Nucleosome Spacing Generated by ISWI and CHD1 Remodelers Is Constant Regardless of Nucleosome Density

Arrays of regularly spaced nucleosomes are a hallmark of chromatin, but it remains unclear how they are generated. Recent genome-wide studies, in vitro and in vivo, showed constant nucleosome spacing even if the histone concentration was experimentally reduced. This counters the long-held assumption that nucleosome density determines spacing and calls for factors keeping spacing constant regardless of nucleosome density. We call this a clamping activity. Here, we show in a purified system that ISWI- and CHD1-type nucleosome remodelers have a clamping activity such that they not only generate regularly spaced nucleosome arrays but also generate constant spacing regardless of nucleosome density. This points to a functionally attractive nucleosome interaction that could be mediated either directly by nucleosome-nucleosome contacts or indirectly through the remodelers. Mutant Drosophila melanogaster ISWI without the HAND-SANT-SLIDE (HSS) domain had no detectable spacing activity even though it is known to remodel and slide nucleosomes. This suggests that the role of ISWI remodelers in generating constant spacing is not just to mediate nucleosome sliding; they actively contribute to the attractive interaction. Additional factors are necessary to set physiological spacing in absolute terms.     

Hyperactivation of the G12-mediated signaling pathway in Caenorhabditis elegans induces a developmental growth arrest via protein kinase C

The G(12) type of heterotrimeric G-proteins play an important role in development and behave as potent oncogenes in cultured cells. However, little is known about the molecular nature of the components that act in the G(12)-signaling pathway in an organism. We characterized a C. elegans Galpha subunit gene, gpa-12, which is a homolog of mammalian G(12)/G(13)alpha, and found that animals defective in gpa-12 are viable. Expression of activated GPA-12 (G(12)QL) results in a developmental growth arrest caused by a feeding behavior defect that is due to a dramatic reduction in pharyngeal pumping. To elucidate the molecular nature of the signaling pathways in which G(12) participates, we screened for suppressors of the G(12)QL phenotype. We isolated 50 suppressors that contain mutations in tpa-1, which encodes two protein kinase C isoforms, TPA-1A and TPA-1B, most similar to PKCtheta/delta. TPA-1 mediates the action of the tumor promoter PMA. Expression of G(12)QL and treatment of wild-type animals with PMA induce an identical growth arrest caused by inhibition of larval feeding, which is dependent on TPA-1A and TPA-1B function. These results suggest that TPA-1 is a downstream target of both G(12) signaling and PMA in modulating feeding and growth in C. elegans. Taken together, our findings provide a potential molecular mechanism for the transforming capability of G(12) proteins.     

Biological nitrogen fixation in resource-poor agriculture in South Africa

Farm lands of resource-poor communities in South Africa are depleted of nutrients due to continuous mono-cropping, limited use of fertilisers, and sometimes leaching caused by high rainfall. Despite the well-known advantages of biological nitrogen fixation (BNF) in cropping systems, less than 10% of the grain crops planted annually in these areas are legumes. Using a participatory research and development approach, resource-poor farmers were introduced to conservation agriculture (CA) practices, including BNF, that promoted zero (or reduced) tillage, increased retention of soil cover, as well as crop diversification. Because crop rotation and intercropping of legumes with cereals are known to contribute to soil fertility while enhancing food security, resource-poor farmers from various Provinces in South Africa were trained on the benefits of legume culture for eight years. As a result, these resource-poor farmers did not only get training in inoculation techniques, but were also supplied with inoculants for use on their farms. Data collected from Farmers Demonstration Trials at Belvedere, Dumbarton and Lusikisiki, showed that the grain and fodder yield of maize planted after legumes, and maize intercropped with legumes, were comparable to those of maize receiving high N fertilizer dose (i.e. 54 kg N at planting and 54 kg N as top-dressing). The same data further showed thatRhizobium inoculation, when combined with application of low levels of P and K, significantly increased crop yields within farmers’ trial plots. BNF therefore offers a great opportunity for resource-poor farmers in South Africa to increase their crop yields and thus improve the quality of their livelihoods through the adoption of affordable and sustainable biological technologies that enhance soil fertility.     

Effect of alemtuzumab-based T-cell depletion on graft compositional change in vitro and immune reconstitution early after allogeneic stem cell transplantation

Background aimsTo reduce the risk of graft-versus-host disease (GVHD) after allogeneic stem cell transplantation (alloSCT), T-cell depletion (TCD) of grafts can be performed by the addition of alemtuzumab (ALT) “to the bag” (in vitro) before transplantation. In this prospective study, the authors analyzed the effect of in vitro incubation with 20 mg ALT on the composition of grafts prior to graft infusion. Furthermore, the authors assessed whether graft composition at the moment of infusion was predictive for T-cell reconstitution and development of GVHD early after TCD alloSCT.MethodsSixty granulocyte colony-stimulating factor-mobilized stem cell grafts were obtained from ≥9/10 HLA-matched related and unrelated donors. The composition of the grafts was analyzed by flow cytometry before and after in vitro incubation with ALT. T-cell reconstitution and incidence of severe GVHD were monitored until 12 weeks after transplantation.ResultsIn vitro incubation of grafts with 20 mg ALT resulted in an initial median depletion efficiency of T-cell receptor (TCR) α/β T cells of 96.7% (range, 63.5–99.8%), followed by subsequent depletion in vivo. Graft volumes and absolute leukocyte counts of grafts before the addition of ALT were not predictive for the efficiency of TCR α/β T-cell depletion. CD4^pos T cells were depleted more efficiently than CD8^pos T cells, and naive and regulatory T cells were depleted more efficiently than memory and effector T cells. This differential depletion of T-cell subsets was in line with their reported differential CD52 expression. In vitro depletion efficiencies and absolute numbers of (naive) TCR α/β T cells in the grafts after ALT incubation were not predictive for T-cell reconstitution or development of GVHD post- alloSCT.ConclusionsThe addition of ALT to the bag is an easy, fast and generally applicable strategy to prevent GVHD in patients receiving alloSCT after myeloablative or non-myeloablative conditioning because of the efficient differential depletion of donor-derived lymphocytes and T cells.     

Lower Cretaceous theropod tracks with the new ichnogenus and combination Lockleypus luanpingensis from the Dabeigou Formation of the Luanping Basin,Hebei Province,China

Theropod footprints from the Jingshang tracksite in the Lower Cretaceous Dabeigou Formation of the Luanping Basin, Hebei Province, China, are re-evaluated after new discoveries at this locality. They occur in a succession with sandstone, mudstone, and calcareous shale. The depositional environment was a shallow lake shore, comparable in age to the famous Jehol Biota. Based on the distinct morphology with peculiar features of the ratio of the outer digits, the footprints formerly assigned to Changpeipus carbonicus are now referred to the new ichnogenus and combination Lockleypus luanpingensis. The possible trackmaker was a relatively large ornithomimosaurian theropod thus far not known from the skeletal record of the Jehol Biota.     

Follistatin antagonizes transforming growth factor-beta3-induced epithelial-mesenchymal transition in vitro: implications for murine palatal development supported by microarray analysis

Abstract Epithelial–mesenchymal transition (EMT) is involved in normal embryonic development as well as in tumor progression and invasiveness. This process is also known to be a crucial step in palatogenesis during fusion of the bi-lateral palatal processes. Disruption of this step results in a cleft palate, which is among the most frequent birth defects in humans. A number of genes and encoded proteins have been shown to play a role in this developmental stage. The central role is attributed to the cytokine transforming growth factor-β3 (TGF-β3), which is expressed in the medial edge epithelium (MEE) already before the fusion process. The MEE covers the tips of the growing palatal shelves and eventually undergoes EMT or programmed cell death (apoptosis). TGF-β3 is described to induce EMT in embryonic palates. With regard to the early expression of this molecule before the fusion process, it is not well understood which mechanisms prevent the TGF-β3 producing epithelial cells from undergoing differentiation precociously. We used the murine palatal fusion to study the regulation of EMT. Specifically, we analyzed the MEE for the expression of known antagonists of TGF-β molecules using in situ hybridization and detected the gene coding for Follistatin to be co-expressed with TGF-β3. Further, we could show that Follistatin directly binds to TGF-β3 and that it completely blocks TGF-β3-induced EMT of the normal murine mammary gland (NMuMG) epithelial cell line in vitro . In addition, we analyzed the gene expression profile of NMuMG cells during TGF-β3-induced EMT by microarray hybridization, detecting strong changes in the expression of apoptosis-regulating genes.     

Translational efficiency of mRNA in yeast cells is not increased by plant viral leader sequences

Summary Synthetic oligonucleotides encoding the 5-non-translated (leader) sequence of the coat protein mRNA of alfalfa mosaic virus RNA 4 or the leader sequence of tobacco mosaic virus RNA were used to replace the natural leader region of the yeast phosphoglycerate kinase (PGK1) mRNAs and the translational efficiency of the chimeric mRNA was determined in yeast cells. In neither case did we observed a significant increase compared to the translational efficiency shown by the wild-type PGK mRNA, in contrast to the known stimulatory effect of these leader sequences on translation in mammalian, plant and bacterial in-vivo and/or in-vitro systems. The same result was obtained when the translational efficiencies in yeast cells of Escherichia coli -galactosidase mRNAs carrying the PGK or either of the two viral leader sequences were compared. Offprint requests to: H. A. Raué     

Sauropod Trackway Reflecting an Unusual Walking Pattern from the Early Cretaceous of Shandong Province,China

The trackway of a quadrupedal dinosaur from the Early Cretaceous (Albian) Qingquan tracksite (Tancheng, Shandong Province) is redescribed, and the trackmaker is identified as a sauropod. The trackway makes a slight turn towards the northwest and is characterized by an extremely narrow gauge pattern and an unusual configuration, i.e., a conspicuous difference between the position of the left and right manus tracks with respect to the position of the preceding pes track. Left manus tracks are located on the inside of the trackway, very close (and sometimes even in connection) to the opposite right pes tracks. So far, the Qingquan trackway is possibly the only extremely narrow-gauge sauropod trackway known from China. However, it is not clear to what extent this extremely narrow gauge pattern is related to the turning or a special behavior, or even linked to an injury (“limping trackway”). We tentatively attribute the Qingquan trackway to cf. Parabrontopodus, even though it has a rather low heteropody that is significantly lower than in Parabrontopodus and not typical for narrow-gauge sauropod trackways, but occurs in the wide-gauge ichnotaxon Brontopodus. Because of this discrepancy, the Qingquan trackway cannot readily be attributed to a more basal sauropod, which is generally considered the producer of narrow-gauge trackways. Therefore, the identification of a distinct sauropod group is not possible presently. The only skeletal remains of sauropods from the Lower Cretaceous of Shandong Province belong to the large titanosauriform, Euhelopus zdanskyi.