. It is thought that these are formed by cohesin complexes via extrusion, either until loop expansion is arrested by CTCF or until cohesin is removed from DNA by WAPL. Although WAPL limits cohesin's chromatin residence time to minutes, it has been reported that some loops exist for hours. How these loops can persist is unknown. We show that during G1-phase, mammalian cells contain acetylated cohesin(STAG1) which binds chromatin for hours, whereas cohesin(STAG2) binds chromatin for minutes. Our results indicate that CTCF and the acetyltransferase ESCO1 protect a subset of cohesin(STAG1) complexes from WAPL, thereby enable formation of long and presumably long-lived loops, and that ESCO1, like CTCF, contributes to boundary formation in chromatin looping. Our data are consistent with a model of nested loop extrusion, in which acetylated cohesin(STAG1) forms stable loops between CTCF sites, demarcating the boundaries of more transient cohesin(STAG2) extrusion activity., reveals, cohesion, binding, mammalian genomes, domains, dna, molecular-dynamics simulations, cohesin-sa1, pds5 promotes, sororin, The publisher's version of record is availible at https://doi.org/10.7554/eLife.52091

: Evaluating The Performance Of De Novo Assembly Methods For Venom-gland Transcriptomics; Venom-gland transcriptomics is a key tool in the study of the evolution, ecology, function, and pharmacology of animal venoms. In particular, gene-expression variation and coding sequences gained through transcriptomics provide key information for explaining functional venom variation over both ecological and evolutionary timescales. The accuracy and usefulness of inferences made through transcriptomics, however, is limited by the accuracy of the transcriptome assembly, which is a bioinformatic problem with several possible solutions. Several methods have been employed to assemble venom-gland transcriptomes, with the Trinity assembler being the most commonly applied among them. Although previous evidence of variation in performance among assembly software exists, particularly regarding recovery of difficult-to-assemble multigene families such as snake venom metalloproteinases, much work to date still employs a single assembly method. We evaluated the performance of several commonly used de novo assembly methods for the recovery of both nontoxin transcripts and complete, high-quality venom-gene transcripts across eleven snake and four scorpion transcriptomes. We varied k-mer sizes used by some assemblers to evaluate the impact of k-mer length on transcript recovery. We showed that the recovery of nontoxin transcripts and toxin transcripts is best accomplished through different assembly software, with SDT at smaller k-mer lengths and Trinity being best for nontoxin recovery and a combination of SeqMan NGen and a seed-and-extend approach implemented in Extender as the best means of recovering a complete set of toxin transcripts. In particular, Extender was the only means tested capable of assembling multiple isoforms of the diverse snake venom metalloproteinase family, while traditional approaches such as Trinity recovered at most one metalloproteinase transcript. Our work demonstrated that traditional metrics of assembly performance are not predictive of performance in the recovery of complete and high quality toxin genes. Instead, effective venom-gland transcriptomic studies should combine and quality-filter the results of several assemblers with varying algorithmic strategies., Keywords: evolution, rna-seq data, genome, proteomics, toxin diversity, expression differentiation, generation sequencing data, reveal, scorpion, snake, snake venomics, transcriptome assembly, venom-gland transcriptome, Publication Note: The publisher’s version of record is available at https://doi.org/10.3390/toxins10060249

: Evaluating the Performance of De Novo Assembly Methods for Venom-Gland Transcriptomics.; Venom-gland transcriptomics is a key tool in the study of the evolution, ecology, function, and pharmacology of animal venoms. In particular, gene-expression variation and coding sequences gained through transcriptomics provide key information for explaining functional venom variation over both ecological and evolutionary timescales. The accuracy and usefulness of inferences made through transcriptomics, however, is limited by the accuracy of the transcriptome assembly, which is a bioinformatic problem with several possible solutions. Several methods have been employed to assemble venom-gland transcriptomes, with the Trinity assembler being the most commonly applied among them. Although previous evidence of variation in performance among assembly software exists, particularly regarding recovery of difficult-to-assemble multigene families such as snake venom metalloproteinases, much work to date still employs a single assembly method. We evaluated the performance of several commonly used de novo assembly methods for the recovery of both nontoxin transcripts and complete, high-quality venom-gene transcripts across eleven snake and four scorpion transcriptomes. We varied -mer sizes used by some assemblers to evaluate the impact of -mer length on transcript recovery. We showed that the recovery of nontoxin transcripts and toxin transcripts is best accomplished through different assembly software, with SDT at smaller -mer lengths and Trinity being best for nontoxin recovery and a combination of SeqMan NGen and a seed-and-extend approach implemented in Extender as the best means of recovering a complete set of toxin transcripts. In particular, Extender was the only means tested capable of assembling multiple isoforms of the diverse snake venom metalloproteinase family, while traditional approaches such as Trinity recovered at most one metalloproteinase transcript. Our work demonstrated that traditional metrics of assembly performance are not predictive of performance in the recovery of complete and high quality toxin genes. Instead, effective venom-gland transcriptomic studies should combine and quality-filter the results of several assemblers with varying algorithmic strategies., Keywords: Scorpion, Snake, Transcriptome assembly, Venom-gland transcriptome, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6024825.

: Evolution In A Community Context; Species that coexist in diverse natural communities interact in complex ways that alter each other's abundances and affect selection on each other's traits. Consequently, predicting trait evolution in natural communities may require understanding ecological and evolutionary dynamics involving a number of species. In August 2016, the American Society of Naturalists sponsored a symposium to explore evolution in a community context, focusing on microevolutionary processes. Here we provide an introduction to our perspectives on this topic by defining the context and describing some examples of when and how microevolutionary responses to multiple species may differ from evolution in isolation or in two-species communities. We find that indirect ecological and evolutionary effects can result in nonadditive selection and evolution that cannot be predicted from pairwise interactions. Genetic correlations of ecological traits in one species can alter trait evolution and adaptation aswell as the abundances of other species. In general, evolution in multispecies communities can change ecological interactions, which then feed back to future evolutionary changes in ways that depend on these indirect effects. We suggest avenues for future research in this field, including determining the circumstances under which pairwise evolution does not adequately describe evolutionary trajectories., Keywords: life-history evolution, rapid evolution, coevolution, character displacement, diffuse coevolution, diffuse selection, ecological communities, g-matrix, indirect effects, intraguild predation, intraspecific variation, local adaptation, natural selection, natural-selection, species interactions, Publication Note: The publisher's version of record is available at https://doi.org/10.1086/695835

: Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life; Background: Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae. Results: Our aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus. As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma. Conclusions: The Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups., Keywords: Anchored Hybrid Enrichment, Anchored phylogenomics, Arachnida, Araneae, Conserved regions, gene trees, genomic perspective, maximum-likelihood, Mygalomorphae, phylogenetic inference, phylogenomics resolves, species trees, Targeted sequence capture, target-enrichment, Ultraconserved elements, web evolution, Publication Note: The publisher’s version of record is available at http://www.dx.doi.org/10.1186/s12862-016-0769-y

: Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life.; Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae. Our aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus. As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma. The Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups., Keywords: Anchored Hybrid Enrichment, Anchored phylogenomics, Arachnida, Araneae, Conserved regions, Mygalomorphae, Targeted sequence capture, Ultraconserved elements, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062932.

: Experimental Study Of Species Invasion; Much of our understanding of natural invasions is retrospective, based on data acquired after invaders become established. As a consequence, we know little about the characteristics of the early population growth and habitat use of the invaders during establishment. Here we report on experimental introductions of guppies into natural streams in which we conducted monthly censuses of each population. Two of the four introductions were in streams with thinned canopies, which mimic a common form of habitat disturbance. We conducted similar censuses of natural populations to characterize natural population densities and generate a null distribution against which we could test a priori hypotheses about the establishment of the experimental invaders. We constructed a pedigree for one population, which enabled us to quantify lifetime reproductive success. Population simulations predict that the nature of the introduced population's life history, in combination with reduced risk of predation in the introduction sites, will result in explosive population growth; however, populations of introduced invaders instead grew to match densities observed in natural streams with intact canopies. Experimental populations in streams with thinned canopies grew to densities that often exceeded those of natural streams with intact canopies. High population densities were associated with the increased use of marginal habitat. Adult females and males that moved into marginal habitat suffered no apparent fitness loss, suggesting lower population densities found there compensated for lower habitat quality. Our results suggest that the ecological setting in which invasions occur plays a role at least comparable in importance to that of the invader's inherent characteristics in shaping early population growth and habitat use., communities, predation, enemy release, establishment, experimental introduction, genetic-basis, guppies poecilia-reticulata, habitat selection, habitat disturbance, habitat selection, introductions, invasive species, life-history evolution, local adaptation, Poecilia reticulata, trinidadian guppies, The publisher's version of record is availible at https://doi.org/10.1002/ecm.1413

: Experimental evidence that dispersal drives ant community assembly in human-altered ecosystems; A key shortcoming in our understanding of exotic species' success is that it is not known how post-introduction dispersal contributes to the success of exotic species and the reassembly of invaded communities. Exotic and native species face poorly understood competition-colonization trade-offs in heterogeneous landscapes of natural and anthropogenic habitats. We conducted three experiments that tested how ant queen behavior during dispersal affects community composition. Using experimental plots, we tested whether (1) different types of habitat disturbance and (2) different sizes of habitat disturbance affected the abundance of newly mated queens landing in the plots. The three most abundant species captured were the exotic fire ant Solenopsis invicta, and the native species Brachymyrmex depilis, and S.pergandei, respectively. When queens were considered collectively, more queens landed in plowed, sand-added, and roadside plots than in control or mow plots, in other words, in the more heavily disturbed plots. We also tested (3) the effect of habitat manipulations on the survival of newly mated fire ant queens (Solenopsis invicta). Soil disturbance (tilling), lack of shade, and removal (poisoning) of the ant community resulted in the greatest fire ant colony survivorship. Collectively, experiments revealed that both exotic and native newly mated ant queens select open, human-altered ecosystems for founding new colonies. The selection of such habitats by fire ant queens leads to their successful colony founding and ultimately to their dominance in those habitats. Selection of disturbed habitats is therefore advantageous for exotic species but is an ecological trap for native species because they do not often succeed in founding colonies in these habitats., Keywords: argentine ant, arthropod-community, biological invasion, disturbance, exotic ants, fire ant, global change, habitat selection, hymenoptera-formicidae, mass effects, Solenopsis invicta, solenopsis-invicta, species coexistence, species sorting, upland ecosystems, Publication Note: The publisher’s version of record is available at http://www.dx.doi.org/10.1890/15-1105.1

: Expression Differentiation Is Constrained to Low-Expression Proteins over Ecological Timescales.; Protein expression level is one of the strongest predictors of protein sequence evolutionary rate, with high-expression protein sequences evolving at slower rates than low-expression protein sequences largely because of constraints on protein folding and function. Expression evolutionary rates also have been shown to be negatively correlated with expression level across human and mouse orthologs over relatively long divergence times (i.e., ∼100 million years). Long-term evolutionary patterns, however, often cannot be extrapolated to microevolutionary processes (and vice versa), and whether this relationship holds for traits evolving under directional selection within a single species over ecological timescales (i.e., <5000 years) is unknown and not necessarily expected. Expression is a metabolically costly process, and the expression level of a particular protein is predicted to be a tradeoff between the benefit of its function and the costs of its expression. Selection should drive the expression level of all proteins close to values that maximize fitness, particularly for high-expression proteins because of the increased energetic cost of production. Therefore, stabilizing selection may reduce the amount of standing expression variation for high-expression proteins, and in combination with physiological constraints that may place an upper bound on the range of beneficial expression variation, these constraints could severely limit the availability of beneficial expression variants. To determine whether rapid-expression evolution was restricted to low-expression proteins owing to these constraints on highly expressed proteins over ecological timescales, we compared venom protein expression levels across mainland and island populations for three species of pit vipers. We detected significant differentiation in protein expression levels in two of the three species and found that rapid-expression differentiation was restricted to low-expression proteins. Our results suggest that various constraints on high-expression proteins reduce the availability of beneficial expression variants relative to low-expression proteins, enabling low-expression proteins to evolve and potentially lead to more rapid adaptation., Keywords: Adaptation, Evolutionary rates, Protein expression, Selective constraints, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4701091.

: ExtraPEG; Initially thought to be a means for cells to eliminate waste, secreted extracellular vesicles, known as exosomes, are now understood to mediate numerous healthy and pathological processes. Though abundant in biological fluids, purifying exosomes has been challenging because their biophysical properties overlap with other secreted cell products. Easy-to-use commercial kits for harvesting exosomes are now widely used, but the relative low-purity and high-cost of the preparations restricts their utility. Here we describe a method for purifying exosomes and other extracellular vesicles by adapting methods for isolating viruses using polyethylene glycol. This technique, called ExtraPEG, enriches exosomes from large volumes of media rapidly and inexpensively using low-speed centrifugation, followed by a single small-volume ultracentrifugation purification step. Total protein and RNA harvested from vesicles is sufficient in quantity and quality for proteomics and sequencing analyses, demonstrating the utility of this method for biomarker discovery and diagnostics. Additionally, confocal microscopy studies suggest that the biological activity of vesicles is not impaired. The ExtraPEG method can be easily adapted to enrich for different vesicle populations, or as an efficient precursor to subsequent purification techniques, providing a means to harvest exosomes from many different biological fluids and for a wide variety of purposes., Keywords: cell-derived exosomes, communication, disease, identification, Microenvironment, microvesicles, proteins, purification, system, trypan blue, Publication Note: The publisher’s version of record is available at http://www.dx.doi.org/10.1038/srep23978

: Extreme warming challenges sentinel status of kelp forests as indicators of climate change.; The desire to use sentinel species as early warning indicators of impending climate change effects on entire ecosystems is attractive, but we need to verify that such approaches have sound biological foundations. A recent large-scale warming event in the North Pacific Ocean of unprecedented magnitude and duration allowed us to evaluate the sentinel status of giant kelp, a coastal foundation species that thrives in cold, nutrient-rich waters and is considered sensitive to warming. Here, we show that giant kelp and the majority of species that associate with it did not presage ecosystem effects of extreme warming off southern California despite giant kelp's expected vulnerability. Our results challenge the general perception that kelp-dominated systems are highly vulnerable to extreme warming events and expose the more general risk of relying on supposed sentinel species that are assumed to be very sensitive to climate change., Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159872.

: FSU_pmch_29391952; Endogenous circadian oscillators orchestrate rhythms at the cellular, physiological, and behavioral levels across species to coordinate activity, for example, sleep/wake cycles, metabolism, and learning and memory, with predictable environmental cycles. The 21st century has seen a dramatic rise in the incidence of circadian and sleep disorders with globalization, technological advances, and the use of personal electronics. The circadian clock modulates alcohol- and drug-induced behaviors with circadian misalignment contributing to increased substance use and abuse. Invertebrate models, such as , have proven invaluable for the identification of genetic and molecular mechanisms underlying highly conserved processes including the circadian clock, drug tolerance, and reward systems. In this review, we highlight the contributions of as a model system for understanding the bidirectional interactions between the circadian system and the drugs of abuse, alcohol and cocaine, and illustrate the highly conserved nature of these interactions between and mammalian systems. Research in provides mechanistic insights into the corresponding behaviors in higher organisms and can be used as a guide for targeted inquiries in mammals., Grant Number: R21 AA021233, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5748135.

: Florida Harvester Ant, Pogonomyrmex badius, Relies on Germination to Consume Large Seeds.; The Florida harvester ant, Pogonomyrmex badius, is one of many ant species and genera that stores large numbers of seeds in damp, underground chambers for later consumption. A comparison of the sizes of seeds recovered from storage chambers with those of seed husks discarded following consumption revealed that the used seeds are far smaller than stored seeds. This difference in use-rate was confirmed in field and laboratory colonies by offering marked seeds of various sizes and monitoring the appearance of size-specific chaff. Because foragers collect a range of seed sizes but only open small seeds, large seeds accumulate, forming 70% or more of the weight of seed stores. Major workers increase the rates at which small and medium seeds are opened, but do not increase the size range of opened seeds. Experiments limiting ant access to portions of natural seed chambers showed that seeds germinate during storage, but that the ants rapidly remove them. When offered alongside non germinating seeds, germinating seeds were preferentially fed to larvae. The rate of germination during the annual cycle was determined by both burial in artificial chambers at various depths and under four laboratory temperatures. The germination rate depends upon the species of seed, the soil/laboratory temperature and/or the elapsed time. The seasonal soil temperature cycle generated germination patterns that vary with the mix of locally-available seeds. Taken together, exploitation of germination greatly increases the resources available to the ants in space and time. While the largest seeds may have the nutritional value of 15 small seeds, the inability of workers to open large seeds at will precludes them from rapid use during catastrophic events. The harvester ant's approach to seed harvesting is therefore two-pronged, with both immediate and delayed payoffs arising from the tendency to forage for a wide variety of seeds sizes., Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5125654.

: Fluorescent Protein-Based Ca2+ Sensor Reveals Global, Divalent Cation-Dependent Conformational Changes in Cardiac Troponin C; Cardiac troponin C (cTnC) is a key effector in cardiac muscle excitation-contraction coupling as the Ca2+ sensing subunit responsible for controlling contraction. In this study, we generated several FRET sensors for divalent cations based on cTnC flanked by a donor fluorescent protein (CFP) and an acceptor fluorescent protein (YFP). The sensors report Ca2+ and Mg2+ binding, and relay global structural information about the structural relationship between cTnC's N- and C-domains. The sensors were first characterized using end point titrations to decipher the response to Ca2+ binding in the presence or absence of Mg2+. The sensor that exhibited the largest responses in end point titrations, CTV-TnC, (Cerulean, TnC, and Venus) was characterized more extensively. Most of the divalent cation-dependent FRET signal originates from the high affinity C-terminal EF hands. CTV-TnC reconstitutes into skinned fiber preparations indicating proper assembly of troponin complex, with only similar to 0.2 pCa unit rightward shift of Ca2+-sensitive force development compared to WT-cTnC. Affinity of CTV-TnC for divalent cations is in agreement with known values for WT-cTnC. Analytical ultracentrifugation indicates that CTV-TnC undergoes compaction as divalent cations bind. C-terminal sites induce ion-specific (Ca2+ versus Mg2+) conformational changes in cTnC. Our data also provide support for the presence of additional, non-EF-hand sites on cTnC for Mg2+ binding. In conclusion, we successfully generated a novel FRET-Ca2+ sensor based on full length cTnC with a variety of cellular applications. Our sensor reveals global structural information about cTnC upon divalent cation binding., Keywords: calcium-binding, genetically encoded indicators, hypertrophic cardiomyopathy, magnesium binding-sites, mutations, myofibrillar adenosine-triphosphatase, neutron-scattering, regulatory domain, skeletal-muscle fibers, thin-filament, Publication Note: The publisher’s version of record is available at http://www.dx.doi.org/10.1371/journal.pone.0164222

: From Growing to Biology; Ready to find out how plants are grown and function? Take a fantastic voyage through plants. From Growing to Biology: Plants 1e brings the latest information for understanding of traditional and modern plant growing, form, and production. Topics covered in 30 chapters include concise and up-to-date ‘big picture’ infographics, student learning outcomes (SLOs), key vocabulary, assessment, as well as identification of 120 species, and more. Moreover, author Dr. G. Hacisalihoglu emphasizes on leaning concepts, binding those concepts together with visuals approach to make learning faster and more memorable.From Growing to Biology: Plants 1e is packed full of horticultural information that is ideal for both academia and industry growers. It is basic enough that if you are just getting started learning plants, you will be able to catch up. Always remember that practice makes permanent and keep going to take your learning plant bio to new levels., Plant biology, This open textbook was funded in part by an Alternative Textbook Grant from FSU Libraries. An author bio and feedback survey are available on the book's Manifold project page: https://doi.org/10.33009/fsop_hacisalihoglu0421 .

: From Shelf to Shelf; Describing patterns of connectivity among populations of species with widespread distributions is particularly important in understanding the ecology and evolution of marine species. In this study, we examined patterns of population differentiation, migration, and historical population dynamics using microsatellite and mitochondrial loci to test whether populations of the epinephelid fish, Gag, Mycteroperca microlepis, an important fishery species, are genetically connected across the Gulf of Mexico and if so, whether that connectivity is attributable to either contemporary or historical processes. Populations of Gag on the Campeche Bank and the West Florida Shelf show significant, but low magnitude, differentiation. Time since divergence/expansion estimates associated with historical population dynamics indicate that any population or spatial expansions indicated by population genetics would have likely occurred in the late Pleistocene. Using coalescent-based approaches, we find that the best model for explaining observed spatial patterns of contemporary genetic variation is one of asymmetric gene flow, with movement from Campeche Bank to the West Florida Shelf. Both estimated migration rates and ecological data support the hypothesis that Gag populations throughout the Gulf of Mexico are connected via present day larval dispersal. Demonstrating this greatly expanded scale of connectivity for Gag highlights the influence of “ghost” populations (sensu Beerli) on genetic patterns and presents a critical consideration for both fisheries management and conservation of this and other species with similar genetic patterns, Publication Note: Publisher's Version also Available at http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0120676, Preferred Citation: Jue, N. K., Brulé, T., Coleman, F. C., & Koenig, C. C. (2015). From Shelf to Shelf: Assessing Historical and Contemporary Genetic Differentiation and Connectivity across the Gulf of Mexico in Gag, Mycteroperca microlepis. PloS one, 10(4), e0120676.

: Function of Succinoglycan Polysaccharide in Sinorhizobium meliloti Host Plant Invasion Depends on Succinylation, Not Molecular Weight; The acidic polysaccharide succinoglycan produced by the rhizobial symbiont Sinorhizobium meliloti 1021 is required for this bacterium to invade the host plant Medicago truncatula and establish a nitrogen-fixing symbiosis. S. meliloti mutants that cannot make succinoglycan cannot initiate invasion structures called infection threads in plant root hairs. S. meliloti exoH mutants that cannot succinylate succinoglycan are also unable to form infection threads, despite the fact that they make large quantities of succinoglycan. Succinoglycan produced by exoH mutants is refractory to cleavage by the glycanases encoded by exoK and exsH, and thus succinoglycan produced by exoH mutants is made only in the high-molecular-weight (HMW) form. One interpretation of the symbiotic defect of exoH mutants is that the low-molecular-weight (LMW) form of succinoglycan is required for infection thread formation. However, our data demonstrate that production of the HMW form of succinoglycan by S. meliloti 1021 is sufficient for invasion of the host M. truncatula and that the LMW form is not required. Here, we show that S. meliloti strains deficient in the exoK- and exsH-encoded glycanases invade M. truncatula and form a productive symbiosis, although they do this with somewhat less efficiency than the wild type. We have also characterized the polysaccharides produced by these double glycanase mutants and determined that they consist of only HMW succinoglycan and no detectable LMW succinoglycan. This demonstrates that LMW succinoglycan is not required for host invasion. These results suggest succinoglycan function is not dependent upon the presence of a small, readily diffusible form. IMPORTANCE Sinorhizobium meliloti is a bacterium that forms a beneficial symbiosis with legume host plants. S. meliloti and other rhizobia convert atmospheric nitrogen to ammonia, a nutrient source for the host plant. To establish the symbiosis, rhizobia must invade plant roots, supplying the proper signals to prevent a plant immune response during invasion. A polysaccharide, succinoglycan, produced by S. meliloti is required for successful invasion. Here, we show that the critical feature of succinoglycan that allows infection to proceed is the attachment of a "succinyl" chemical group and that the chain length of succinoglycan is much less important for its function. We also show that none of the short-chain versions of succinoglycan is produced in the absence of two chain-cleaving enzymes., Keywords: calcofluor-binding exopolysaccharide, capsular polysaccharide, deficient mutants, form ineffective nodules, k-polysaccharide, leguminosarum bv trifolii, medicago-truncatula, rhizobium-meliloti, structural-characterization, symbiotically important exopolysaccharide, Publication Note: The publisher’s version of record is available at http://www.dx.doi.org/10.1128/mBio.00606-16

: Function of Succinoglycan Polysaccharide in Sinorhizobium meliloti Host Plant Invasion Depends on Succinylation, Not Molecular Weight.; The acidic polysaccharide succinoglycan produced by the rhizobial symbiont Sinorhizobium meliloti 1021 is required for this bacterium to invade the host plant Medicago truncatula and establish a nitrogen-fixing symbiosis. S. meliloti mutants that cannot make succinoglycan cannot initiate invasion structures called infection threads in plant root hairs. S. meliloti exoH mutants that cannot succinylate succinoglycan are also unable to form infection threads, despite the fact that they make large quantities of succinoglycan. Succinoglycan produced by exoH mutants is refractory to cleavage by the glycanases encoded by exoK and exsH, and thus succinoglycan produced by exoH mutants is made only in the high-molecular-weight (HMW) form. One interpretation of the symbiotic defect of exoH mutants is that the low-molecular-weight (LMW) form of succinoglycan is required for infection thread formation. However, our data demonstrate that production of the HMW form of succinoglycan by S. meliloti 1021 is sufficient for invasion of the host M. truncatula and that the LMW form is not required. Here, we show that S. meliloti strains deficient in the exoK- and exsH-encoded glycanases invade M. truncatula and form a productive symbiosis, although they do this with somewhat less efficiency than the wild type. We have also characterized the polysaccharides produced by these double glycanase mutants and determined that they consist of only HMW succinoglycan and no detectable LMW succinoglycan. This demonstrates that LMW succinoglycan is not required for host invasion. These results suggest succinoglycan function is not dependent upon the presence of a small, readily diffusible form. Sinorhizobium meliloti is a bacterium that forms a beneficial symbiosis with legume host plants. S. meliloti and other rhizobia convert atmospheric nitrogen to ammonia, a nutrient source for the host plant. To establish the symbiosis, rhizobia must invade plant roots, supplying the proper signals to prevent a plant immune response during invasion. A polysaccharide, succinoglycan, produced by S. meliloti is required for successful invasion. Here, we show that the critical feature of succinoglycan that allows infection to proceed is the attachment of a "succinyl" chemical group and that the chain length of succinoglycan is much less important for its function. We also show that none of the short-chain versions of succinoglycan is produced in the absence of two chain-cleaving enzymes., Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4916376.

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