Outcrossing potential between 11 important genetically modified crops and the Chilean vascular flora

The potential impact of genetically modified (GM) crops on biodiversity is one of the main concerns in an environmental risk assessment (ERA). The likelihood of outcrossing and pollen‐mediated gene flow from GM crops and non‐GM crops are explained by the same principles and depend primarily on the biology of the species. We conducted a national‐scale study of the likelihood of outcrossing between 11 GM crops and vascular plants in Chile by use of a systematized database that included cultivated, introduced and native plant species in Chile. The database included geographical distributions and key biological and agronomical characteristics for 3505 introduced, 4993 native and 257 cultivated (of which 11 were native and 246 were introduced) plant species. Out of the considered GM crops (cotton, soya bean, maize, grape, wheat, rice, sugar beet, alfalfa, canola, tomato and potato), only potato and tomato presented native relatives (66 species total). Introduced relative species showed that three GM groups were formed having: a) up to one introduced relative (cotton and soya bean), b) up to two (rice, grape, maize and wheat) and c) from two to seven (sugar beet, alfalfa, canola, tomato and potato). In particular, GM crops presenting introduced noncultivated relative species were canola (1 relative species), alfalfa (up to 4), rice (1), tomato (up to 2) and potato (up to 2). The outcrossing potential between species [OP; scaled from ‘very low’ (1) to ‘very high’ (5)] was developed, showing medium OPs (3) for GM–native relative interactions when they occurred, low (2) for GMs and introduced noncultivated and high (4) for the grape‐Vitis vinifera GM–introduced cultivated interaction. This analytical tool might be useful for future ERA for unconfined GM crop release in Chile.     

Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana)

Patterns of genomic divergence between hybridizing taxa can be heterogeneous along the genome. Both differential introgression and local adaptation may contribute to this pattern. Here, we analysed two teosinte subspecies, Zea mays ssp. parviglumis and ssp. mexicana, to test whether their divergence has occurred in the face of gene flow and to infer which environmental variables have been important drivers of their ecological differentiation. We generated 9,780 DArTseqTM SNPs for 47 populations, and used an additional data set containing 33,454 MaizeSNP50 SNPs for 49 populations. With these data, we inferred features of demographic history and performed genome wide scans to determine the number of outlier SNPs associated with climate and soil variables. The two data sets indicate that divergence has occurred or been maintained despite continuous gene flow and/or secondary contact. Most of the significant SNP associations were to temperature and to phosphorus concentration in the soil. A large proportion of these candidate SNPs were located in regions of high differentiation that had been identified previously as putative inversions. We therefore propose that genomic differentiation in teosintes has occurred by a process of adaptive divergence, with putative inversions contributing to reduced gene flow between locally adapted populations.     

Monitoring attributes for ecological restoration in Latin America and the Caribbean region

Ecological restoration is becoming mainstreamed worldwide but target ecosystems' responses to restorative interventions are not sufficiently monitored, in terms of the wide range of ecological, social, and economic attributes available. In order to highlight and better understand this problem, we conducted a literature review of the ecological, social, and economic attributes cited in the scientific literature used for monitoring the success of ecological restoration projects in Latin America and the Caribbean region, where no regional study of this kind has previously been conducted. In 84 of the 91 articles retained for the study, ecological indicators were evaluated, while only seven articles included measurements of socioeconomic indicators. Regarding the Society for Ecological Restoration Primer attributes of restored ecosystems, we only found indicators measuring attributes 1–6, with attribute 1 (species assemblages) predominating (73%), followed by physical conditions (54%) and ecological functions (51%). Brazil was the country in the region where most monitoring was being carried out (51% of the articles), and tropical rainforest (33%) and tropical dry forest (25%) were the ecosystem types where ecological restoration was most frequently monitored. Highly vulnerable ecosystems such as mangroves and paramos were underrepresented. Attributes related to ecosystem stability or to governance and education of communities were not monitored at all. More real long‐term monitoring, instead of chronosequences, is needed, especially where understanding socioeconomic implications of, and barriers to, effective ecological restoration is a top priority.     

Variation in Sexual Expression in Jacaratia mexicana (Caricaceae) in Southern Mexico: Frequency and Relative Seed Performance of Fruit-Producing Males

Dioecy, the segregation of male and female structures among individuals, is widespread in tropical plants, encompassing 10–30 percent of species in some sites. In many cases, interindividual sex separation is not complete, as individual plants, although nominally dioecious, may produce both types of reproductive structures. A common form of this sexual variation is the production of female structures in otherwise male individuals, commonly referred to as fruiting males. Here we report the existence of fruiting males in the dioecious tropical tree Jacaratia mexicana (Caricaceae). We show that fruiting males can constitute up to 45 percent of all males in some populations of a tropical forest in Southern Mexico. In order to determine the functional significance of fruiting males for the breeding system of J. mexicana , we compared the relative performance of male- and female-borne seeds. Our results show that seeds from fruiting males are three times less likely to germinate and survive than seeds from female trees. Based on relative seed fitness data, and sex ratios in natural populations, we estimate that 6–15 percent of the genes contributed by fruiting males to the next generation are transmitted via ovules, meaning that morphological variation in gender is at least partially accompanied by functional gender variation. Finally, our seed fitness estimates for fruiting males suggest that fruiting males will not replace female plants in natural populations.
Abstract in Spanish is available at http://www.blackwell-synergy.com/loi/btp .     

Patient contrastive learning: A performant,expressive, and practical approach to electrocardiogram modeling

Supervised machine learning applications in health care are often limited due to a scarcity of labeled training data. To mitigate the effect of small sample size, we introduce a pre-training approach, Patient Contrastive Learning of Representations (PCLR), which creates latent representations of electrocardiograms (ECGs) from a large number of unlabeled examples using contrastive learning. The resulting representations are expressive, performant, and practical across a wide spectrum of clinical tasks. We develop PCLR using a large health care system with over 3.2 million 12-lead ECGs and demonstrate that training linear models on PCLR representations achieves a 51% performance increase, on average, over six training set sizes and four tasks (sex classification, age regression, and the detection of left ventricular hypertrophy and atrial fibrillation), relative to training neural network models from scratch. We also compared PCLR to three other ECG pre-training approaches (supervised pre-training, unsupervised pre-training with an autoencoder, and pre-training using a contrastive multi ECG-segment approach), and show significant performance benefits in three out of four tasks. We found an average performance benefit of 47% over the other models and an average of a 9% performance benefit compared to best model for each task. We release PCLR to enable others to extract ECG representations at https://github.com/broadinstitute/ml4h/tree/master/model_zoo/PCLR.     

Tyrosine phosphorylation of alpha-actinin in activated platelets

The integrin alpha(IIb)beta(3) mediates tyrosine phosphorylation of a 105-kDa protein (pp105) in activated platelets. We have partially purified a 105-kDa tyrosine-phosphorylated protein from platelets stimulated with phorbol 12-myristate 13-acetate and obtained the sequence of an internal 12-mer peptide derived from this protein. The sequence was identical to human alpha-actinin sequences deposited in the Swiss Protein Database. alpha-Actinin, a 105-kDa protein in platelets, was subsequently purified from activated platelets by four sequential chromatographic steps. Fractions were analyzed by Western blotting and probed with alpha-actinin and anti-phosphotyrosine antibodies. The distribution of alpha-actinin and pp105 overlapped throughout the purification. Furthermore, in the course of this purification, a 105-kDa tyrosine-phosphorylated protein was only detected in fractions that contained alpha-actinin. The purified alpha-actinin protein was immunoprecipitated with antibodies to phosphotyrosine in the absence but not in the presence of phenyl phosphate. alpha-Actinin resolved by two-dimensional gel electrophoresis of activated platelet lysates was recognized by the antibodies to phosphotyrosine, whereas pretreatment of the platelets with bisindolylmaleimide, a protein kinase C inhibitor that prevents tyrosine phosphorylation of pp105, inhibited the reactivity of the antibodies to phosphotyrosine with alpha-actinin. Taken together, these data demonstrate that a fraction of alpha-actinin is tyrosine-phosphorylated in activated platelets.