Cell-type specialization is encoded by specific chromatin topologies.

The three-dimensional (3D) structure of chromatin is intrinsically associated with gene regulation and cell function1-3. Methods based on chromatin conformation capture have mapped chromatin structures in neuronal systems such as in vitro differentiated neurons, neurons isolated through fluorescence-activated cell sorting from cortical tissues pooled from different animals and from dissociated whole hippocampi4-6. However, changes in chromatin organization captured by imaging, such as the relocation of Bdnf away from the nuclear periphery after activation7, are invisible with such approaches8. Here we developed immunoGAM, an extension of genome architecture mapping (GAM)2,9, to map 3D chromatin topology genome-wide in specific brain cell types, without tissue disruption, from single animals. GAM is a ligation-free technology that maps genome topology by sequencing the DNA content from thin (about 220 nm) nuclear cryosections. Chromatin interactions are identified from the increased probability of co-segregation of contacting loci across a collection of nuclear slices. ImmunoGAM expands the scope of GAM to enable the selection of specific cell types using low cell numbers (approximately 1,000 cells) within a complex tissue and avoids tissue dissociation2,10. We report cell-type specialized 3D chromatin structures at multiple genomic scales that relate to patterns of gene expression. We discover extensive 'melting' of long genes when they are highly expressed and/or have high chromatin accessibility. The contacts most specific of neuron subtypes contain genes associated with specialized processes, such as addiction and synaptic plasticity, which harbour putative binding sites for neuronal transcription factors within accessible chromatin regions. Moreover, sensory receptor genes are preferentially found in heterochromatic compartments in brain cells, which establish strong contacts across tens of megabases. Our results demonstrate that highly specific chromatin conformations in brain cells are tightly related to gene regulation mechanisms and specialized functions.

Mpox outbreak in Rio de Janeiro, Brazil: A translational approach.

Mpox is a zoonotic disease historically reported in Africa. Since 2003, limited outbreaks have occurred outside Africa. In 2022, the global spread of cases with sustained interhuman transmission and unusual disease features raised public health concerns. We explore the mpox outbreak in Rio de Janeiro (RJ) state, Brazil, in an observational study of mpox-suspected cases from June to December 2022. Data collection relied on a public healthcare notification form. Diagnosis was determined by MPXV-PCR. In 46 confirmed cases, anti-OPXV IgG was determined by ELISA, and seven MPXV genomes were sequenced. A total of 3095 cases were included, 816 (26.3%) with positive MPXV-PCR results. Most positive cases were men in their 30 s and MSM. A total of 285 (34.9%) MPXV-PCR+ patients live with HIV. Eight were coinfected with varicella-zoster virus. Anogenital lesions and adenomegaly were associated with the diagnosis of mpox. Females and individuals under 18 represented 9.4% and 5.4% of all confirmed cases, respectively, showing higher PCR cycle threshold (Ct) values and fewer anogenital lesions compared to adult men. Anti-OPXV IgG was detected in 29/46 (63.0%) patients. All analyzed sequences belonged to clade IIb. In RJ state, mpox presented a diverse clinical picture, represented mainly by mild cases with low complication rates and prominent genital involvement. The incidence in females and children was higher than usually reported. The observation of a bimodal distribution of Ct values, with few positive results, may suggest the need to review the diagnostic criteria in these groups.

Structure-activity relationship study of small-molecule inhibitor of Atg12-Atg3 protein-protein interaction.

Autophagy is a catabolic process that was described to play a critical role in advanced stages of cancer, wherein it maintains tumor cell homeostasis and growth by supplying nutrients. Autophagy is also described to support alternative cellular trafficking pathways, providing a non-canonical autophagy-dependent inflammatory cytokine secretion mechanism. Therefore, autophagy inhibitors have high potential in the treatment of cancer and acute inflammation. In our study, we identified compound 1 as an inhibitor of the ATG12-ATG3 protein-protein interaction. We focused on the systematic modification of the original hit 1, a casein kinase 2 (CK2) inhibitor, to find potent disruptors of ATG12-ATG3 protein-protein interaction. A systematic modification of the hit structure led us to a wide plethora of compounds that maintain its ATG12-ATG3 inhibitory activity, which could act as a viable starting point to design new compounds with diverse therapeutic applications.

Overcoming insecticide resistance through computational inhibitor design.

Insecticides allow control of agricultural pests and disease vectors and are vital for global food security and health. The evolution of resistance to insecticides, such as organophosphates (OPs), is a serious and growing concern. OP resistance often involves sequestration or hydrolysis of OPs by carboxylesterases. Inhibiting carboxylesterases could, therefore, restore the effectiveness of OPs for which resistance has evolved. Here, we use covalent virtual screening to produce nano-/picomolar boronic acid inhibitors of the carboxylesterase αE7 from the agricultural pest Lucilia cuprina as well as a common Gly137Asp αE7 mutant that confers OP resistance. These inhibitors, with high selectivity against human acetylcholinesterase and low to no toxicity in human cells and in mice, act synergistically with the OPs diazinon and malathion to reduce the amount of OP required to kill L. cuprina by up to 16-fold and abolish resistance. The compounds exhibit broad utility in significantly potentiating another OP, chlorpyrifos, against the common pest, the peach-potato aphid (Myzus persicae). These compounds represent a solution to OP resistance as well as to environmental concerns regarding overuse of OPs, allowing significant reduction of use without compromising efficacy.

Software for prioritizing conservation actions based on probabilistic information.

Marxan is the most common decision-support tool used to inform the design of protected-area systems. The original version of Marxan does not consider risk and uncertainty associated with threatening processes affecting protected areas, including uncertainty about the location and condition of species' populations and habitats now and in the future. We described and examined the functionality of a modified version of Marxan, Marxan with Probability. This software explicitly considers 4 types of uncertainty: probability that a feature exists in a particular place (estimated based on species distribution models or spatially explicit population models); probability that features in a site will be lost in the future due to a threatening process, such as climate change, natural catastrophes, and uncontrolled human interventions; probability that a feature will exist in the future due to natural successional processes, such as a fire or flood; and probability the feature exists but has been degraded by threatening processes, such as overfishing or pollution, and thus cannot contribute to conservation goals. We summarized the results of 5 studies that illustrate how each type of uncertainty can be used to inform protected area design. If there were uncertainty in species or habitat distribution, users could maximize the chance that these features were represented by including uncertainty using Marxan with Probability. Similarly, if threatening processes were considered, users minimized the chance that species or habitats were lost or degraded by using Marxan with Probability. Marxan with Probability opens up substantial new avenues for systematic conservation planning research and application by agencies.

Marxan es la herramienta de apoyo a las decisiones que más comúnmente se usa para orientar el diseño de los sistemas de áreas protegidas. La versión original de Marxan no considera el riesgo y la incertidumbre asociados con los procesos amenazantes que afectan a las áreas protegidas, incluyendo la incertidumbre sobre la ubicación y la condición de las poblaciones de las especies y su hábitat ahora y en el futuro. Describimos y analizamos la funcionalidad de una versión modificada de Marxan: Marxan con Probabilidad. Este software considera explícitamente cuatro tipos de incertidumbre: probabilidad de que una característica exista en un lugar en particular (estimada con base en los modelos de distribución de especies o con modelos de población espacialmente explícitos); probabilidad de que las características de un sitio se pierdan en el futuro debido a un proceso amenazante, como el cambio climático, las catástrofes naturales y las intervenciones humanas descontroladas; probabilidad de que una característica existirá en el futuro debido a los procesos naturales de sucesión; como los incendios o las inundaciones; y probabilidad de que una característica exista pero haya sido degradada por los procesos amenazantes, como la sobrepesca y la contaminación, y por lo tanto no puede contribuir a los objetivos de conservación. Sintetizamos los resultados de cinco estudios que ilustraron cómo cada tipo de incertidumbre puede usarse para orientar el diseño del área protegida. Si hubiera incertidumbre en la distribución de la especie o de su hábitat, los usuarios podrían maximizar la posibilidad de que estas características estuvieran representadas mediante la inclusión de Marxan con Probabilidad. De manera similar, si los procesos amenazantes estuvieran considerados, los usuarios minimizarían la posibilidad de que se pierda la especie o degrade el hábitat usando Marxan con Probabilidad. Marxan con Probabilidad abre nuevas vías importantes para la investigación sobre la planeación sistemática de la conservación y su aplicación por parte de las agencias.

Evaluating surrogates of genetic diversity for conservation planning.

Protected-area systems should conserve intraspecific genetic diversity. Because genetic data require resources to obtain, several approaches have been proposed for generating plans for protected-area systems (prioritizations) when genetic data are not available. Yet such surrogate-based approaches remain poorly tested. We evaluated the effectiveness of potential surrogate-based approaches based on microsatellite genetic data collected across the Iberian Peninsula for 7 amphibian and 3 reptilian species. Long-term environmental suitability did not effectively represent sites containing high genetic diversity (allelic richness). Prioritizations based on long-term environmental suitability had similar performance to random prioritizations. Geographic distances and resistance distances based on contemporary environmental suitability were not always effective surrogates for identification of combinations of sites that contain individuals with different genetic compositions. Our results demonstrate that population genetic data based on commonly used neutral markers can inform prioritizations, and we could not find an adequate substitute. Conservation planners need to weigh the potential benefits of genetic data against their acquisition costs.

Evaluación de los Sustitutos de la Diversidad Genética para la Planeación de la Conservación Resumen Los sistemas de áreas protegidas deberían conservar la diversidad genética intraespecífica. Ya que para obtener datos genéticos se requieren recursos, se han propuesto distintas estrategias para generar los planes para los sistemas de áreas protegidas (priorizaciones) cuando los datos genéticos no están disponibles. A pesar de lo anterior, dichas estrategias basadas en sustitutos han sido poco evaluadas. Evaluamos la efectividad del potencial de las estrategias basadas en sustitutos cuya base son los datos genéticos de microsatélites obtenidos en toda la Península Ibérica y correspondientes a siete especies de anfibios y a tres de reptiles. La idoneidad ambiental a largo plazo no representó efectivamente los sitios que contienen una diversidad genética alta (riqueza de alelos). Las priorizaciones basadas en la idoneidad ambiental a largo plazo tuvieron un desempeño similar a las priorizaciones aleatorias. Las distancias geográficas y las distancias de resistencia basadas en la idoneidad ambiental contemporánea no siempre fueron sustitutos efectivos para la identificación de las combinaciones de sitios que contienen individuos con composiciones genéticas diferentes. Nuestros resultados demuestran que los datos genéticos de una población basados en marcadores neutrales de uso común pueden informar a las priorizaciones y que no pudimos encontrar un sustituto adecuado. Los planificadores de la conservación necesitan sopesar los beneficios potenciales de los datos genéticos contra sus costos de adquisición.

Assessment of the environmental compatibility and antifouling performance of an innovative biocidal and foul-release multifunctional marine coating.

The control of marine biofouling has raised serious environmental concerns, thus the continuous release of toxic and persistent biocidal agents applied as anti-biofouling coatings have triggered the search for non-toxic strategies. However, most of them still lack rigorous evaluation of their ecotoxicity and antifouling effects under real scenarios and their correlation with simulated assays. In this work, the biocide releasing risk and ecotoxicity of a biocidal and foul-release polydimethylsiloxane (PDMS)-based marine coating containing grafted Econea biocide (<0.6 wt.%) were evaluated under simulated real mechanical wear conditions at a pilot-scale system, and under extreme wear scenarios (washability settings). The coating system demonstrated low environmental impact against the model Vibrio fischeri bacterium and marine algae, associated with the effective biocide grafting in the coating matrix and subsequent biocide release minimization. This multifunctional coating system also showed auspicious antifouling (AF) effects, with an AF performance index significantly higher (API > 89) than a single foul-release system (AF < 40) after two and half years at a real immersion scenario in the Portuguese shore of the Atlantic Ocean. These field results corroborated the antibiofilm performance evaluated with Pseudoalteromonas tunicata at simulated dynamic marine conditions after seven-week assays. This eco-friendly multifunctional strategy, validated by both simulated testing conditions and real field tests, is believed to be a powerful tool for the development of AF technologies and a potential contribution to the quest for new environmentally friendly antifouling solutions.

Critical range of soil organic carbon in southern Europe lands under desertification risk.

Soil quality is fundamental for ecosystem long term functionality, productivity and resilience to current climatic changes. Despite its importance, soil is lost and degraded at dramatic rates worldwide. In Europe, the Mediterranean areas are a hotspot for soil erosion and land degradation due to a combination of climatic conditions, soils, geomorphology and anthropic pressure. Soil organic carbon (SOC) is considered a key indicator of soil quality as it relates to other fundamental soil functions supporting crucial ecosystem services. In the present study, the functional relationships among SOC and other important soil properties were investigated in the topsoil of 38 sites under different land cover and management, distributed over three Mediterranean regions under strong desertification risk, with the final aim to define critical SOC ranges for fast loss of important soil functionalities. The study sites belonged to private and public landowners seeking to adopt sustainable land management practices to support ecosystem sustainability and productivity of their land. Data showed a very clear relationship between SOC concentrations and the other analyzed soil properties: total nitrogen, bulk density, cation exchange capacity, available water capacity, microbial biomass, C fractions associated to particulate organic matter and to the mineral soil component and indirectly with net N mineralization. Below 20 g SOC kg-1, additional changes of SOC concentrations resulted in a steep variation of all the analyzed soil indicators, an order of magnitude higher than the changes occurring between 50 and 100 g SOC kg-1 and 3-4 times the changes observed at 20-50 g SOC kg-1. About half of the study sites showed average SOC concentration of the topsoil centimetres <20 g SOC kg-1. For these areas the level of SOC might hence be considered critical and immediate and effective recovery management plans are needed to avoid complete land degradation in the next future.

Development of a Library of Thiophene-Based Drug-Like Lego Molecules: Evaluation of Their Anion Binding, Transport Properties, and Cytotoxicity.

The anion-binding and transport properties of an extensive library of thiophene-based molecules are reported. Seventeen bis-urea positional isomers, with different binding conformations and lipophilicities, have been synthesized by appending α- or ß-thiophene or α-, ß-, or γ-benzo[b]thiophene moieties to an ortho-phenylenediamine central core, yielding six subsets of positional isomers. Through 1 H NMR, X-ray crystallography, molecular modelling, and anion efflux studies, it is demonstrated that the most active transporters adopt a pre-organized binding conformation capable of promoting the recognition of chloride, using urea and C-H binding groups in a cooperative fashion. Additional large unilamellar vesicle-based assays, carried out under electroneutral and electrogenic conditions, together with N-methyl-d-glucamine chloride assays, have indicated that anion efflux occurs mainly through an H+ /Cl- symport mechanism. On the other hand, the most efficient anion transporter displays cytotoxicity against tumor cell lines, while having no effects on a cystic fibrosis cell line.

Characterization of serum cytokines and circulating microRNAs that are predicted to regulate inflammasome genes in cutaneous leishmaniasis patients.

Leishmaniasis is a neglected disease caused by an intracellular protozoan parasite of the genus Leishmania. Infection starts when this protozoan replicates in a phagolysosomal compartment in macrophages, after evading host immune responses. The balance of Th1 and Th2 immune responses is crucial in leishmaniasis because it will determine whether the infection will be under control or if clinical complications will occur. The inflammasome, which is activated during Leishmania infection, involves the action of caspase-1 and release of the proinflammatory cytokines interleukin-1ß and interleukin-18. Together, they contribute to the maintenance of an inflammatory response and pyroptosis. Here, we evaluated the serum levels of cytokines and the expression of circulating microRNAs related to inflammasome regulation in twenty-seven patients with cutaneous leishmaniasis in comparison to nine healthy individuals, in the context of the inflammasome activation. Evaluation of serum cytokines activation (IL-1ß, IL-2, IL-4, IL-6, IL-10, and IL-17) was performed by flow cytometry using CBA kits (cytometric beads array) while the expression of circulating microRNAs (miR-7, miR-133a, miR-146b, miR-155, miR-223, miR-328, and miR-342) in plasma was measured by quantitative polymerase chain reaction. Our results showed an increase of the expression of miR-7-5p (p < 10-5), miR-133a (p = 0.034), miR-146b (p = 0.003), miR-223-3p (p = 10-5), and miR-328-3p (p = 0.002), and cytokine levels for IL-1ß (p = 0.0005), IL-6 (p = 0.001), and IL-17 (p = 0.001) in patients with cutaneous leishmaniasis compared to the controls. These results suggest that microRNAs and cytokines can play an important role in regulating the human immune responses to Leishmania infection. Our findings may contribute to the understanding of the mechanisms of the gene regulation during the cutaneous leishmaniasis and to the identification of possible biomarkers of the infection.

One Step Forward towards the Development of Eco-Friendly Antifouling Coatings: Immobilization of a Sulfated Marine-Inspired Compound.

Marine biofouling represents a global economic and ecological challenge and few eco-friendly antifouling agents are available. The aim of this work was to establish the proof of concept that a recently synthesized nature-inspired compound (gallic acid persulfate, GAP) can act as an eco-friendly and effective antifoulant when immobilized in coatings through a non-release strategy, promoting a long-lasting antifouling effect. The synthesis of GAP was optimized to provide quantitative yields. GAP water solubility was assessed, showing values higher than 1000 mg/mL. GAP was found to be stable in sterilized natural seawater with a half-life (DT50) of 7 months. GAP was immobilized into several commercial coatings, exhibiting high compatibility with different polymeric matrices. Leaching assays of polydimethylsiloxane and polyurethane-based marine coatings containing GAP confirmed that the chemical immobilization of GAP was successful, since releases up to fivefold lower than the conventional releasing systems of polyurethane-based marine coatings were observed. Furthermore, coatings containing immobilized GAP exhibited the most auspicious anti-settlement effect against Mytilus galloprovincialis larvae for the maximum exposure period (40 h) in laboratory trials. Overall, GAP promises to be an agent capable of improving the antifouling activity of several commercial marine coatings with desirable environmental properties.

Inhibition of a pancreatic cancer model by cooperative pairs of clinically approved and experimental antibodies.

By year 2025 pancreatic ductal adenocarcinoma (PDAC) is expected to become the second leading cause of cancer related death. However, other than improved chemotherapy and a small molecule inhibitor of the epidermal growth factor receptor (EGFR), no targeted drugs are currently available. Repurposing of approved drugs might offer a rapid solution. We employed an animal PDAC model, expressing a mutant and a wild type form of p53 and KRAS, respectively. Cetuximab, a clinically approved anti-EGFR monoclonal antibody (mAb) weakly inhibited PDAC xenografts, similar to trastuzumab, a mAb against HER2, a co-receptor of EGFR. Because the combination of cetuximab and trastuzumab only moderately enhanced the anti-tumor effects, we combined each with a home-made mAb to the same receptor and identified two cooperative pairs. The pair of trastuzumab and a murine anti-HER2 mAb better than the anti-EGFR pair inhibited PDAC xenografts, although HER2's abundance in our model is 15-fold lower than the level of EGFR. In vitro studies attribute cooperation to forced receptor endocytosis/degradation and inhibition of both DNA synthesis and cell migration. Taken together, our results identify cooperative pairs of anti-PDAC antibodies and highlight potential mechanisms of anti-tumor effects.

Genes on the edge: A framework to detect genetic diversity imperiled by climate change.

Ongoing global warming is disrupting several ecological and evolutionary processes, spanning different levels of biological organization. Species are expected to shift their ranges as a response to climate change, with relevant implications to peripheral populations at the trailing and leading edges. Several studies have analyzed the exposure of species to climate change but few have explored exposure at the intraspecific level. We introduce a framework to forecast exposure to climate change at the intraspecific level. We build on existing methods by combining correlative species distribution models, a model of species range dynamics, and a model of phylogeographic interpolation. We demonstrate the framework by applying it to 20 Iberian amphibian and reptile species. Our aims were to: (a) identify which species and intraspecific lineages will be most exposed to future climate change; (b) test if nucleotide diversity at the edges of species ranges are significantly higher or lower than on the overall range; and (c) analyze if areas of higher species gain, loss, and turnover coincide with those predicted for lineages richness and nucleotide diversity. We found that about 80% of the studied species are predicted to contract their range. Within each species, some lineages were predicted to contract their range, while others were predicted to maintain or expand it. Therefore, estimating the impacts of climate change at the species level only can underestimate losses at the intraspecific level. Some species had significant high amount of nucleotide at the trailing or leading edge, or both, but we did not find a consistent pattern across species. Spatial patterns of species richness, gain, loss, and turnover were fairly concurrent with lineages richness and nucleotide diversity. Our results support the need for increased attention to intraspecific diversity regarding monitoring and conservation strategies under climate change.

American tegumentary leishmaniasis in Brazil: a critical review of the current therapeutic approach with systemic meglumine antimoniate and short-term possibilities for an alternative treatment.

OBJECTIVES: Meglumine antimoniate (MA; Glucantime®), the 80-year-old first-line systemic treatment for all forms of American tegumentary leishmaniasis (ATL) caused by Leishmania (Viannia) braziliensis, Leishmania (Viannia) guyanensis and Leishmania (Leishmania) amazonensis, is highly toxic, presents adverse side-effects and may not attain clinical and parasitological cure. This critical review examines the necessity for intramuscular/intravenous administration of MA, the alternatives to this approach, and the possibilities of developing affordable, accessible and non-toxic drugs or new delivery methods. METHOD: PubMed searches were performed using the terms 'cutaneous leishmaniasis' or 'American tegumentary leishmaniasis' in combination with 'meglumine antimoniate' or 'N-methyl glucamine' or 'drug repositioning' or 'nanotechnology'. Searches covered a period of 20 years of peer reviewed journals and technical bulletins. We explored the mode of action, pharmacokinetics, toxicity and efficacy of MA, evaluated the progress of ATL therapy in Brazil, and examined the potential of drug repositioning and nanotechnology in accelerating the introduction and/or optimisation of an alternative treatment. RESULTS: The evidence suggests that ATL therapy will continue to rely on systemic MA in the foreseeable future even though an intralesional subcutaneous route has evolved over the last 10 years. The chances of developing a novel drug for ATL or a new mode of delivery of MA are low. While MA nanocarriers afford a promising approach, this technology is still in its infancy. A more immediate solution would be the production of a bioequivalent of miltefosine, an efficacious oral agent no longer protected by patent. CONCLUSION: Development of a contemporary treatment requires governmental commitment in bringing together private and public sectors.

OBJECTIFS: L'antimoniate de méglumine (AM; Glucantime®), le traitement systémique de première intention vieux de 80 ans pour toutes les formes de la leishmaniose tégumentaire américaine (LTA) causée par Leishmania (Viannia) braziliensis, L. (V.) guyanensis et L. (Leishmania) amazonensis, est hautement toxique, présente des effets secondaires indésirables et peut ne pas aboutir à une guérison clinique et parasitologique. Cette analyse critique examine la nécessité d'une administration intramusculaire/intraveineuse d'AM, les alternatives à cette approche et les possibilités de développement de médicaments abordables, accessibles et non toxiques ou de nouvelles méthodes d'administration. MÉTHODE: Des recherches sur PubMed ont été effectuées en utilisant les termes «leishmaniose cutanée¼ ou «leishmaniose tégumentaire américaine¼ en combinaison avec «antimoniate de méglumine ¼ ou «N-méthyl glucamine¼ ou «repositionnement de médicament¼ ou «nanotechnologie¼. Les recherches ont porté sur une période de 20 ans d'articles revue par des pairs et de bulletins techniques. Nous avons exploré le mode d'action, la pharmacocinétique, la toxicité et l'efficacité de l'AM, évalué les progrès du traitement de la LTA au Brésil et examiné le potentiel du repositionnement de médicaments et de la nanotechnologie pour accélérer l'introduction et/ou l'optimisation d'un traitement alternatif. RÉSULTATS: Les données suggèrent que le traitement de la LTA continuera à s'appuyer sur l'AM systémique dans un avenir proche, même si une voie sous-cutanée intralésionnelle a évolué au cours des 10 dernières années. Les chances de développer un nouveau médicament pour la LTA ou un nouveau mode d'administration d'AM sont faibles. Alors que les nanocarriers d'AM offrent une approche prometteuse, cette technologie en est encore à ses balbutiements. Une solution plus immédiate consisterait à produire un bioéquivalent de miltéfosine, un agent oral efficace, qui n'est plus protégé par un brevet. CONCLUSION: Le développement d'un traitement contemporain nécessite un engagement gouvernemental pour réunir les secteurs privés et publiques.

Construction of a full-length infectious cDNA clone of Cowpea mild mottle virus.

Infectious cDNA clones are an important tool to study the molecular and cellular process of RNA virus infection. In vitro and in vivo transcription systems are the two main strategies used in the generation of infectious cDNA clones for RNA viruses. This study describes the first generation of a full-length infectious cDNA clone of Cowpea mild mottle virus (CPMMV), a Carlavirus. The full-length genome was synthesized by Overlap Extension PCR of two overlapping fragments and cloned in a pUC-based vector under control of the SP6 RNA polymerase promoter. After in vitro run-off transcription, the produced RNA was mechanically inoculated into soybean plants cv. CD206. The systemic infection was confirmed by RT-PCR and further sequencing of amplified cDNA fragments. To simplify the transfection process, the complete genome was subcloned into a binary vector under control of the 35S promoter of cauliflower mosaic virus by the Gibson Assembly protocol. The resulting clones were inoculated by particle bombardment onto soybean seedlings and the recovery of the virus was confirmed 2 weeks later by RT-PCR. Our results indicate the constructs of the full-length cDNA of CPMMV are fully infectious in both in vitro and in vivo transcription strategies.

Not the time or the place: the missing spatio-temporal link in publicly available genetic data.

Genetic data are being generated at unprecedented rates. Policies of many journals, institutions and funding bodies aim to ensure that these data are publicly archived so that published results are reproducible. Additionally, publicly archived data can be 'repurposed' to address new questions in the future. In 2011, along with other leading journals in ecology and evolution, Molecular Ecology implemented mandatory public data archiving (the Joint Data Archiving Policy). To evaluate the effect of this policy, we assessed the genetic, spatial and temporal data archived for 419 data sets from 289 articles in Molecular Ecology from 2009 to 2013. We then determined whether archived data could be used to reproduce analyses as presented in the manuscript. We found that the journal's mandatory archiving policy has had a substantial positive impact, increasing genetic data archiving from 49 (pre-2011) to 98% (2011-present). However, 31% of publicly archived genetic data sets could not be recreated based on information supplied in either the manuscript or public archives, with incomplete data or inconsistent codes linking genetic data and metadata as the primary reasons. While the majority of articles did provide some geographic information, 40% did not provide this information as geographic coordinates. Furthermore, a large proportion of articles did not contain any information regarding date of sampling (40%). Although the inclusion of spatio-temporal data does require an increase in effort, we argue that the enduring value of publicly accessible genetic data to the molecular ecology field is greatly compromised when such metadata are not archived alongside genetic data.

Recognition of bio-relevant dicarboxylate anions by an azacalix[2]arene[2]triazine derivative decorated with urea moieties.

A new dichloroazacalix[2]arene[2]triazine receptor (1) with two chiral urea binding moieties is reported. The binding affinity of this macrocycle was evaluated by (1)H NMR titrations in CDCl3 for the dicarboxylate anions oxalate (ox(2-)), malonate (mal(2-)), succinate (suc(2-)), glutarate (glu(2-)), diglycolate (dg(2-)), fumarate (fum(2-)), maleate (male(2-)), and (R,R)- and (S,S)-tartarate (tart(2-)) enantiomers. Among the first five linear anions, the higher association constants were calculated for the larger anions glu(2-) and dg(2-) and for the smallest anion ox(2-), with Kass values following the sequence dg(2-) > glu(2-) > ox(2-) > suc(2-) > mal(2-). Despite the high binding affinity 1 of for both tart(2-) enantiomers, no enantioselectivity was observed. By contrast, Kass for fum(2-) is ca. 8.9 times greater than that for male(2-), showing the selectivity of 1 for the trans isomer. These binding preferences were further elucidated by theoretical methods. Molecular dynamics simulations showed that the linear anions are lodged between both pendant arms and that each anion can assume two distinct binding poses, with one or two carboxylate groups establishing intermittent hydrogen bonds with both urea binding units. On the other hand, the recognition of male(2-) ensues in an alternative scenario, characterised by the interaction between a carboxylate group and a single urea binding unit, mirroring the lower experimental binding affinity relatively to fum(2-). A linear increase of the receptor's Nurea···Nurea and the anions' (-)O2C···CO2(-) distances versus experimental Kass was established for mal(2-), suc(2-), glu(2-) and dg(2-) associations, indicating that the match between these two distances determines the anion binding strength. The affinity for ox(2-) was associated with the most negative values of electrostatic potential positioned near carboxylate groups.

Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription.

Histone H3 of nucleosomes positioned on active genes is trimethylated at Lys36 (H3K36me3) by the SETD2 (also termed KMT3A/SET2 or HYPB) methyltransferase. Previous studies in yeast indicated that H3K36me3 prevents spurious intragenic transcription initiation through recruitment of a histone deacetylase complex, a mechanism that is not conserved in mammals. Here, we report that downregulation of SETD2 in human cells leads to intragenic transcription initiation in at least 11% of active genes. Reduction of SETD2 prevents normal loading of the FACT (FAcilitates Chromatin Transcription) complex subunits SPT16 and SSRP1, and decreases nucleosome occupancy in active genes. Moreover, co-immunoprecipitation experiments suggest that SPT16 is recruited to active chromatin templates, which contain H3K36me3-modified nucleosomes. Our results further show that within minutes after transcriptional activation, there is a SETD2-dependent reduction in gene body occupancy of histone H2B, but not of histone H3, suggesting that SETD2 coordinates FACT-mediated exchange of histone H2B during transcription-coupled nucleosome displacement. After inhibition of transcription, we observe a SETD2-dependent recruitment of FACT and increased histone H2B occupancy. These data suggest that SETD2 activity modulates FACT recruitment and nucleosome dynamics, thereby repressing cryptic transcription initiation.