Expression of epidermal growth factor in the rat kidney

Summary The renal localization and the site of synthesis of epidermal growth factor (EGF) were investigated in the rat kidney by immunohistochemistry and in situ hybridization techniques. EGF was localized in the cells of the thick ascending limb of Henle (TAL) and distal convoluted tubule (DCT). At the ultrastructural level, EGF immunoreactivity was distributed on the apical membrane and trans-Golgi complex of the TAL and DCT cells. These segments of the rat nephron also hybridized to prepro-EGF cRNA probes in a specific manner, indicating that TAL and DCT are the sites of EGF synthesis in the rat kidney.     

MicroRNA signatures of iPSCs and endoderm-derived tissues

MicroRNAs (miRNAs), small non-coding RNAs that fine-tune gene expression, play multiple roles in the cell, including cell fate specification. We have analyzed the differential expression of miRNAs during fibroblast reprogramming into induced pluripotent stem cells (iPSCs) and endoderm induction from iPSCs upon treatment with high concentrations of Activin-A. The reprogrammed iPSCs assumed an embryonic stem cell (ESC)-like miRNA signature, marked by the induction of pluripotency clusters miR-290–295 and miR-302/367 and conversely the downregulation of the let-7 family. On the other hand, endoderm induction in iPSCs resulted in the upregulation of 13 miRNAs. Given that the liver and the pancreas are common derivatives of the endoderm, analysis of the expression of these 13 upregulated miRNAs in hepatocytes and pancreatic islets revealed a tendency for these miRNAs to be expressed more in pancreatic islets than in hepatocytes. These observations provide insights into how differentiation may be guided more efficiently towards the endoderm and further into the liver or pancreas. Moreover, we also report novel miRNAs enriched for each of the cell types analyzed.     

Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases

Engineered polyketide synthases (PKSs) are promising synthetic biology platforms for the production of chemicals with diverse applications. The dehydratase (DH) domain within modular type I PKSs generates an α,β-unsaturated bond in nascent polyketide intermediates through a dehydration reaction. Several crystal structures of DH domains have been solved, providing important structural insights into substrate selection and dehydration. Here, we present two DH domain structures from two chemically diverse PKSs. The first DH domain, isolated from the third module in the borrelidin PKS, is specific towards a trans-cyclopentane-carboxylate-containing polyketide substrate. The second DH domain, isolated from the first module in the fluvirucin B₁ PKS, accepts an amide-containing polyketide intermediate. Sequence-structure analysis of these domains, in addition to previously published DH structures, display many significant similarities and key differences pertaining to substrate selection. The two major differences between BorA DH M3, FluA DH M1 and other DH domains are found in regions of unmodeled residues or residues containing high B-factors. These two regions are located between α3–β11 and β7–α2. From the catalytic Asp located in α3 to a conserved Pro in β11, the residues between them form part of the bottom of the substrate-binding cavity responsible for binding to acyl-ACP intermediates.

     

Air-pollutant chemicals and oxidized lipids exhibit genome-wide synergistic effects on endothelial cells

Background  

Ambient air pollution is associated with increased cardiovascular morbidity and mortality. We have found that exposure to ambient ultrafine particulate matter, highly enriched in redox cycling organic chemicals, promotes atherosclerosis in mice. We hypothesize that these pro-oxidative chemicals could synergize with oxidized lipid components generated in low-density lipoprotein particles to enhance vascular inflammation and atherosclerosis.     

Upstream kinases of plant SnRKs are involved in salt stress tolerance

Sucrose non‐fermenting 1‐related protein kinases (SnRKs) are important for plant growth and stress responses. This family has three clades: SnRK1, SnRK2 and SnRK3. Although plant SnRKs are thought to be activated by upstream kinases, the overall mechanism remains obscure. Geminivirus Rep‐Interacting Kinase (GRIK)1 and GRIK2 phosphorylate SnRK1s, which are involved in sugar/energy sensing, and the grik1‐1 grik2‐1 double mutant shows growth retardation under regular growth conditions. In this study, we established another Arabidopsis mutant line harbouring a different allele of gene GRIK1 (grik1‐2 grik2‐1) that grows similarly to the wild‐type, enabling us to evaluate the function of GRIKs under stress conditions. In the grik1‐2 grik2‐1 double mutant, phosphorylation of SnRK1.1 was reduced, but not eliminated, suggesting that the grik1‐2 mutation is a weak allele. In addition to high sensitivity to glucose, the grik1‐2 grik2‐1 mutant was sensitive to high salt, indicating that GRIKs are also involved in salinity signalling pathways. Salt Overly Sensitive (SOS)2, a member of the SnRK3 subfamily, is a critical mediator of the response to salinity. GRIK1 phosphorylated SOS2 in vitro, resulting in elevated kinase activity of SOS2. The salt tolerance of sos2 was restored to normal levels by wild‐type SOS2, but not by a mutated form of SOS2 lacking the T168 residue phosphorylated by GRIK1. Activation of SOS2 by GRIK1 was also demonstrated in a reconstituted system in yeast. Our results indicate that GRIKs phosphorylate and activate SnRK1 and other members of the SnRK3 family, and that they play important roles in multiple signalling pathways in vivo.     

Species‐specific disturbance tolerance,competition and positive interactions along an anthropogenic disturbance gradient

Question: As it has been found that stress promotes positive interactions mediated by physical amelioration of the environment, is it possible that interactions may turn positive with increasing chronic anthropogenic disturbance (CAD) intensity? Also, is it possible that species that do not tolerate disturbance may require environmental amelioration by their neighbours in disturbed areas, whereas tolerant species may not? Location: The semi‐arid grassland in Concepción Buenavista, Oaxaca, southern Mexico. Methods: We assessed interaction intensity and importance through a neighbour removal experiment along a CAD gradient for three species differing in disturbance tolerance. Water potential was monitored on vegetated and bare soil. Results: A shift from competitive effects in low CAD sites to positive interactions in degraded sites was found. The disturbance‐tolerant species did not respond to CAD, whereas the less tolerant species changed its interactions drastically in terms of growth and reproduction. The species with medium tolerance had an intermediate response. Neighbours promoted germination in all species. Vegetation removal reduced soil humidity. Conclusions: Positive interactions seemingly resulted from the amelioration of the abiotic stresses induced by vegetation removal. The dependence on neighbours to germinate, grow, or reproduce suggests that if CAD eliminates the plant cover, vegetation will hardly recover. Irreversible changes are known to occur in communities where positive interactions predominate, but CAD may set the conditions for irreversible shifts even in communities where interactions are normally competitive.     

Co-opted Oxysterol-Binding ORP and VAP Proteins Channel Sterols to RNA Virus Replication Sites via Membrane Contact Sites

Viruses recruit cellular membranes and subvert cellular proteins involved in lipid biosynthesis to build viral replicase complexes and replication organelles. Among the lipids, sterols are important components of membranes, affecting the shape and curvature of membranes. In this paper, the tombusvirus replication protein is shown to co-opt cellular Oxysterol-binding protein related proteins (ORPs), whose deletion in yeast model host leads to decreased tombusvirus replication. In addition, tombusviruses also subvert Scs2p VAP protein to facilitate the formation of membrane contact sites (MCSs), where membranes are juxtaposed, likely channeling lipids to the replication sites. In all, these events result in redistribution and enrichment of sterols at the sites of viral replication in yeast and plant cells. Using in vitro viral replication assay with artificial vesicles, we show stimulation of tombusvirus replication by sterols. Thus, co-opting cellular ORP and VAP proteins to form MCSs serves the virus need to generate abundant sterol-rich membrane surfaces for tombusvirus replication.

Authors Summary

Cellular proteins and cellular membranes are usurped by positive-stranded RNA viruses to assemble viral replicase complexes required for their replication. Tombusviruses, which are small RNA viruses of plants, depend on sterol-rich membranes for replication. The authors show that the tombusviral replication protein binds to cellular oxysterol-binding ORP proteins. Moreover, the endoplasmic reticulum resident cellular VAP proteins also co-localize with viral replication proteins. These protein interactions likely facilitate the formation of membrane contact sites that are visible in cells replicating tombusvirus RNA. The authors also show that sterols are recruited and enriched to the sites of viral replication. In vitro replication assay was used to show that sterols indeed stimulate tombusvirus replication. In summary, tombusviruses use subverted cellular proteins to build sterol-rich membrane microdomain to promote the assembly of the viral replicase complex. The paper connects efficient virus replication with cellular lipid transport and membrane structures.     

Diving deeper into the underlying white shark behaviors at Guadalupe Island,Mexico

1. Fine‐scale movement patterns are driven by both biotic (hunting, physiological needs) and abiotic (environmental conditions) factors. The energy balance governs all movement‐related strategic decisions.
2. Marine environments can be better understood by considering the vertical component. From 24 acoustic trackings of 10 white sharks in Guadalupe Island, this study linked, for the first time, horizontal and vertical movement data and inferred six different behavioral states along with movement states, through the use of hidden Markov models, which allowed to draw a comprehensive picture of white shark behavior.
3. Traveling was the most frequent state of behavior for white sharks, carried out mainly at night and twilight. In contrast, area‐restricted searching was the least used, occurring primarily in daylight hours.
4. Time of day, distance to shore, total shark length, and, to a lesser extent, tide phase affected behavioral states. Chumming activity reversed, in the short term and in a nonpermanent way, the behavioral pattern to a general diel vertical pattern.

     

A role for the carbohydrate‐binding module (CBM) in regulatory SnRK1 subunits: the effect of maltose on SnRK1 activity

SnRK1 is a protein kinase complex that is involved in several aspects of plant growth and development. There are published data indicative of a participation of SnRK1 in the regulation of the synthesis and degradation of starch, although the molecular mechanism is not known. In this work, we performed electron microscopy to explore the in vivo localization of the regulatory and catalytic subunits that constitute the SnRK1 complex. The results indicated that all the subunits are present in the chloroplast and, in particular, the SnRK1 βγ and SnRK1 β3 subunits are associated with starch. Furthermore, the regulatory subunits bind maltose, a relevant product of starch degradation. The kinase activity of immunoprecipitated complexes containing the βγ regulatory subunit was positively regulated by maltose only in the complexes obtained from Arabidopsis leaves collected at dusk. Recombinant complexes with the SnRK1α1 catalytic subunit, SnRK1βγ and three different β subunits showed that maltose only had an effect on a complex formed with the β3 subunit. Truncation of the CBM domain form SnRK1 βγ abolished the maltose activation of the complex and the activity was significantly reduced, indicating that the CBM is a positive regulator of SnRK1. A model of the SnRK1α1/βγ/β3 complex suggests the presence of two putative maltose‐binding sites, both involving ligand interactions with the βγ subunit and the α subunit.