Timing is everything: early degradation of abscission layer is associated with increased seed shattering in U.S. weedy rice

Background Seed shattering, or shedding, is an important fitness trait for wild and weedy grasses. U.S. weedy rice (Oryza sativa) is a highly shattering weed, thought to have evolved from non-shattering cultivated ancestors. All U.S. weedy rice individuals examined to date contain a mutation in the sh4 locus associated with loss of shattering during rice domestication. Weedy individuals also share the shattering trait with wild rice, but not the ancestral shattering mutation at sh4; thus, how weedy rice reacquired the shattering phenotype is unknown. To establish the morphological basis of the parallel evolution of seed shattering in weedy rice and wild, we examined the abscission layer at the flower-pedicel junction in weedy individuals in comparison with wild and cultivated relatives. Results Consistent with previous work, shattering wild rice individuals possess clear, defined abscission layers at flowering, whereas non-shattering cultivated rice individuals do not. Shattering weedy rice from two separately evolved populations in the U.S. (SH and BHA) show patterns of abscission layer formation and degradation distinct from wild rice. Prior to flowering, the abscission layer has formed in all weedy individuals and by flowering it is already degrading. In contrast, wild O. rufipogon abscission layers have been shown not to degrade until after flowering has occurred. Conclusions Seed shattering in weedy rice involves the formation and degradation of an abscission layer in the flower-pedicel junction, as in wild Oryza, but is a developmentally different process from shattering in wild rice. Weedy rice abscission layers appear to break down earlier than wild abscission layers. The timing of weedy abscission layer degradation suggests that unidentified regulatory genes may play a critical role in the reacquisition of shattering in weedy rice, and sheds light on the morphological basis of pa

Efecto del enriquecimiento ambiental sobre la ansiedad: estudio experimental en un modelo animal

Anxiety is a global health problem; therefore, it is necessary to study new therapeutics alternatives, including environmental enrichment (EE). In the present paper the effect of EE on anxiety were studied. EE was evaluated in 20 C57BL/6 mice divided into 2 groups: Control Group (CG, n=10) and Experimental Group (EG, n=10). EG received EE with various sensory stimuli (olfatoy, gustatory, visual and tactile) and dark niches. CG was housed individually in a restricted environment. Mice were evaluated in the Elevated Plus Maze (EPM), Light/Dark Box (LDB) and Preference for Sucrose (PS). EE caused hypermotility in EPM with preference for shifts between closed arms (p<0.05), increased the unit residence time in both compartments of LDB (p<005) and significantly increased the PS (p<0.05). In conclusion; the EE based on including dark niches induces hyperactivity with decreased levels of anxiety, allowing the expression of instinctive behaviors to dark places.  La ansiedad es unroblema de salud mundial que amerita el estudio de nuevas alternativas para su tratamiento terapéutico, entre ellas el enriquecimiento ambiental (EA). El presente trabajo estudió el efecto del EA sobre la ansiedad. 20 ratones C57BL/6 fueron divididos en 2 grupos: Grupo Control (GC, n=10) Grupo Experimental (GE, n=10). El GE recibió EA basado en estímulos sensoriales (olfativos, gustativos, visuales y táctiles) y nichos oscuros, mientras que el GC fue hospedado individualmente en un ambiente restringido de EA. Los ratones fueron evaluados en el Laberinto Elevado en Cruz (LEC), Caja Luz/Oscuridad (CLO) y mediante la prueba preferencia por sacarosa (PS). El EA causó hipermotilidad en LEC con preferencia por los desplazamientos entre brazos cerrados (p<0.05); aumentó el tiempo unitario de permanencia en ambos compartimientos de CLO (p<0.05) e incrementó significativamente el consumo de sacarosa en PS (p<0.05). En conclusión; la técnica del EA basado en incluir nichos oscuros induce hiperactividad con niveles de ansiedad disminuidos, permitiendo la expresión de conductas instintivas

nucleAIzer : A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer

Single-cell segmentation is typically a crucial task of image-based cellular analysis. We present nucleAIzer, a deep-learning approach aiming toward a truly general method for localizing 2D cell nuclei across a diverse range of assays and light microscopy modalities. We outperform the 739 methods submitted to the 2018 Data Science Bowl on images representing a variety of realistic conditions, some of which were not represented in the training data. The key to our approach is that during training nucleAIzer automatically adapts its nucleus-style model to unseen and unlabeled data using image style transfer to automatically generate augmented training samples. This allows the model to recognize nuclei in new and different experiments efficiently without requiring expert annotations, making deep learning for nucleus segmentation fairly simple and labor free for most biological light microscopy experiments. It can also be used online, integrated into CellProfiler and freely downloaded at www.nucleaizer.org. A record of this paper's transparent peer review process is included in the Supplemental Information.Peer reviewe

Bone Marrow Transplantation Transfers Age-Related Susceptibility to Neovascular Remodeling in Murine Laser- Induced Choroidal Neovascularization

Citation: Espinosa-Heidmann DG, Malek G, Mettu PS, et al. Bone marrow transplantation transfers age-related susceptibility to neovascular remodeling in murine laser-induced choroidal neovascularization. Invest Ophthalmol Vis Sci. 2013;54:7439-7449. DOI:10.1167/iovs.13-12546 PURPOSE. Neovascular remodeling (NVR), the progression of small capillaries into large-caliber arterioles with perivascular fibrosis, represents a major therapeutic challenge in neovascular age-related macular degeneration (AMD). Neovascular remodeling occurs after laser-induced choroidal neovascularization (CNV) in aged but not young mice. Additionally, bone marrowderived cells, including macrophages, endothelial precursor cells, and mesenchymal precursor cells, contribute to CNV severity. In this study, we investigated the impact of aged bone marrow transplantation (BMT) on the degree of fibrosis, size, and vascular morphology of CNV lesions in a mouse model of laser-induced CNV. METHODS. Young (2 months) and old (16 months) mice were transplanted with green fluorescent protein (GFP)-labeled bone marrow isolated from either young or old donors. Laser CNV was induced 1 month following transplant, and eyes were analyzed via choroidal flat mounts and immunohistochemistry 1 month postlaser. The identity of cells infiltrating CNV lesions was determined using specific markers for the labeled transplanted cells (GFPþ), macrophages (F4/80þ), perivascular mesenchymal-derived cells (smooth muscle actin, SMAþ), and endothelial cells (CD31þ). RESULTS. Bone marrow transplantation from aged mice transferred susceptibility to NVR into young recipients. Inversely, transplantation of young marrow into old mice prevented NVR, preserving small size and minimal fibrosis. Mice with NVR demonstrated a greater relative contribution of marrow-derived SMAþ perivascular mesenchymal cells as compared to other cells. CONCLUSIONS. Our findings indicate that the status of bone marrow is an important determining factor of neovascular severity. Furthermore, we find that perivascular mesenchymal cells, rather than endothelial cells, derived from aged bone marrow may contribute to increased CNV severity in this murine model of experimental neovascularization

Amount of Information Needed for Model Choice in Approximate Bayesian Computation

Approximate Bayesian Computation (ABC) has become a popular technique in evolutionary genetics for elucidating population structure and history due to its flexibility. The statistical inference framework has benefited from significant progress in recent years. In population genetics, however, its outcome depends heavily on the amount of information in the dataset, whether that be the level of genetic variation or the number of samples and loci. Here we look at the power to reject a simple constant population size coalescent model in favor of a bottleneck model in datasets of varying quality. Not only is this power dependent on the number of samples and loci, but it also depends strongly on the level of nucleotide diversity in the observed dataset. Whilst overall model choice in an ABC setting is fairly powerful and quite conservative with regard to false positives, detecting weaker bottlenecks is problematic in smaller or less genetically diverse datasets and limits the inferences possible in non-model organism where the amount of information regarding the two models is often limited. Our results show it is important to consider these limitations when performing an ABC analysis and that studies should perform simulations based on the size and nature of the dataset in order to fully assess the power of the study

Epidemiología molecular y análisis filogenético de la infección por el virus del papiloma humano en mujeres con lesiones cervicales y cáncer en la región litoral del Ecuador

The aim of the present study was to gather information regarding the molecular epidemiology of Human papillomavirus (HPV) and related risk factors in a group of women with low- and high-grade cervical lesions and cancer from the coastal region of Ecuador. In addition, we studied the evolution of HPV variants from the most prevalent types and provided a temporal framework for their emergence, which may help to trace the source of dissemination within the region. We analyzed 166 samples, including 57 CIN1, 95 CIN2/3 and 14 cancer cases. HPV detection and typing was done by PCR-sequencing (MY09/MY11). HPV variants and estimation of the time to most recent common ancestor (tMRCA) was assessed through phylogeny and coalescence analysis. HPV DNA was found in 54.4% of CIN1, 74.7% of CIN2/3 and 78.6% of cancer samples. HPV16 (38.9%) and HPV58 (19.5%) were the most prevalent types. Risk factors for the development of cervical lesions/cancer were the following: three or more pregnancies (OR = 4.3), HPV infection (OR = 3.7 for high-risk types; OR = 3.5 for HPV16), among others. With regard to HPV evolution, HPV16 isolates belonged to lineages A (69%) and D (31%) whereas HPV58 isolates belonged only to lineage A. The period of emergence of HPV16 was in association with human populations (tMRCA = 91. 052 years for HPV16A and 27. 000 years for HPV16D), whereas HPV58A preceded Homo sapiens evolution (322. 257 years). This study provides novel data on HPV epidemiology and evolution in Ecuador, which will be fundamental in the vaccine era.Fil: Bedoya Pilozo, Cesar H.. Escuela Superior Politécnica del Litoral; Ecuador. Instituto Nacional de Investigaciones en Salud Pública; EcuadorFil: Medina Magües, Lex G.. Escuela Superior Politécnica del Litoral; EcuadorFil: Espinosa García, Maylen. Instituto Nacional de Investigaciones en Salud Pública; EcuadorFil: Sánchez, Martha. Instituto Nacional de Investigaciones en Salud Pública; EcuadorFil: Parrales Valdiviezo, Johanna V.. Instituto Nacional de Investigaciones en Salud Pública; EcuadorFil: Molina, Denisse. Instituto Nacional de Investigaciones en Salud Pública; EcuadorFil: Ibarra, María A.. Instituto Nacional de Investigaciones en Salud Pública; EcuadorFil: Quimis Ponce, María. Instituto Nacional de Investigaciones en Salud Pública; EcuadorFil: España, Karool. Instituto Nacional de Investigaciones en Salud Pública; EcuadorFil: Párraga Macias, Karla E.. Instituto Nacional de Investigaciones en Salud Pública; EcuadorFil: Cajas Flores, Nancy V.. Instituto Nacional de Investigaciones en Salud Pública; EcuadorFil: Solon, Orlando A.. Instituto Nacional de Investigaciones en Salud Pública; Ecuador. Universidad Agraria del Ecuador; EcuadorFil: Robalino Penaherrera, Jorge A.. Instituto Nacional de Investigaciones en Salud Pública; EcuadorFil: Chedraui, Peter. Hospital Gineco-Obstétrico Enrique C. Sotomayor; EcuadorFil: Escobar, Saul. Universidad Católica de Guayaquil; EcuadorFil: Loja Chango, Rita D.. Universidad Católica de Guayaquil; EcuadorFil: Ramirez Morán, Cecibel. Universidad Católica de Guayaquil; EcuadorFil: Espinoza Caicedo, Jasson. Universidad Católica de Guayaquil; EcuadorFil: Sánchez Giler, Sunny. Universidad Especialidades Espíritu Santo. Facultad de Ciencias Médicas; EcuadorFil: Limia, Celia M.. Instituto de Medicina Tropical Pedro Kouri; CubaFil: Alemán, Yoan. Instituto de Medicina Tropical Pedro Kouri; CubaFil: Soto, Yudira. Instituto de Medicina Tropical Pedro Kouri; CubaFil: Kouri, Vivian. Instituto de Medicina Tropical Pedro Kouri; CubaFil: Culasso, Andrés Carlos Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; ArgentinaFil: Badano, Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; Argentina. Secretaría de Educación Superior, Ciencia, Tecnología e Innovación; Ecuador. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada; Argentin

The Effect of Variation in the Effective Population Size on the Rate of Adaptive Molecular Evolution in Eukaryotes

The role of adaptation is a fundamental question in molecular evolution. Theory predicts that species with large effective population sizes should undergo a higher rate of adaptive evolution than species with low effective population sizes if adaptation is limited by the supply of mutations. Previous analyses have appeared to support this conjecture because estimates of the proportion of nonsynonymous substitutions fixed by adaptive evolution, α, tend to be higher in species with large N(e). However, α is a function of both the number of advantageous and effectively neutral substitutions, either of which might depend on N(e). Here, we investigate the relationship between N(e) and ω(a), the rate of adaptive evolution relative to the rate of neutral evolution, using nucleotide polymorphism and divergence data from 13 independent pairs of eukaryotic species. We find a highly significant positive correlation between ω(a) and N(e). We also find some evidence that the rate of adaptive evolution varies between groups of organisms for a given N(e). The correlation between ω(a) and N(e) does not appear to be an artifact of demographic change or selection on synonymous codon use. Our results suggest that adaptation is to some extent limited by the supply of mutations and that at least some adaptation depends on newly occurring mutations rather than on standing genetic variation. Finally, we show that the proportion of nearly neutral nonadaptive substitutions declines with increasing N(e). The low rate of adaptive evolution and the high proportion of effectively neutral substitution in species with small N(e) are expected to combine to make it difficult to detect adaptive molecular evolution in species with small N(e)

A multicentre outcome analysis to define global benchmarks for donation after circulatory death liver transplantation

BACKGROUND: To identify the best possible outcomes in liver transplantation from donation after circulatory death donors (DCD) and to propose outcome values, which serve as reference for individual liver recipients or patient groups. METHODS: Based on 2219 controlled DCD liver transplantations, collected from 17 centres in North America and Europe, we identified 1012 low-risk, primary, adult liver transplantations with a laboratory MELD of ≤20points, receiving a DCD liver with a total donor warm ischemia time of ≤30minutes and asystolic donor warm ischemia time of ≤15minutes. Clinically relevant outcomes were selected and complications were reported according to the Clavien-Dindo-Grading and the Comprehensive Complication Index (CCI). Corresponding benchmark cut-offs were based on median values of each centre, where the 75(th)-percentile was considered. RESULTS: Benchmark cases represented between 19.7% and 75% of DCD transplantations in participating centers. The one-year retransplant and mortality rate was 5.23% and 9.01%, respectively. Within the first year of follow-up, 51.1% of recipients developed at least one major complication (≥Clavien-Dindo-Grade-III). Benchmark cut-offs were ≤3days and ≤16days for ICU and hospital stay, ≤66% for severe recipient complications (≥Grade-III), ≤16.8% for ischemic cholangiopathy, and ≤38.9CCI points at one-year posttransplant. Comparisons with higher risk groups showed more complications and impaired graft survival, outside the benchmark cut-offs. Organ perfusion techniques reduced the complications to values below benchmark cut-offs, despite higher graft risk. CONCLUSIONS: Despite excellent 1-year survival, morbidity in benchmark cases remains high with more than half of recipients developing severe complications during 1-year follow-up. Benchmark cut-offs targeting morbidity parameters offer a valid tool to assess the protective value of new preservation technologies in higher risk groups, and provide a valid comparator cohort for future clinical trials. LAY SUMMARY: The best possible outcomes after liver transplantation of grafts donated after circulatory death (DCD) were defined using the concept of benchmarking. These were based on 2219 liver transplantations following controlled DCD donation in 17 centres worldwide. The following benchmark cut-offs for the most relevant outcome parameters were developed: ICU and hospital stay: ≤3 and ≤16 days; primary non function: ≤2.5%; renal replacement therapy: ≤9.6%; ischemic cholangiopathy: ≤16.8% and anastomotic strictures ≤28.4%. One-year graft loss and mortality were defined as ≤14.4% and 9.6%, respectively. Donor and recipient combinations with higher risk had significantly worse outcomes. The use of novel organ perfusion technology achieved similar, good results in this high-risk group with prolonged donor warm ischemia time, when compared to the benchmark cohort