BUSCADOR RECOLECTA

Improved bioinformatics tools for annotating gene function are becoming increasingly available, but such information must be considered theoretical until further experimental evidence proves it. In the work reported here, the genes for the main components of the translocons of the outer membrane of chloroplasts (Toc) and mitochondria (Tom), including preprotein receptors and protein-conducting channels of N. benthamiana, were identified. Sequence identity searches and phylogenetic relationships with functionally annotated sequences such as those of A. thaliana revealed that N. benthamiana orthologs mainly exist as recently duplicated loci. Only a Toc34 ortholog was found (NbToc34), while Toc159 receptor family was composed of four orthologs but somewhat different from those of A. thaliana. Except for NbToc90, the rest (NbToc120, NbToc159A and NbToc159B) had a molecular weight of about 150 kDa and an acidic domain similar in length. Only two orthologs of the Tom20 receptors, NbTom20-1 and NbTom20-2, were found. The number of the Toc and Tom receptor isoforms in N. benthamiana was comparable to that previously reported in tomato and what we found in BLAST searches in other species in the genera Nicotiana and Solanum. After cloning, the subcellular localization of N. benthamiana orthologs was studied, resulting to be identical to that of A. thaliana receptors. Phenotype analysis after silencing together with relative expression analysis in roots, stems and leaves revealed that, except for the Toc and Tom channel-forming components (NbToc75 and NbTom40) and NbToc34, functional redundancy could be observed either among Toc159 or mitochondrial receptors. Finally, heterodimer formation between NbToc34 and the NbToc159 family receptors was confirmed by two alternative techniques indicating that different Toc complexes could be assembled. Additional work needs to be addressed to know if this results in a functional specialization of each Toc complex., Peer reviewed

Improved bioinformatics tools for annotating gene function are becoming increasingly available, but such information must be considered theoretical until further experimental evidence proves it. In the work reported here, the genes for the main components of the translocons of the outer membrane of chloroplasts (Toc) and mitochondria (Tom), including preprotein receptors and protein-conducting channels of N. benthamiana, were identified. Sequence identity searches and phylogenetic relationships with functionally annotated sequences such as those of A. thaliana revealed that N. benthamiana orthologs mainly exist as recently duplicated loci. Only a Toc34 ortholog was found (NbToc34), while Toc159 receptor family was composed of four orthologs but somewhat different from those of A. thaliana. Except for NbToc90, the rest (NbToc120, NbToc159A and NbToc159B) had a molecular weight of about 150 kDa and an acidic domain similar in length. Only two orthologs of the Tom20 receptors, NbTom20-1 and NbTom20-2, were found. The number of the Toc and Tom receptor isoforms in N. benthamiana was comparable to that previously reported in tomato and what we found in BLAST searches in other species in the genera Nicotiana and Solanum. After cloning, the subcellular localization of N. benthamiana orthologs was studied, resulting to be identical to that of A. thaliana receptors. Phenotype analysis after silencing together with relative expression analysis in roots, stems and leaves revealed that, except for the Toc and Tom channel-forming components (NbToc75 and NbTom40) and NbToc34, functional redundancy could be observed either among Toc159 or mitochondrial receptors. Finally, heterodimer formation between NbToc34 and the NbToc159 family receptors was confirmed by two alternative techniques indicating that different Toc complexes could be assembled. Additional work needs to be addressed to know if this results in a functional specialization of each Toc complex., Peer reviewed

Figures, original raw data, of the above paper., Peer reviewed

Ecological systems are facing major diversity losses in this century due to Anthropogenic effects. Habitat loss, overexploitation of resources, invasion and pollution are rapidly jeopardizing the survival of whole communities. It has been recently suggested that a potential approach to flatten the curve of species extinction and prevent catastrophic shifts would involve the engineering of one selected species within one of these communities. Such possibility has started to become part of potential intervention scenarios to preserve biodiversity. Despite its potential, very little is known about the actual dynamic responses of complex ecological networks to the introduction of a synthetic strains derived from a resident species. In this paper, we address this problem by modelling the response of a community to the addition of a synthetic strain derived from a member of a stable ecosystem. We show that the community interaction matrix largely limits the spread of the engineered strain, thus suggesting that species diversity acts as an ecological firewall. The implications for future scenarios of ecosystem engineering are outlined.This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’., Peer reviewed

Supplementary movie S1: 3D time-course analysis of IO neuron migration in wildtype mice. Supplementary movie S2: 3D time-course analysis of IO neuron migration in Robo3 knockout mice. Supplementary movie S3: Morphology of Tomato+/Foxp2+ IO neurons in a E13 Ptf1a:CreERT2 ;RosaTom embryo. Supplementary movie S4: Morphology of Tomato+/Foxp2+ IO neurons in a E13 Ptf1a:CreERT2; Robo3-/- ;RosaTom embryo., Peer reviewed

The file “ctd_remedios_tlp.mat” includes data recorded by the CTD during the REMEDIOS-TLP cruise. Specifically it includes the following variables: - ‘latitude’ and ‘longitude’: in degrees (1x366 rowsxcols each variable). - ‘chla’: chlorophyll a in μg L-1. Columns are the different profiles, whereas rows are the chlorophyll values averaged every 1 m (142x366). - ‘date’: YY:MM:DD:hh:mm:ss of each CTD profile (366x6). - ‘sample’: text variable that associates each profile to its kind of sampling. ‘I01’, ’I02’ and ‘I03’ are the intensive samplings, whereas surveys samplings are named as ‘S01’, ’S02’, ‘S03’ and ‘S04’. - ‘pres’: pressure (dbar) from surface (0 m) to maximum bottom pressure (142 m). - ‘sigma’: density-1000 in kg-3. Columns are the different profiles, whereas rows are the density values averaged every 1 m (142x366). - ‘st’: code of stations sampled during the cruise (1x366). CTD data recorded with a MSS90 microstructure profiler during the intensive samplings are included in the file “profiler_remedios.mat” and contains the following variables: - ‘date’: YY:MM:DD:hh:mm:ss of each CTD profile (1658x6). - ‘dens’: density-1000 in kg-3. Columns correspond to the different profiles, whereas rows are the density values averaged every 1 m (45x1658). - ‘fluo’: fluorescence profiles. Columns correspond to the different profiles, whereas rows are the fluorescence values averaged every 1 m (45x1658). - ‘T’: temperature in oC. Columns correspond to the different profiles, whereas rows are the temperature values averaged every 1 m (45x1658). Nitrate data measured during the intensive samplings are included in the file ‘nitrate.mat’ and it includes the following variables: - ‘cruise’: code of the intensive sampling. 1 corresponds to intensive I01, 2 to I02 and 3 to I03 (134x1). - ‘date’: YY:MM:DD:hh:mm:ss of each CTD profile (134x6). - ‘pres’: pressure (dbar) in m (134x1). - ‘NO3’: nitrate values in μM. Values are displayed in an unique column and are associated to the variables ‘date’ and ‘pres’ (134x1), Dataset used for analyses in the publication "Rapid Fluctuations of the Subsurface Chlorophyll Maximum in Response to Wind Forcing in a Long, Narrow Bay", ESS Open Achive, 2021, No

Supplemental information: Document S1. Figures S1–S7. Table S1. GO analysis. Table S2. KEGG cLTP down-regulated. Table S3. KEGG cLTP up-regulated. Document S2. Article plus supplemental information., Peer reviewed

Source data 1: Graphs source data. Source data 2: RNAseq source data. Source data 3: ChIPseq source data. Source data 4: Western blot source data., Peer reviewed

Supplementary Table 9. Genomic region on Chromosome 8 detected using Fst and the mercury leaf accumulation phentoype. The region contains MtCAX9 and several ATPase binding, ion transporters, and stress response., Heavy metals are an increasing problem due to contamination from human sources that and can enter the food chain by being taken up by plants. Understanding the genetic basis of accumulation and tolerance in plants is important for reducing the uptake of toxic metals in crops and crop relatives, as well as for removing heavy metals from soils by means of phytoremediation. Following exposure of Medicago truncatula seedlings to cadmium (Cd) and mercury (Hg), we conducted a genome-wide association study using relative root growth (RRG) and leaf accumulation measurements. Cd and Hg accumulation and RRG had heritability ranging 0.44 – 0.72 indicating high genetic diversity for these traits. The Cd and Hg trait associations were broadly distributed throughout the genome, indicated the traits are polygenic and involve several quantitative loci. For all traits, candidate genes included several membrane associated ATP-binding cassette transporters, P-type ATPase transporters, oxidative stress response genes, and stress related UDP-glycosyltransferases. The P-type ATPase transporters and ATP-binding cassette protein-families have roles in vacuole transport of heavy metals, and our findings support their wide use in physiological plant responses to heavy metals and abiotic stresses. We also found associations between Cd RRG with the genes CAX3 and PDR3, two linked adjacent genes, and leaf accumulation of Hg associated with the genes NRAMP6 and CAX9. When plant genotypes with the most extreme phenotypes were compared, we found significant divergence in genomic regions using population genomics methods that contained metal transport and stress response gene ontologies. Several of these genomic regions show high linkage disequilibrium (LD) among candidate genes suggesting they have evolved together. Minor allele frequency (MAF) and effect size of the most significant SNPs was negatively correlated with large effect alleles being most rare. This is consistent with purifying selection against alleles that increase toxicity and abiotic stress. Conversely, the alleles with large affect that had higher frequencies that were associated with the exclusion of Cd and Hg. Overall, macroevolutionary conservation of heavy metal and stress response genes is important for improvement of forage crops by harnessing wild genetic variants in gene banks such as the Medicago HapMap collection., Peer reviewed

R script to generate Figure 3B in Cid, Marquez-Galera et al., (2021) (https://doi.org/10.1016/j.celrep.2021.109229)., Peer reviewed