Protrusive waves guide 3D cell migration along nanofibers

In vivo, cells migrate on complex three-dimensional (3D) fibrous matrices, which has made investigation of the key molecular and physical mechanisms that drive cell migration difficult. Using reductionist approaches based on 3D electrospun fibers, we report for various cell types that single-cell migration along fibronectin-coated nanofibers is associated with lateral actin-based waves. These cyclical waves have a fin-like shape and propagate up to several hundred micrometers from the cell body, extending the leading edge and promoting highly persistent directional movement. Cells generate these waves through balanced activation of the Rac1/N-WASP/Arp2/3 and Rho/formins pathways. The waves originate from one major adhesion site at leading end of the cell body, which is linked through actomyosin contractility to another site at the back of the cell, allowing force generation, matrix deformation and cell translocation. By combining experimental and modeling data, we demonstrate that cell migration in a fibrous environment requires the formation and propagation of dynamic, actin based fin-like protrusions.     

Targeting the late component of the cardiac L-type Ca2+ current to suppress early afterdepolarizations

Early afterdepolarizations (EADs) associated with prolongation of the cardiac action potential (AP) can create heterogeneity of repolarization and premature extrasystoles, triggering focal and reentrant arrhythmias. Because the L-type Ca²⁺ current (I_Ca,L) plays a key role in both AP prolongation and EAD formation, L-type Ca²⁺ channels (LTCCs) represent a promising therapeutic target to normalize AP duration (APD) and suppress EADs and their arrhythmogenic consequences. We used the dynamic-clamp technique to systematically explore how the biophysical properties of LTCCs could be modified to normalize APD and suppress EADs without impairing excitation–contraction coupling. Isolated rabbit ventricular myocytes were first exposed to H₂O₂ or moderate hypokalemia to induce EADs, after which their endogenous I_Ca,L was replaced by a virtual I_Ca,L with tunable parameters, in dynamic-clamp mode. We probed the sensitivity of EADs to changes in the (a) amplitude of the noninactivating pedestal current; (b) slope of voltage-dependent activation; (c) slope of voltage-dependent inactivation; (d) time constant of voltage-dependent activation; and (e) time constant of voltage-dependent inactivation. We found that reducing the amplitude of the noninactivating pedestal component of I_Ca,L effectively suppressed both H₂O₂- and hypokalemia-induced EADs and restored APD. These results, together with our previous work, demonstrate the potential of this hybrid experimental–computational approach to guide drug discovery or gene therapy strategies by identifying and targeting selective properties of LTCC.     

Expression of a Catalytically Inactive Mutant Form of Glutathione Peroxidase 4 (Gpx4) Confers a Dominant-negative Effect in Male Fertility

The selenoenzyme Gpx4 is essential for early embryogenesis and cell viability for its unique function to prevent phospholipid oxidation. Recently, the cytosolic form of Gpx4 was identified as an upstream regulator of a novel form of non-apoptotic cell death, called ferroptosis, whereas the mitochondrial isoform of Gpx4 was previously shown to be crucial for male fertility. Here, we generated and analyzed mice with a targeted mutation of the active site selenocysteine of Gpx4 (Gpx4_U46S). Mice homozygous for Gpx4_U46S died at the same embryonic stage (E7.5) as Gpx4^−/− embryos as expected. Surprisingly, male mice heterozygous for Gpx4_U46S presented subfertility. Subfertility was manifested in a reduced number of litters from heterozygous breeding and an impairment of spermatozoa to fertilize oocytes in vitro. Morphologically, sperm isolated from heterozygous Gpx4_U46S mice revealed many structural abnormalities particularly in the spermatozoa midpiece due to improper oxidation and polymerization of sperm capsular proteins and malformation of the mitochondrial capsule surrounding and stabilizing sperm mitochondria. These findings are reminiscent of sperm isolated from selenium-deprived rodents or from mice specifically lacking mitochondrial Gpx4. Due to a strongly facilitated incorporation of Ser in the polypeptide chain as compared with selenocysteine at the UGA codon, expression of the catalytically inactive Gpx4_U46S was found to be strongly increased. Because the stability of the mitochondrial capsule of mature spermatozoa depends on the moonlighting function of Gpx4 both as an enzyme oxidizing capsular protein thiols and as a structural protein, tightly controlled expression of functional Gpx4 emerges as a key for full male fertility.     

Systematic assessment of the Atelostomata (Spatangoida and Holasteroida; irregular echinoids) based on spine microstructure

Spines of irregular echinoids occur in very high abundance in each specimen, and display distinct architecture as a result of the specialized functions of the spines; however, studies on spine microstructure in atelostomate echinoids have rarely been carried out. Accordingly, little is known about their specific morphology. This work aims to elaborate differences in the spine morphology of selected Atelostomata (Spatangoida and Holasteroida) in detail, and to discuss spine microstructure for its potential systematic value. Based on 82 atelostomate species (56 spatangoids and 26 holasteroids), we show that the perforation pattern in the internal cylinder of the spine (helicoidal versus horizontal pattern) provides a safe distinction between the Spatangoida and Holasteroida. According to this character we discuss the geological history of atelostomate echinoids, in particular their migration into the deep sea, based on well‐preserved records of fossil spines. © 2015 The Linnean Society of London     

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0582-8) contains supplementary material, which is available to authorized users.     

Age‐dependent decline in fin regenerative capacity in the short‐lived fish Nothobranchius furzeri

The potential to regenerate declines with age in a wide range of organisms. A popular model system to study the mechanisms of regeneration is the fin of teleost fish, which has the ability to fully regrow upon amputation. Here, we used the short‐lived killifish Nothobranchius furzeri to analyse the impact of aging on fin regeneration in more detail. We observed that young fish were able to nearly completely (98%) regenerate their amputated caudal fins within 4 weeks, whereas middle‐aged fish reached 78%, old fish 57% and very old fish 46% of their original fin size. The difference in growth rate between young and old fish was already significant at 3 days post amputation (dpa) and increased with time. We therefore hypothesized that early events are crucial for the age‐related differences in regenerative capacity. Indeed, we could observe a higher percentage of proliferating cells in early regenerating fin tissue of young fish compared with aged fish and larger fractions of apoptotic cells in aged fish. Furthermore, young fish showed peak upregulation of several genes involved in fgf and wnt/β‐catenin signalling at an earlier time point than old fish. Our findings suggest that regenerative processes are initiated earlier and that regeneration overall is more efficient in younger fish.     

Assessment of regional and local biodiversity in tropical and subtropical coastal habitats in the East African Marine Ecoregion

The transboundary networks of Marine Protected Areas (MPAs) project, TRANSMAP, assessed local turnover and regional biodiversity across the East African Marine Ecoregion, where inter-governmental co-operation has been working to connect local MPAs. The benthic fauna in the three most dominant habitats on this coastline??beaches, mangroves and seagrasses??were studied in two Regions (Northern Region, 10?C13°S; Southern Region, 25?C28°S). Meiofaunal taxa were used as the model faunal group owing to their diversity and abundance across habitat types and environmental conditions. Meiofaunal abundance averaged 2,500 individuals 10 cm^?2 and was generally higher in mangrove and seagrass sediments than on the beaches, and was significantly different between habitats × Regions. In total, 18 taxa were recorded with highest diversity in the beach samples. Diversity indices and assemblage structure were significantly different between habitats, but also Regions. Specific granulometric 1?? size classes, shore-height and number of rain days were the factors most significantly correlating with the observed assemblage patterns. Additionally, the size of a MPA and latitude (which correlated with MPA age, but not number of rain days), were the factors fitting best with meiofaunal assemblage patterns across the beaches, the habitat for which the most comprehensive data were generated. Sample diversity was higher in the Southern Region, and although within- and across-habitats diversity were similar across the Regions, the two Regions appeared to provide complementary habitats and supported different assemblages. Within the Regions, beaches (the only habitat for which more than one location was sampled) were significantly different between Locations, supporting the establishment of multiple protected locations of the same habitat within each transboundary MPA.