Metastatic risk and resistance to BRAF inhibitors in melanoma defined by selective allelic loss of ATG5

Melanoma is a paradigm of aggressive tumors with a complex and heterogeneous genetic background. Still, melanoma cells frequently retain developmental traits that trace back to lineage specification programs. In particular, lysosome-associated vesicular trafficking is emerging as a melanoma-enriched lineage dependency. However, the contribution of other lysosomal functions such as autophagy to melanoma progression is unclear, particularly in the context of metastasis and resistance to targeted therapy. Here we mined a broad spectrum of cancers for a meta-analysis of mRNA expression, copy number variation and prognostic value of 13 core autophagy genes. This strategy identified heterozygous loss of ATG5 at chromosome band 6q21 as a distinctive feature of advanced melanomas. Importantly, partial ATG5 loss predicted poor overall patient survival in a manner not shared by other autophagy factors and not recapitulated in other tumor types. This prognostic relevance of ATG5 copy number was not evident for other 6q21 neighboring genes. Melanocyte-specific mouse models confirmed that heterozygous (but not homozygous) deletion of Atg5 enhanced melanoma metastasis and compromised the response to targeted therapy (exemplified by dabrafenib, a BRAF inhibitor in clinical use). Collectively, our results support ATG5 as a therapeutically relevant dose-dependent rheostat of melanoma progression. Moreover, these data have important translational implications in drug design, as partial blockade of autophagy genes may worsen (instead of counteracting) the malignant behavior of metastatic melanomas.     

A biomechanical analysis on the impact of episiotomy during childbirth

Episiotomy is still a controversy issue among physicians, despite the enormous growth of clinical research. Therefore, the potential of numerical modeling of anatomical structures to simulate biomechanical processes was exploited to realize quantitatively the real effects of the episiotomy and its consequences on the pelvic floor muscle. As such, a numerical model was used composed of pelvic floor muscles, a surface delimiting the anterior region, and a fetus body. A normal vaginal delivery without and with different episiotomies was simulated with the fetus in vertex presentation and occipitoanterior position. According to our numerical results, a mediolateral episiotomy has a protective effect, reducing the stress on the muscles, and the force required to delivery successfully up to 52.2 %. The intervention also has benefits on muscle injury, reducing the damage to a small zone. This study demonstrates the feasibility of using a computational modeling approach to study parturition, namely the capability to isolate and evaluate the mechanical significance of a single feature. It must, however, be taken into account that the numerical model does not assess problems that may occur as blood loss, infections and others, so it is necessary to examine whether the benefits of an intervention outweigh the risks.     

Integrating Genetic,Neuropsychological and Neuroimaging Data to Model Early-Onset Obsessive Compulsive Disorder Severity

We propose an integrative approach that combines structural magnetic resonance imaging data (MRI), diffusion tensor imaging data (DTI), neuropsychological data, and genetic data to predict early-onset obsessive compulsive disorder (OCD) severity. From a cohort of 87 patients, 56 with complete information were used in the present analysis. First, we performed a multivariate genetic association analysis of OCD severity with 266 genetic polymorphisms. This association analysis was used to select and prioritize the SNPs that would be included in the model. Second, we split the sample into a training set (N = 38) and a validation set (N = 18). Third, entropy-based measures of information gain were used for feature selection with the training subset. Fourth, the selected features were fed into two supervised methods of class prediction based on machine learning, using the leave-one-out procedure with the training set. Finally, the resulting model was validated with the validation set. Nine variables were used for the creation of the OCD severity predictor, including six genetic polymorphisms and three variables from the neuropsychological data. The developed model classified child and adolescent patients with OCD by disease severity with an accuracy of 0.90 in the testing set and 0.70 in the validation sample. Above its clinical applicability, the combination of particular neuropsychological, neuroimaging, and genetic characteristics could enhance our understanding of the neurobiological basis of the disorder.     

Effects of different arbuscular mycorrhizal fungal backgrounds and soils on olive plants growth and water relation properties under well‐watered and drought conditions

The adaptation capacity of olive trees to different environments is well recognized. However, the presence of microorganisms in the soil is also a key factor in the response of these trees to drought. The objective of the present study was to elucidate the effects of different arbuscular mycorrhizal (AM) fungi coming from diverse soils on olive plant growth and water relations. Olive plants were inoculated with native AM fungal populations from two contrasting environments, that is, semi‐arid – Freila (FL) and humid – Grazalema (GZ) regions, and subjected to drought stress. Results showed that plants grew better on GZ soil inoculated with GZ fungi, indicating a preference of AM fungi for their corresponding soil. Furthermore, under these conditions, the highest AM fungal diversity was found. However, the highest root hydraulic conductivity (Lp_r) value was achieved by plants inoculated with GZ fungi and growing in FL soil under drought conditions. So, this AM inoculum also functioned in soils from different origins. Nine novel aquaporin genes were also cloned from olive roots. Diverse correlation and association values were found among different aquaporin expressions and abundances and Lp_r, indicating how the interaction of different aquaporins may render diverse Lp_r values.     

Chloride as a macronutrient increases water‐use efficiency by anatomically driven reduced stomatal conductance and increased mesophyll diffusion to CO2

Chloride (Cl^?) has been recently described as a beneficial macronutrient, playing specific roles in promoting plant growth and water‐use efficiency (WUE). However, it is still unclear how Cl^? could be beneficial, especially in comparison with nitrate (NO₃^?), an essential source of nitrogen that shares with Cl^? similar physical and osmotic properties, as well as common transport mechanisms. In tobacco plants, macronutrient levels of Cl^? specifically reduce stomatal conductance (g_s) without a concomitant reduction in the net photosynthesis rate (A_N). As stomata‐mediated water loss through transpiration is inherent in the need of C₃ plants to capture CO₂, simultaneous increase in photosynthesis and WUE is of great relevance to achieve a sustainable increase in C₃ crop productivity. Our results showed that Cl^?‐mediated stimulation of larger leaf cells leads to a reduction in stomatal density, which in turn reduces g_s and water consumption. Conversely, Cl^? improves mesophyll diffusion conductance to CO₂ (g_m) and photosynthetic performance due to a higher surface area of chloroplasts exposed to the intercellular airspace of mesophyll cells, possibly as a consequence of the stimulation of chloroplast biogenesis. A key finding of this study is the simultaneous improvement of A_N and WUE due to macronutrient Cl^? nutrition. This work identifies relevant and specific functions in which Cl^? participates as a beneficial macronutrient for higher plants, uncovering a sustainable approach to improve crop yield.     

Use of classical bird census transects as spatial replicates for hierarchical modeling of an avian community

New monitoring programs are often designed with some form of temporal replication to deal with imperfect detection by means of occupancy models. However, classical bird census data from earlier times often lack temporal replication, precluding detection‐corrected inferences about occupancy. Historical data have a key role in many ecological studies intended to document range shifts, and so need to be made comparable with present‐day data by accounting for detection probability. We analyze a classical bird census conducted in the region of Murcia (SE Spain) in 1991 and 1992 and propose a solution to estimating detection probability for such historical data when used in a community occupancy model: the spatial replication of subplots nested within larger plots allows estimation of detection probability. In our study, the basic sample units were 1‐km transects, which were considered spatial replicates in two aggregation schemes. We fit two Bayesian multispecies occupancy models, one for each aggregation scheme, and evaluated the linear and quadratic effect of forest cover and temperature, and a linear effect of precipitation on species occupancy probabilities. Using spatial rather than temporal replicates allowed us to obtain individual species occupancy probabilities and species richness accounting for imperfect detection. Species‐specific occupancy and community size decreased with increasing annual mean temperature. Both aggregation schemes yielded estimates of occupancy and detectability that were highly correlated for each species, so in the design of future surveys ecological reasons and cost‐effective sampling designs should be considered to select the most suitable aggregation scheme. In conclusion, the use of spatial replication may often allow historical survey data to be applied formally hierarchical occupancy models and be compared with modern‐day data of the species community to analyze global change process.     

Variable actin dynamics requirement for the exit of different cargo from the trans-Golgi network

Efficient post-Golgi trafficking depends on microtubules, but actin filaments and actin-associated proteins are also postulated. Here we examined, by inverse fluorescence recovery after photobleaching, the role of actin dynamics in the exit from the TGN of fluorescent-tagged apical or basolateral and raft or non-raft-associated cargoes. Either the actin-stabilizing jasplakinolide or the actin-depolymerising latrunculin B variably but significantly inhibited post-Golgi traffic of non-raft associated apical p75NTR and basolateral VSV-G cargoes. The TGN-exit of the apical-destined VSV-G mutant was impaired only by latrunculin B. Strikingly, the raft-associated GPI-anchor protein was not affected by either actin toxin. Results indicate that actin dynamics participates in the TGN egress of both apical- and basolateral-targeted proteins but is not needed for apical raft-associated cargo.     

Root exudation of carbohydrates and cations from barley in response to drought and elevated CO2

Plant and Soil - Citrate secretion is a kind of typical strategy for plant against aluminum (Al) toxicity. However, the signaling process in Al-activated citrate secretion needs to be clarified....