Soil carbon stock impacts following reversion of Miscanthus × giganteus and short rotation coppice willow commercial plantations into arable cropping

There are posited links between the establishment of perennial bioenergy, such as short rotation coppice (SRC) willow and Miscanthus × giganteus, on low carbon soils and enhanced soil C sequestration. Sequestration provides additional climate mitigation, however, few studies have explored impacts on soil C stocks of bioenergy crop removal; thus, the permanence of any sequestered C is unclear. This uncertainty has led some authors to question the handling of soil C stocks with carbon accounting, for example, through life cycle assessments. Here, we provide additional data for this debate, reporting on the soil C impacts of the reversion (removal and return) to arable cropping of commercial SRC willow and Miscanthus across four sites in the UK, two for each bioenergy crop, with eight reversions nested within these sites. Using a paired‐site approach, soil C stocks (0–1 m) were compared between 3 and 7 years after bioenergy crop removal. Impacts on soil C stocks varied, ranging from an increase of 70.16 ± 10.81 Mg C/ha 7 years after reversion of SRC willow to a decrease of 33.38 ± 5.33 Mg C/ha 3 years after reversion of Miscanthus compared to paired arable land. The implications for carbon accounting will depend on the method used to allocate this stock change between current and past land use. However, with published life cycle assessment values for the lifetime C reduction provided by these crops ranging from 29.50 to 138.55 Mg C/ha, the magnitude of these changes in stock are significant. We discuss the potential underlying mechanisms driving variability in soil C stock change, including the age of bioenergy crop at removal, removal methods, and differences in the recalcitrant of the crop residues, and highlight the need to design management methods to limit negative outcomes.     

A comparative and phylogenetic analysis of the alpha-actinin rod domain

Alpha-actinin is a ubiquitous actin-binding protein, composed of 3 domains; an actin-binding domain and a calcium-binding domain at the termini, connected by a rod domain composed by 1, 2, or 4 spectrin repeats (SRs). To understand how the rod domain has evolved during evolution, we have analyzed and compared the amino acid residue heterogeneity and phylogeny of the SRs of alpha-actinins of vertebrates, invertebrates, fungi, and several protozoa. The repeats of vertebrate alpha-actinins show a high degree of similarity, whereas repeats of invertebrates, fungi, and, in particular, of protozoa are more divergent. In the phylogeny, SR1 of all species were clustered together, independent of the number of repeats in the protein. It was also obvious that the second and last repeat in fungi (SR2) grouped with the fourth and last repeat of vertebrates and invertebrates (SR4). Therefore, the phylogeny implied that the rod domain of the cenancestral alpha-actinin only contained one SR. It was also obvious that SR2 of fungi are related to SR4 of vertebrates and invertebrates, implying that in the second intragenic duplication 2 repeats (i.e., what become SR2 and SR3) were inserted between the initial 2 repeats that become SR1 and SR4.     

Structural insight into the specific interaction between murine SHPS-1/SIRP alpha and its ligand CD47

SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1 (SHPS-1 or SIRPα/BIT) is an immunoglobulin (Ig) superfamily transmembrane receptor and a member of the signal regulatory protein (SIRP) family involved in cell-cell interaction. SHPS-1 binds to its ligand CD47 to relay an inhibitory signal for cellular responses, whereas SIRPβ, an activating member of the same family, does not bind to CD47 despite sharing a highly homologous ligand-binding domain with SHPS-1. To address the molecular basis for specific CD47 recognition by SHPS-1, we present the crystal structure of the ligand-binding domain of murine SHPS-1 (mSHPS-1). Folding topology revealed that mSHPS-1 adopts an I2-set Ig fold, but its overall structure resembles IgV domains of antigen receptors, although it has an extended loop structure (C′E loop), which forms a dimer interface in the crystal. Site-directed mutagenesis studies of mSHPS-1 identified critical residues for CD47 binding including sites in the C′E loop and regions corresponding to complementarity-determining regions of antigen receptors. The structural and functional features of mSHPS-1 are consistent with the human SHPS-1 structure except that human SHPS-1 has an additional β-strand D. These results suggest that the variable complementarity-determining region-like loop structures in the binding surface of SHPS-1 are generally required for ligand recognition in a manner similar to that of antigen receptors, which may explain the diverse ligand-binding specificities of SIRP family receptors.     

Production and characterization of transgenic mice systemically expressing endo-beta-galactosidase C

The alphaGal epitope (Galalpha1-3Gal) is a sugar structure expressed on the cell surface of almost all organisms except humans and old-world-monkeys, which express natural anti-alphaGal antibodies. The presence of these antibodies elicits a hyper acute rejection (HAR) upon xenotransplantation of cellular materials, such as from pigs to human beings. Endo-beta-galactosidase C (EndoGalC), an enzyme isolated from Clostridium perfringens, removes the alphaGal epitope by cleaving the Galbeta1-4GlcNAc linkage in the Galalpha1-3Galbeta1-4GlcNAc sequence. To explore the possibility that cells or organs from transgenic pigs systemically expressing EndoGalC might be suitable for xenotransplantation, we first introduced the EndoGalC transgene into the mouse genome via pronuclear injection. The progeny of the resulting transgenics expressed EndoGalC mRNA and protein. Flow cytometry and histochemical analyses revealed a dramatic reduction in the expression of the alphaGal epitope in these mice. They also exhibited abnormal phenotypes, such as occasional death immediately after birth, growth retardation, and transient skin lesions. Interestingly, the phenotypic abnormalities seen in these transgenics were similar to those observed in beta1,4-galactosyltransferase 1 (beta4GalT-1) knockout (KO) mice. Most probably, these phenotypes were caused by exposure of the internal N-acetylglucosamine residue at the end of the sugar chain on the cell surface. The present findings also provide some basis for evaluating possible application of the transgenic approach for xenotranplantation.     

Cell migration by a FRS2-adaptor dependent membrane relocation of ret receptors

During development neural progenitor cells migrate with extraordinary precision to inhabit tissues and organs far from their initial position. Little is known about the cellular basis for directional guidance by tyrosine kinase receptors (RTKs). RET is a RTK with important functions in guiding the migration of neuronal cells, and RET dysregulation leads to clinical disease such as agangliosis of the colon. We show here that RET migration in neuroepitheliomal and non-neuronal cells is elicited by the activation of specific signaling pathways initiated by the competitive recruitment of the FRS2 adaptor molecule to tyrosine 1062 (Y1062) in RET. FRS2 selectively recruited RET to focal complexes and led to activation of SRC family kinases and focal adhesion kinase (FAK). Activation of SRC depended on its direct interaction with RET at a different intracellular tyrosine (Y981) and activation of molecular signaling from these two separate sites in concert regulated migration. Our data suggest that an important function for FRS2 is to concentrate RET in membrane foci, leading to an engagement of specific signaling complexes localized in these membrane domains.     

Rapid rates of lineage-specific gene duplication and deletion in the alpha-globin gene family

Phylogeny reconstructions of the globin gene families have revealed that paralogous genes within species are often more similar to one another than they are to their orthologous counterparts in closely related species. This pattern has been previously attributed to mechanisms of concerted evolution such as interparalog gene conversion that homogenize sequence variation between tandemly duplicated genes and therefore create the appearance of recent common ancestry. Here we report a comparative genomic analysis of the alpha-globin gene family in mammals that reveal a surprisingly high rate of lineage-specific gene duplication and deletion via unequal crossing-over. Results of our analysis reveal that patterns of sequence similarity between paralogous alpha-like globin genes from the same species are only partly explained by concerted evolution between preexisting gene duplicates. In a number of cases, sequence similarity between paralogous sequences from the same species is attributable to recent ancestry between the products of de novo gene duplications. As a result of this surprisingly rapid rate of gene gain and loss, many mammals possess alpha-like globin genes that have no orthologous counterparts in closely related species. The resultant variation in gene copy number among species may represent an important source of regulatory variation that affects physiologically important aspects of blood oxygen transport and aerobic energy metabolism.