Epipelagic siphonophore assemblages associated with water masses along a transect between Chile and Easter Island (eastern South Pacific Ocean)

We analyze for the first time the spatial distribution of siphonophoresin relation to water masses along a 3750-km oceanic transectbetween the Chilean coast and the Easter Island (27° S),a sector scarcely known of eastern South Pacific Ocean. Thirty-onesiphonophore species were identified; Sulculeolaria turgidaand Vogtia glabra were recorded for the first time in this sector.The most abundant species were Muggiaea atlantica (29.2%), Eudoxoidesspiralis (24.5%) and Lensia subtilis (13.1%). Two differentsiphonophore assemblages east and west of 76 W, associated respectivelywith Subantarctic Water and Subtropical Water masses, can beused as water mass indicators. The former included the threemost abundant species, whereas the latter showed greater speciesrichness. This study provides basic knowledge on spatial distributionof siphonophores, which is important to develop future researchfocused on understanding the ecological role and biologicalprocesses driven by planktonic organisms in the southeasternPacific Ocean.     

2-D DIGE analysis of UV-C radiation-responsive proteins in globe artichoke leaves

Plants respond to ultraviolet stress inducing a self-defence through the regulation of specific gene family members. The UV acclimation is the result of biochemical and physiological processes, such as enhancement of the antioxidant enzymatic system and accumulation of UV-absorbing phenolic compounds (e.g. flavonoids). Globe artichoke is an attractive species for studying the protein network involved in UV stress response, being characterized by remarkable levels of inducible antioxidants. Proteomic tools can assist the evaluation of the expression patterns of UV-responsive proteins and we applied the difference in-gel electrophoresis (DIGE) technology for monitoring the globe artichoke proteome variation at four time points following an acute UV-C exposure. A total of 145 UV-C-modulated proteins were observed and 119 were identified by LC-MS/MS using a ～144,000 customized Compositae protein database, which included about 19,000 globe artichoke unigenes. Proteins were Gene Ontology (GO) categorized, visualized on their pathways and their behaviour was discussed. A predicted protein interaction network was produced and highly connected hub-like proteins were highlighted. Most of the proteins differentially modulated were chloroplast located, involved in photosynthesis, sugar metabolisms, protein folding and abiotic stress. The identification of UV-C-responsive proteins may contribute to shed light on the molecular mechanisms underlying plant responses to UV stress.     

Use of degenerate primers and touchdown PCR for construction of cDNA libraries

Optimized construction of low-redundancy cDNA mini-libraries using low-stringency RT-PCR is described cDNAs are generated using arbitrary consensus-degenerate hybrid oligonucleotide primers and nanogram amounts of Schistosoma mansoni mRNA. A number of conditions such as temperature and salt concentration are combined to create balanced, low-stringency conditions that permit a normalized amplification of a diversified, random set of sequences. On average, 350 different sequences are obtained per mini-library, which represents a significantly higher diversity of messages per library when compared to previously published conditions (ie., 20-40 sequences/ mini-library). The optimized high-throughput approach described here is likely to help in the discovery of expressed genes in any complex organism.     

De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks

With the emergence of high throughput single cell techniques, the understanding of the molecular and cellular diversity of mammalian organs have rapidly increased. In order to understand the spatial organization of this diversity, single cell data is often integrated with spatial data to create probabilistic cell maps. However, targeted cell typing approaches relying on existing single cell data achieve incomplete and biased maps that could mask the true diversity present in a tissue slide. Here we applied a de novo technique to spatially resolve and characterize cellular diversity of in situ sequencing data during human heart development. We obtained and made accessible well defined spatial cell-type maps of fetal hearts from 4.5 to 9 post conception weeks, not biased by probabilistic cell typing approaches. With our analysis, we could characterize previously unreported molecular diversity within cardiomyocytes and epicardial cells and identified their characteristic expression signatures, comparing them with specific subpopulations found in single cell RNA sequencing datasets. We further characterized the differentiation trajectories of epicardial cells, identifying a clear spatial component on it. All in all, our study provides a novel technique for conducting de novo spatial-temporal analyses in developmental tissue samples and a useful resource for online exploration of cell-type differentiation during heart development at sub-cellular image resolution.     

TGFβ Governs the Pleiotropic Activity of NDRG1 in Triple-Negative Breast Cancer Progression

In triple-negative breast cancer (TNBC), the pleiotropic NDRG1 (N-Myc downstream regulated gene 1) promotes progression and worse survival, yet contradictory results were documented, and the mechanisms remain unknown. Phosphorylation and localization could drive NDRG1 pleiotropy, nonetheless, their role in TNBC progression and clinical outcome was not investigated. We found enhanced p-NDRG1 (Thr346) by TGFβ1 and explored whether it drives NDRG1 pleiotropy and TNBC progression. In tissue microarrays of 81 TNBC patients, we identified that staining and localization of NDRG1 and p-NDRG1 (Thr346) are biomarkers and risk factors associated with shorter overall survival. We found that TGFβ1 leads NDRG1, downstream of GSK3β, and upstream of NF-κB, to differentially regulate migration, invasion, epithelial-mesenchymal transition, tumor initiation, and maintenance of different populations of cancer stem cells (CSCs), depending on the progression stage of tumor cells, and the combination of TGFβ and GSK3β inhibitors impaired CSCs. The present study revealed the striking importance to assess both total NDRG1 and p-NDRG1 (Thr346) positiveness and subcellular localization to evaluate patient prognosis and their stratification. NDRG1 pleiotropy is driven by TGFβ to differentially promote metastasis and/or maintenance of CSCs at different stages of tumor progression, which could be abrogated by the inhibition of TGFβ and GSK3β.     

Phosphate limitation as crucial factor to enhance yeast lipid production from short‐chain fatty acids

Microbial lipids for chemical synthesis are commonly obtained from sugar‐based substrates which in most cases is not economically viable. As a low‐cost carbon source, short‐chain fatty acids (SCFAs) that can be obtained from food wastes offer an interesting alternative for achieving an affordable lipid production process. In this study, SCFAs were employed to accumulate lipids using Yarrowia lipolytica ACA DC 50109. For this purpose, different amounts of SCFAs, sulfate, phosphate and carbon: phosphate ratios were used in both synthetic and real SCFAs‐rich media. Although sulfate limitation did not increase lipid accumulation, phosphate limitation was proved to be an optimal strategy for increasing lipid content and lipid yields in both synthetic and real media, reaching a lipid productivity up to 8.95 g/L h. Remarkably, the highest lipid yield (0.30 g/g) was achieved under phosphate absence condition (0 g/L). This fact demonstrated the suitability of using low‐phosphate concentrations to boost lipid production from SCFAs.

Microbial lipids for chemical synthesis are commonly obtained from sugar‐based substrates which in most cases is not economically viable. As a low‐cost carbon source, short‐chain fatty acids (SCFAs) that can be obtained from food‐wastes offer an interesting alternative for achieving an affordable lipid production process. In this study, SCFAs were employed to accumulate lipids using Yarrowia lipolytica ACA DC 50109.     

Corporate and Product Carbon Footprint under Compound Hybrid Analysis: Application to a Spanish Timber Company

The European Union (EU) is advancing steadily toward the stabilization of atmospheric greenhouse gas concentrations. Various sectors are now obliged to make reductions, and new policies based on the carbon footprint are being encouraged. However, voluntary reporting of so‐called scope 3 emissions is hindering successful implementation of these policies. In this study, we present a tiered hybrid analysis to report emissions according to the ISO/TR 14069 standards and to obtain complete measures of scope 3 emissions. A process analysis for scope 1 and scope 2 emissions is complemented with a multiregional input‐output analysis for upstream scope 3 emissions. This novel approach is applied to the case study of a Spanish timber company. Its total carbon footprint in 2011 was 783,660 kilograms of carbon‐dioxide equivalent, of which 88% correspond to scope 3 emissions. These emissions are globally distributed; 71% are from European countries, followed by 8% from emerging economies (Brazil, Russia, India, Indonesia, Australia, and Turkey), 5% from China, and, finally, 16% from the rest of the world. We identify and discuss the advantages and disadvantages of this novel approach, the European implementation of which could be highly effective in reducing global carbon emissions.     

An 86Y-labeled mirror-image oligonucleotide: influence of Y-DOTA isomers on the biodistribution in rats

A mirror-image oligonucleotide (L-RNA) was radiolabeled with the positron emitting radionuclide (86)Y (t(1/2) = 14.7 h) via the bifunctional chelator approach. DOTA-modification of the L-RNA (sequence: 5'-aminohexyl UGA CUG ACU GAC-3'; MW 3975) was performed using (S)-p-SCN-Bn-DOTA. (86)Y radiolabeling of the DOTA-L-RNA produced more than one species as evidenced by HPLC radiometric detection. For the identification of the (86)Y-labeled L-RNA, the structural analogue nonradioactive precursor [Y((S)-p-NH2-Bn-DOTA)](-) was synthesized. Two coordination isomers were separated via HPLC adopting the square antiprismatic (SAP) and the twisted square antiprismatic (TSAP) geometry, respectively. Their stereochemical configuration in the solution state was assessed by NMR and circular dichroism spectroscopy. Both [Y((S)-p-NH2-Bn-DOTA)](-) isomers were converted into isothiocyanate derivatives [Y((S)-p-SCN-Bn-DOTA)](-) and conjugated to the L-RNA. The identity of the [(86)Y-DOTA]-L-RNA species was finally established by comparison of the radiometric ((86)Y) and UV-visible chromatographic profiles. Biodistribution studies in Wistar rats showed minor changes in the biodistribution profile of the [(86)Y((S)-p-NH2-Bn-DOTA)](-) complex isomers, while no significant differences were observed for the [(86)Y-DOTA]-L-RNA isomers. High renal excretions were found for the [(86)Y((S)-p-NH 2-Bn-DOTA)](-) complex isomers as well as for the L-RNA isomers.     

Comparative Energy, Environmental, and Economic Analysis of Traditional and E-commerce DVD Rental Networks

This study is a comparative life-cycle assessment (LCA) of two competing digital video disc (DVD) rental networks: the e-commerce option, where the customer orders the movies online, and the traditional business option, where the customer goes to the rental store to rent a movie. The analytical framework proposed is for a customer living in the city of Ann Arbor, Michigan in the United States. The primary energy and environmental performance for both networks are presented using a multicriterion LCA. The package selected by the traditional network is responsible for 67% of the difference in total energy consumption of the two alternatives. Results show that the e-commerce alternative consumed 33% less energy and emitted 40% less CO2 than the traditional option. A set of sensitivity analyses test the influence of distance traveled, transportation mode, and reuse of DVD and DVD packaging on the final results. The mode of transportation used by the customer in the traditional business model also affects global emissions and energy consumption. The customer walking to the store is by far the best option in the traditional network; however, the e-commerce option performed comparatively better despite all transportation modes tested. A novel economic indicator, ESAL, is used to compare different transportation modes based on the level of stress exerted on the pavement. The two networks are compared on the basis of cost accounting; consistent with its energy and environmental advantages, the e-commerce network also exerts lesser economic impact, by $1.17, for the functional unit tested.