Springing forward: Migrating songbirds catch up with the start of spring in North America.

In temperate regions, the annual pattern of spring onset can be envisioned as a 'green wave' of emerging vegetation that moves across continents from low to high latitudes, signifying increasing food availability for consumers. Many herbivorous migrants 'surf' such resource waves, timing their movements to exploit peak vegetation resources in early spring. Although less well studied at the individual level, secondary consumers such as insectivorous songbirds can track vegetation phenology during migration as well. We hypothesized that four species of ground-foraging songbirds in eastern North America-two warblers and two thrushes-time their spring migrations to coincide with later phases of vegetation phenology, corresponding to increased arthropod prey, and predicted they would match their migration rate to the green wave but trail behind it rather than surfing its leading edge. We further hypothesized that the rate at which spring onset progresses across the continent influences bird migration rates, such that individuals adjust migration timing within North America to phenological conditions they experience en route. To test our hypotheses, we used a continent-wide automated radio telemetry network to track individual songbirds on spring migration between the U.S. Gulf Coast region and northern locations closer to their breeding grounds. We measured vegetation phenology using two metrics of spring onset, the spring index first leaf date and the normalized difference vegetation index (NDVI), then calculated the rate and timing of spring onset relative to bird detections. All individuals arrived in the southeastern United States well after local spring onset. Counter to our expectations, we found that songbirds exhibited a 'catching up' pattern: Individuals migrated faster than the green wave of spring onset, effectively closing in on the start of spring as they approached breeding areas. While surfing of resource waves is a well-documented migration strategy for herbivorous waterfowl and ungulates, individual songbirds in our study migrated faster than the green wave and increasingly caught up to its leading edge en route. Consequently, songbirds experience a range of vegetation phenophases while migrating through North America, suggesting flexibility in their capacity to exploit variable resources in spring.

En las regiones templadas, el patrón anual de inicio de la primavera puede concebirse como una "ola verde" de vegetación emergente que se desplaza por los continentes desde las latitudes bajas a las altas, lo que significa una mayor disponibilidad de alimento para los consumidores. Muchos herbívoros migratorios "surfean" estas olas de recursos, programando sus movimientos para aprovechar los picos de vegetación a principios de primavera. Aunque menos estudiados a nivel de individuo, los consumidores secundarios, como las aves terrestres insectívoras, también pueden seguir la fenología de la vegetación durante la migración. Hipotetizamos es que cuatro especies de aves terrestres que se alimentan en el suelo en el este de Norteamérica - dos reinitas y dos zorzales - programan sus migraciones primaverales para que coincidan con las fases más tardías de la fenología de la vegetación, que se corresponden con un aumento de artrópodos, y predijimos que sincronizarian su ritmo de migración con la ola verde, pero que irían detrás de ella en lugar de surfear su borde delantero. También hipotetizamos que el ritmo al que avanza la primavera en el continente influye en las tasas de migración de las aves, de modo que los individuos ajustan la fecha de migración dentro de Norteamérica a las condiciones fenológicas que experimentan en ruta. Para comprobar nuestras hipótesis, utilizamos una red automatizada de radiotelemetría a escala continental para seguir individuos en su migración primaveral entre la región de la costa del Golfo de EEUU y las localidades septentrionales más cercanas a sus zonas de cría. Medimos la fenología de la vegetación utilizando dos métricas del inicio de la primavera, el índice de la fecha de la primera hoja primaveral y el índice de vegetación de diferencia normalizada (NDVI), luego calculamos la tasa y el tiempo de la aparaciòn de la primavera relativo a las detecciones de aves. Todos los individuos llegaron al sureste de EEUU bastante después del inicio de la primavera local. Contrario a nuestras expectativas, descubrimos que las aves terrestres mostraron un patrón de Carrera para "ponerse al día": los individuos migraron frente a la ola verde del inicio de la primavera, acercándose efectivamente al inicio de la primavera a medida que llegaban a las zonas de cría. Mientras que el surfing de las olas de recursos es una estrategia migratoria bien documentada para las aves acuáticas herbívoras y los ungulados, los individuos de aves terrestres de nuestro estudio migraron más rápido que la ola verde y alcanzaron cada vez más el borde delantero en ruta. En consecuencia, las aves terrestres experimentan una serie de fases fenológicas de la vegetación mientras migran a través de Norteamérica, lo que sugiere flexibilidad en su capacidad para explotar recursos variables en primavera.

Post-transcriptional control of executioner caspases by RNA-binding proteins.

Caspases are key components of apoptotic pathways. Regulation of caspases occurs at several levels, including transcription, proteolytic processing, inhibition of enzymatic function, and protein degradation. In contrast, little is known about the extent of post-transcriptional control of caspases. Here, we describe four conserved RNA-binding proteins (RBPs)-PUF-8, MEX-3, GLD-1, and CGH-1-that sequentially repress the CED-3 caspase in distinct regions of the Caenorhabditis elegans germline. We demonstrate that GLD-1 represses ced-3 mRNA translation via two binding sites in its 3' untranslated region (UTR), thereby ensuring a dual control of unwanted cell death: at the level of p53/CEP-1 and at the executioner caspase level. Moreover, we identified seven RBPs that regulate human caspase-3 expression and/or activation, including human PUF-8, GLD-1, and CGH-1 homologs PUM1, QKI, and DDX6. Given the presence of unusually long executioner caspase 3' UTRs in many metazoans, translational control of executioner caspases by RBPs might be a strategy used widely across the animal kingdom to control apoptosis.

SWI/SNF complexes in hematological malignancies: biological implications and therapeutic opportunities.

Hematological malignancies are a highly heterogeneous group of diseases with varied molecular and phenotypical characteristics. SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling complexes play significant roles in the regulation of gene expression, being essential for processes such as cell maintenance and differentiation in hematopoietic stem cells. Furthermore, alterations in SWI/SNF complex subunits, especially in ARID1A/1B/2, SMARCA2/4, and BCL7A, are highly recurrent across a wide variety of lymphoid and myeloid malignancies. Most genetic alterations cause a loss of function of the subunit, suggesting a tumor suppressor role. However, SWI/SNF subunits can also be required for tumor maintenance or even play an oncogenic role in certain disease contexts. The recurrent alterations of SWI/SNF subunits highlight not only the biological relevance of SWI/SNF complexes in hematological malignancies but also their clinical potential. In particular, increasing evidence has shown that mutations in SWI/SNF complex subunits confer resistance to several antineoplastic agents routinely used for the treatment of hematological malignancies. Furthermore, mutations in SWI/SNF subunits often create synthetic lethality relationships with other SWI/SNF or non-SWI/SNF proteins that could be exploited therapeutically. In conclusion, SWI/SNF complexes are recurrently altered in hematological malignancies and some SWI/SNF subunits may be essential for tumor maintenance. These alterations, as well as their synthetic lethal relationships with SWI/SNF and non-SWI/SNF proteins, may be pharmacologically exploited for the treatment of diverse hematological cancers.

Anatomy and development of the edible fruits of Cordiera concolor (Rubiaceae).

A comprehensive study on the fruit anatomy and development of Cordiera concolor was carried out to establish the origin of the gelatinous tissue surrounding the seeds at maturity. Cordiera currently belongs to tribe Cordiereae, forming part of the species-rich lineage called Gardenieae complex. Most genera of Gardenieae complex has many-seeded fleshy fruits, with seeds usually imbedded in a pulp, which historically was considered of a placental nature. For the histological analyses, fruits at different stages of development were fixed in formalin-acetic acid-alcohol and examined with light microscopy. The endocarp has no woody consistency, it is what classifies a fruit as berry. The pericarp is differentiated into three histological zones: 1) the exocarp, formed of the epidermis and the sub-epidermal tannin cells, 2) the mesocarp, consisting of parenchyma with tannins and druses, and 3) the endocarp, derived from the internal epidermis of the ovary. The placental tissue has little development during the formation of the pericarp. We concluded that the gelatinous tissue surrounding the seeds in the ripe fruit is formed of the mesocarp and endocarp. The present results disagree with the widely accepted conception of the placental origin of the gelatinous pulp surrounding the seeds in Gardenieae Complex species.

Anther structure and pollen development in species of Rubiaceae and anatomical evidence of pathway to morphological dioecy.

we conducted anatomical analysis of anthers with the aim to establish the differences in the development pattern of microsporophytes and microgametophytes between perfect and imperfect flowers in the tribe Gardenieae (Rubiaceae). The species studied were: Tocoyena formosa (monoecious with perfect flowers), Cordiera concolor, Genipa americana, Randia calycina, and Randia heteromera (dioecious with imperfect flowers). Flowers in successive stages of development were collected and fixed. The material was processed and examined using light microscopy and scanning electron microscopy. The present study revealed the stage when pollen is arrested in the functionally pistillate flowers of the dioecious taxa. Based on these observations an evolutionary sequence of changes towards the reduction of non-functional anthers in Rubiaceae is proposed. In addition, we describe and discuss characters that might be of importance in future phylogenetic studies in Rubiaceae (e.g., pollen morphology and its dispersal unit, the presence of orbicules, and a new type of placentoid).

Decoding Gene Expression Signatures Underlying Vegetative to Inflorescence Meristem Transition in the Common Bean.

The tropical common bean (Phaseolus vulgaris L.) is an obligatory short-day plant that requires relaxation of the photoperiod to induce flowering. Similar to other crops, photoperiod-induced floral initiation depends on the differentiation and maintenance of meristems. In this study, the global changes in transcript expression profiles were analyzed in two meristematic tissues corresponding to the vegetative and inflorescence meristems of two genotypes with different sensitivities to photoperiods. A total of 3396 differentially expressed genes (DEGs) were identified, and 1271 and 1533 were found to be up-regulated and down-regulated, respectively, whereas 592 genes showed discordant expression patterns between both genotypes. Arabidopsis homologues of DEGs were identified, and most of them were not previously involved in Arabidopsis floral transition, suggesting an evolutionary divergence of the transcriptional regulatory networks of the flowering process of both species. However, some genes belonging to the photoperiod and flower development pathways with evolutionarily conserved transcriptional profiles have been found. In addition, the flower meristem identity genes APETALA1 and LEAFY, as well as CONSTANS-LIKE 5, were identified as markers to distinguish between the vegetative and reproductive stages. Our data also indicated that the down-regulation of the photoperiodic genes seems to be directly associated with promoting floral transition under inductive short-day lengths. These findings provide valuable insight into the molecular factors that underlie meristematic development and contribute to understanding the photoperiod adaptation in the common bean.

Amaranth Seeds and Sprouts as Functional Ingredients for the Development of Dietary Fiber, Betalains, and Polyphenol-Enriched Minced Tilapia Meat Gels.

There is an increasing interest in the development of meat processed products enriched with antioxidant dietary fiber to augment the consumption of these health beneficial compounds. This study aimed to evaluate the nutritional, nutraceutical, and antioxidant potential, as well as the physicochemical properties of minced tilapia fillets (meat) gels with added amaranth seed or sprout flours (0%, 2%, 4%, 8%, and 10% w/w). Dietary fiber content was significantly increased with the addition of amaranth seed (1.25-1.75-fold) and sprout flours (1.99-3.21-fold). Tilapia gels with added 10% amaranth seed flour showed a high content of extractable dihydroxybenzoic acid and cinnamic acid, whereas the addition of 10% amaranth sprout flour provided a high and wide variety of bioactive compounds, mainly amaranthine and bound ferulic acid. The addition of amaranth seed and sprout flours increased hardness (1.01-1.73-fold) without affecting springiness, decreased luminosity (1.05-1.15-fold), and increased redness and yellowness. Therefore, amaranth seed and sprout flours could be used as functional ingredients for the development of fish products rich in bioactive compounds.

Synthetase of the methyl donor S-adenosylmethionine from nitrogen-fixing α-rhizobia can bind functionally diverse RNA species.

Function of bacterial small non-coding RNAs (sRNAs) and overall RNA metabolism is largely shaped by a vast diversity of RNA-protein interactions. However, in non-model bacteria with defined non-coding transcriptomes the sRNA interactome remains almost unexplored. We used affinity chromatography to capture proteins associated in vivo with MS2-tagged trans-sRNAs that regulate nutrient uptake (AbcR2 and NfeR1) and cell cycle (EcpR1) mRNAs by antisense-based translational inhibition in the nitrogen-fixing α-rhizobia Sinorhizobium meliloti. The three proteomes were rather distinct, with that of EcpR1 particularly enriched in cell cycle-related enzymes, whilst sharing several transcription/translation-related proteins recurrently identified associated with sRNAs. Strikingly, MetK, the synthetase of the major methyl donor S-adenosylmethionine, was reliably recovered as a binding partner of the three sRNAs, which reciprocally co-immunoprecipitated with a FLAG-tagged MetK variant. Induced (over)expression of the trans-sRNAs and MetK depletion did not influence canonical riboregulatory traits, `for example, protein titration or sRNA stability, respectively. An in vitro filter assay confirmed binding of AbcR2, NfeR1 and EcpR1 to MetK and further revealed interaction of the protein with other non-coding and coding transcripts but not with the 5S rRNA. These findings uncover a broad specificity for RNA binding as an unprecedented feature of this housekeeping prokaryotic enzyme.

Ecological mechanisms explaining interactions within plant-hummingbird networks: morphological matching increases towards lower latitudes.

Interactions between species are influenced by different ecological mechanisms, such as morphological matching, phenological overlap and species abundances. How these mechanisms explain interaction frequencies across environmental gradients remains poorly understood. Consequently, we also know little about the mechanisms that drive the geographical patterns in network structure, such as complementary specialization and modularity. Here, we use data on morphologies, phenologies and abundances to explain interaction frequencies between hummingbirds and plants at a large geographical scale. For 24 quantitative networks sampled throughout the Americas, we found that the tendency of species to interact with morphologically matching partners contributed to specialized and modular network structures. Morphological matching best explained interaction frequencies in networks found closer to the equator and in areas with low-temperature seasonality. When comparing the three ecological mechanisms within networks, we found that both morphological matching and phenological overlap generally outperformed abundances in the explanation of interaction frequencies. Together, these findings provide insights into the ecological mechanisms that underlie geographical patterns in resource specialization. Notably, our results highlight morphological constraints on interactions as a potential explanation for increasing resource specialization towards lower latitudes.

Earlier and slower or later and faster: Spring migration pace linked to departure time in a Neotropical migrant songbird.

Migratory birds travel vast distances and the timing of migratory flights can affect survival and the ability to reproduce. For Neotropical migrant songbirds, early spring departure from wintering sites, early arrival to the breeding grounds and higher reproductive success have been related to the use of suitable habitats and environmental conditions during the non-breeding season. However, how migratory strategies are shaped by winter habitat choice is largely unknown due to the general inability to track birds from specific wintering habitats to stopovers or breeding destinations. We assessed how winter habitat (native forest vs. shade-grown coffee plantations) relates to spring departure date and migration pace in Swainson's Thrush Catharus ustulatus. We also determined the effect of departure date and total migration duration on the arrival date of birds detected near or within their breeding range. We used a novel application of Motus radiotelemetry arrays to track individuals from their wintering grounds in the Andes of South America along their migratory journey to North America. We found variation in migratory strategies between habitats, with birds wintering in native forest departing later than birds in coffee. We present isotopic evidence for native forest being of higher quality than shade-coffee for Swainson's Thrush and hypothesize that moister conditions in forest, as shown by stable isotope (δ13 C) analysis of thrush whole blood, provides favourable pre-migratory conditions allowing birds to delay departure from wintering grounds. Habitat, between-site and -year variation in departure date, suggests that birds made facultative adjustments to winter habitat quality and environmental conditions. Independent of habitat, birds that departed later migrated faster and this pattern was maintained along the migration route (n = 44). Migrating earlier and slower or later and faster was unlikely to result in significant differences in arrival time to breeding destinations. Our findings reveal underappreciated complexity in migratory decisions by long-distance migrants that contrast with the current paradigm of earlier departures and arrival from optimal habitats. The next step is to understand the relative fitness benefits of early versus late schedules or whether each strategy is an equally good response to experienced conditions.

Las aves migratorias viajan largas distancias y la fecha de sus vuelos migratorios puede afectar su supervivencia y habilidad para reproducirse. Para las aves migratorias Neotropicales canoras, salir más temprano de los sitios de invernada, llegar más temprano a los sitios de reproducción y tener mayor éxito reproductivo, está relacionado con el uso de hábitats y condiciones medioambientales adecuadas durante la época no reproductiva. Sin embargo, la forma en que las estrategias migratorias son moldeadas por la selección del hábitat invernal es en gran parte desconocida debido a la inhabilidad general de rastrear las aves desde hábitats de invernada específicos hasta los sitios de descanso o de reproducción. Determinamos la relación entre el hábitat de invierno (bosque nativo vs. plantaciones de café con sombra), la fecha de salida durante la migración de primavera y el número de días usados durante la migración por la mirla buchipecosa Catharus ustulatus. También determinamos el efecto de la fecha de salida y la duración total de la migración en la fecha de llegada de las aves detectadas cerca o dentro de su rango de reproducción. Usamos la novedosa red de radio telemetría Motus para rastrear individuos desde sus sitios de invernada en las montañas de los Andes en Sudamérica a lo largo de su viaje migratorio hasta Norte América. Encontramos variación en las estrategias migratorias entre hábitats, las aves invernando en bosque nativo salieron más tarde que las aves invernando en cafetales. Presentamos evidencia isotópica, que sugiere que el bosque nativo es de mejor calidad que las plantaciones de café con sombra. Hipotetizamos que condiciones más húmedas en el bosque, indicadas por análisis de isotopos estables (δ13 C) de la sangre de las mirlas, proveen condiciones favorables antes de la migración permitiendo a las aves retrasar su salida de los territorios de invernada. La variación en la fecha de salida entre hábitats, años y sitios, sugiere que las aves hicieron ajustes facultativos a la calidad del hábitat de invierno y a las condiciones medio ambientales. Independientemente del hábitat, las aves que salieron más tarde migraron más rápido, y este patrón fue mantenido a lo largo de la ruta migratoria (n = 44). Fue poco probable que migrar más temprano y más lento o más tarde y más rápido resultara en diferencias significativas en la fecha de llegada a los sitios de reproducción. Nuestros resultados revelan una subestimada complejidad en las decisiones migratorias de las aves y contrastan con el paradigma actual de salida y llegada más temprana en aves que usan hábitats óptimos. El siguiente paso es entender los beneficios relativos de migrar temprano versus tarde en el desempeño o si cada estrategia es una respuesta igualmente buena a las condiciones experimentadas.

Tandem RNA isolation reveals functional rearrangement of RNA-binding proteins on CDKN1B/p27Kip1 3'UTRs in cisplatin treated cells.

Post-transcriptional control of gene expression is mediated via RNA-binding proteins (RBPs) that interact with mRNAs in a combinatorial fashion. While recent global RNA interactome capture experiments expanded the repertoire of cellular RBPs quiet dramatically, little is known about the assembly of RBPs on particular mRNAs; and how these associations change and control the fate of the mRNA in drug-treatment conditions. Here we introduce a novel biochemical approach, termed tobramycin-based tandem RNA isolation procedure (tobTRIP), to quantify proteins associated with the 3'UTRs of cyclin-dependent kinase inhibitor 1B (CDKN1B/p27Kip1) mRNAs in vivo. P27Kip1 plays an important role in mediating a cell's response to cisplatin (CP), a widely used chemotherapeutic cancer drug that induces DNA damage and cell cycle arrest. We found that p27Kip1 mRNA is stabilized upon CP treatment of HEK293 cells through elements in its 3'UTR. Applying tobTRIP, we further compared the associated proteins in CP and non-treated cells, and identified more than 50 interacting RBPs, many functionally related and evoking a coordinated response. Knock-downs of several of the identified RBPs in HEK293 cells confirmed their involvement in CP-induced p27 mRNA regulation; while knock-down of the KH-type splicing regulatory protein (KHSRP) further enhanced the sensitivity of MCF7 adenocarcinoma cancer cells to CP treatment. Our results highlight the benefit of specific in vivo mRNA-protein interactome capture to reveal post-transcriptional regulatory networks implicated in cellular drug response and adaptation.

Fiber-reinforced composite fixed dental prosthesis using an additive manufactured silicone index.

OBJECTIVE: Digital tools such as facial and intraoral digitizers and additive manufacturing (AM) technologies assist restorative treatments. The objective of the present manuscript was to describe a workflow procedure for treatment planning and fabricating a fiber-reinforced composite fixed dental prosthesis (FDP) replacing an absent maxillary lateral incisor, using additively manufactured silicone indices to facilitate the clinical intervention. CLINICAL CONSIDERATIONS: The elaboration of a direct fiber-reinforced composite restoration is a technique sensitive procedure which might be time-consuming for the clinician. The digital waxing helped to determine the exact position and size of the lingual wings and connectors of the fiber-reinforced FDP and to design a three-piece index. And the AM of the index helped to transfer the information to the patient's dentition accurately. CONCLUSIONS: The protocol minimizes the time of clinical intervention by facilitating the transference of the virtual diagnostic waxing teeth into the patient's mouth. The three-piece silicone index provides an individualized path of insertion of each index part while also providing a customized space and location of the lingual wings of the restoration. CLINICAL SIGNIFICANCE: The usage of AM silicone indices facilitates the clinical intervention by translating the size and position of the diagnostic wax-up teeth into the patient's mouth, minimizing clinical procedure's time.

Parallel origins of photoperiod adaptation following dual domestications of common bean.

Common bean (Phaseolus vulgaris L.) is an important grain legume domesticated independently in Mexico and Andean South America approximately 8000 years ago. Wild forms are obligate short-day plants, and relaxation of photoperiod sensitivity was important for expansion to higher latitudes and subsequent global spread. To better understand the nature and origin of this key adaptation, we examined its genetic control in progeny of a wide cross between a wild accession and a photoperiod-insensitive cultivar. We found that photoperiod sensitivity is under oligogenic control, and confirm a major effect of the Ppd locus on chromosome 1. The red/far-red photoreceptor gene PHYTOCHROME A3 (PHYA3) was identified as a strong positional candidate for Ppd, and sequencing revealed distinct deleterious PHYA3 mutations in photoperiod-insensitive Andean and Mesoamerican accessions. These results reveal the independent origins of photoperiod insensitivity within the two major common bean gene pools and demonstrate the conserved importance of PHYA genes in photoperiod adaptation of short-day legume species.

Trait evolution, resource specialization and vulnerability to plant extinctions among Antillean hummingbirds.

Species traits are thought to predict feeding specialization and the vulnerability of a species to extinctions of interaction partners, but the context in which a species evolved and currently inhabits may also matter. Notably, the predictive power of traits may require that traits evolved to fit interaction partners. Furthermore, local abiotic and biotic conditions may be important. On islands, for instance, specialized and vulnerable species are predicted to be found mainly in mountains, whereas species in lowlands should be generalized and less vulnerable. We evaluated these predictions for hummingbirds and their nectar-food plants on Antillean islands. Our results suggest that the rates of hummingbird trait divergence were higher among ancestral mainland forms before the colonization of the Antilles. In correspondence with the limited trait evolution that occurred within the Antilles, local abiotic and biotic conditions-not species traits-correlate with hummingbird resource specialization and the vulnerability of hummingbirds to extinctions of their floral resources. Specifically, hummingbirds were more specialized and vulnerable in conditions with high topographical complexity, high rainfall, low temperatures and high floral resource richness, which characterize the Antillean Mountains. These findings show that resource specialization and species vulnerability to extinctions of interaction partners are highly context-dependent.

Meta-networks for the study of biogeographical traits in ecological networks: the Mexican hummingbird-plant assemblage.

Recent studies on ecological networks have quantified the contribution of ecological, historical, and evolutionary factors on the structure of local communities of interacting species. However, the influence of species' biogeographical traits, such as migratory habits or phylogeographical history, on ecological networks is poorly understood. Meta-networks, i.e., networks that cover large spatial extensions and include species not co-occurring locally, enable us to investigate mechanisms that operate at larger spatial scales such as migratory patterns or phylogeographical distributions, as well as indirect relationships among species through shared partners. Using a meta-network of hummingbird-plant interaction across Mexico, we illustrate the usefulness of this approach by investigating (1) how biogeographical and morphological factors associate with observed interactions and (2) how species-specific biogeographical characteristics associate with species' network roles. Our results show that all studied hummingbird and plant species in the meta-network were interrelated, either directly or through shared partners. The meta-network was structured into modules, resulting from hummingbirds and plants interacting preferentially with subsets of species, which differed in biogeographical, and, to a lesser extent, morphological traits. Furthermore, migrants and hummingbirds from Nearctic, Transition, and widespread regions had a higher topological importance in the meta-network. Our study illustrates how meta-networks may contribute to our current knowledge on species' biogeographical traits and biotic interactions, providing a perspective complementary to local-scale networks.

A versatile tandem RNA isolation procedure to capture in vivo formed mRNA-protein complexes.

We describe a tandem RNA isolation procedure (TRIP) that enables purification of in vivo formed messenger ribonucleoprotein (mRNP) complexes. The procedure relies on the purification of polyadenylated mRNAs with oligo(dT) beads from cellular extracts, followed by the capture of specific mRNAs with 3'-biotinylated 2'-O-methylated antisense RNA oligonucleotides, which are recovered with streptavidin beads. TRIP was applied to isolate in vivo crosslinked mRNP complexes from yeast, nematodes and human cells for subsequent analysis of RNAs and bound proteins. The method provides a basis for adaptation to other types of polyadenylated RNAs, enabling the comprehensive identification of bound proteins/RNAs, and the investigation of dynamic rearrangement of mRNPs imposed by cellular or environmental cues.

Dissection of Resistance Genes to Pseudomonas syringae pv. phaseolicola in UI3 Common Bean Cultivar.

Few quantitative trait loci have been mapped for resistance to Pseudomonas syringae pv. phaseolicola in common bean. Two F2 populations were developed from the host differential UI3 cultivar. The objective of this study was to further characterize the resistance to races 1, 5, 7 and 9 of Psp included in UI3. Using a QTL mapping approach, 16 and 11 main-effect QTLs for pod and primary leaf resistance were located on LG10, explaining up to 90% and 26% of the phenotypic variation, respectively. The homologous genomic region corresponding to primary leaf resistance QTLs detected tested positive for the presence of resistance-associated gene cluster encoding nucleotide-binding and leucine-rich repeat (NL), Natural Resistance Associated Macrophage (NRAMP) and Pentatricopeptide Repeat family (PPR) proteins. It is worth noting that the main effect QTLs for resistance in pod were located inside a 3.5 Mb genomic region that included the Phvul.010G021200 gene, which encodes a protein that has the highest sequence similarity to the RIN4 gene of Arabidopsis, and can be considered an important candidate gene for the organ-specific QTLs identified here. These results support that resistance to Psp from UI3 might result from the immune response activated by combinations of R proteins, and suggest the guard model as an important mechanism in pod resistance to halo blight. The candidate genes identified here warrant functional studies that will help in characterizing the actual defense gene(s) in UI3 genotype.

Guayusa (Ilex guayusa L.) new tea: phenolic and carotenoid composition and antioxidant capacity.

BACKGROUND: Guayusa (Ilex guayusa Loes) is an evergreen tree native of South America that grows particularly in the upper Amazon region of Ecuador. For its health benefits, it has been cultivated and consumed since ancient times by Amazon indigenous tribes. RESULTS: A total of 14 phenolic compounds were identified and quantified. Chlorogenic acid and quercetin-3-O-hexose were the main representatives of the hydroxycinnamic acids and flavonols, respectively. Five carotenoids were identified, showing lutein the highest concentration. Guayusa leaves revealed high antioxidant capacity determined by two analytical methods, DPPH and ORAC. The industrial processing applied to the leaves modified the composition of bioactive compounds and antioxidant capacity of guayusa. In general, blanched guayusa retained the concentration of phenolic compounds and some carotenoids and similar antioxidant capacity as untreated green leaves. In contrast, fermentation reduced the content of bioactive compounds and showed the lowest antioxidant capacity. CONCLUSION: Therefore, blanched guayusa has potential for product development as a functional ingredient in the food industry. © 2017 Society of Chemical Industry.

High proportion of smaller ranged hummingbird species coincides with ecological specialization across the Americas.

Ecological communities that experience stable climate conditions have been speculated to preserve more specialized interspecific associations and have higher proportions of smaller ranged species (SRS). Thus, areas with disproportionally large numbers of SRS are expected to coincide geographically with a high degree of community-level ecological specialization, but this suggestion remains poorly supported with empirical evidence. Here, we analysed data for hummingbird resource specialization, range size, contemporary climate, and Late Quaternary climate stability for 46 hummingbird-plant mutualistic networks distributed across the Americas, representing 130 hummingbird species (ca 40% of all hummingbird species). We demonstrate a positive relationship between the proportion of SRS of hummingbirds and community-level specialization, i.e. the division of the floral niche among coexisting hummingbird species. This relationship remained strong even when accounting for climate, furthermore, the effect of SRS on specialization was far stronger than the effect of specialization on SRS, suggesting that climate largely influences specialization through species' range-size dynamics. Irrespective of the exact mechanism involved, our results indicate that communities consisting of higher proportions of SRS may be vulnerable to disturbance not only because of their small geographical ranges, but also because of their high degree of specialization.

Inhibitory Effect of Individual or Combinations of Broadly Neutralizing Antibodies and Antiviral Reagents against Cell-Free and Cell-to-Cell HIV-1 Transmission.

UNLABELLED: To date, most therapeutic and vaccine candidates for human immunodeficiency virus type 1 (HIV-1) are evaluated preclinically for efficacy against cell-free viral challenges. However, cell-associated HIV-1 is suggested to be a major contributor to sexual transmission by mucosal routes. To determine if neutralizing antibodies or inhibitors block cell-free and cell-associated virus transmission of diverse HIV-1 strains with different efficiencies, we tested 12 different antibodies and five inhibitors against four green fluorescent protein (GFP)-labeled HIV-1 envelope (Env) variants from transmitted/founder (T/F) or chronic infection isolates. We evaluated antibody/inhibitor-mediated virus neutralization using either TZM-bl target cells, in which infectivity was determined by virus-driven luciferase expression, or A3R5 lymphoblastoid target cells, in which infectivity was evaluated by GFP expression. In both the TZM-bl and A3R5 assays, cell-free virus or infected CD4+ lymphocytes were used as targets for neutralization. We further hypothesized that the combined use of specific neutralizing antibodies targeting HIV-1 Env would more effectively prevent cell-associated virus transmission than the use of individual antibodies. The tested antibody combinations included two gp120-directed antibodies, VRC01 and PG9, or VRC01 with the gp41-directed antibody 10E8. Our results demonstrated that cell-associated virus was less sensitive to neutralizing antibodies and inhibitors, particularly using the A3R5 neutralization assay, and the potencies of these neutralizing agents differed among Env variants. A combination of different neutralizing antibodies that target specific sites on gp120 led to a significant reduction in cell-associated virus transmission. These assays will help identify ideal combinations of broadly neutralizing antibodies to use for passive preventive antibody administration and further characterize targets for the most effective neutralizing antibodies/inhibitors. IMPORTANCE: Prevention of the transmission of human immunodeficiency virus type 1 (HIV-1) remains a prominent goal of HIV research. The relative contribution of HIV-1 within an infected cell versus cell-free HIV-1 to virus transmission remains debated. It has been suggested that cell-associated virus is more efficient at transmitting HIV-1 and more difficult to neutralize than cell-free virus. Several broadly neutralizing antibodies and retroviral inhibitors are currently being studied as potential therapies against HIV-1 transmission. The present study demonstrates a decrease in neutralizing antibody and inhibitor efficiencies against cell-associated compared to cell-free HIV-1 transmission among different strains of HIV-1. We also observed a significant reduction in virus transmission using a combination of two different neutralizing antibodies that target specific sites on the outermost region of HIV-1, the virus envelope. Therefore, our findings support the use of antibody combinations against both cell-free and cell-associated virus in future candidate therapy regimens.