Exome sequencing identifies a nonsense mutation in <Emphasis Type="Italic">Fam46a</Emphasis> associated with bone abnormalities in a new mouse model for skeletal dysplasia

We performed exome sequencing for mutation discovery of an ENU (N-ethyl-N-nitrosourea)-derived mouse model characterized by significant elevated plasma alkaline phosphatase (ALP) activities in female and male mutant mice, originally named BAP014 (bone screen alkaline phosphatase #14). We identified a novel loss-of-function mutation within the Fam46a (family with sequence similarity 46, member A) gene (NM_001160378.1:c.469G>T, NP_001153850.1:p.Glu157*). Heterozygous mice of this mouse line (renamed Fam46a ^E157*Mhda) had significantly high ALP activities and apparently no other differences in morphology compared to wild-type mice. In contrast, homozygous Fam46a ^E157*Mhda mice showed severe morphological and skeletal abnormalities including short stature along with limb, rib, pelvis, and skull deformities with minimal trabecular bone and reduced cortical bone thickness in long bones. ALP activities of homozygous mutants were almost two-fold higher than in heterozygous mice. Fam46a is weakly expressed in most adult and embryonic tissues with a strong expression in mineralized tissues as calvaria and femur. The FAM46A protein is computationally predicted as a new member of the superfamily of nucleotidyltransferase fold proteins, but little is known about its function. Fam46a ^E157*Mhda mice are the first mouse model for a mutation within the Fam46a gene.     

Review and advancement of the marine biotic resource use metric in seafood LCAs: a case study of Norwegian salmon feed

Purpose

Seafood life cycle assessment (LCA) studies have adopted the primary production required (PPR) indicator to account for the impact of these production systems (e.g., capture fisheries or aquaculture) on the ecosystems they harvest wild inputs from. However, there exists a large diversity in the application of methods to calculate PPR, and current practice often does not consider species- and ecosystem-specific factors. Here, we critically examine current practice and propose a refined method for applying the PPR metric in seafood LCAs.

Methods

We surveyed seafood LCAs that quantify PPR, or its derivatives, to examine the diversity of practice. We then defined and applied a refined method to a case study of the average Norwegian salmon feed in 2012. This refined method incorporates species-specific fishmeal and oil yields, source ecosystem-specific transfer efficiencies and expresses results as a percentage of total ecosystem production that PPR represents. Results were compared to those using previously applied methods based on the literature review, and the impact of uncertainty and natural variability of key input parameters was also assessed using Monte Carlo simulation.

Results and discussion

From the literature review, most studies do not incorporate species-specific fishmeal and oil yields or ecosystem-specific transfer efficiencies when calculating PPR. Our proposed method, which incorporated source species- and ecosystem-specific values for these parameters, provides far greater resolution of PPR than when employing global average values. When alternative methods to calculate PPR were applied to marine inputs to Norwegian salmon feeds, resulting PPR values were similar for some sources of fishmeal and oil. For other species, such as Atlantic herring from ecosystems with low transfer efficiencies, there was a large divergence in resulting PPR values. For combined inputs to Norwegian salmon feeds in 2012, the refined method resulted in a total PPR value that is three times higher than would result using the currently standard method signaling that previous LCA research may have substantially underestimated the marine biotic impacts of fishery products.

Conclusions

While there exists a great diversity of practice in the application of the PPR indicator in seafood LCA, the refined method should be adopted for future LCA studies to be more specific to the context of the study.

     

Structures of the dI2dIII1 complex of proton-translocating transhydrogenase with bound, inactive analogues of NADH and NADPH reveal active site geometries

Transhydrogenase couples the redox reaction between NADH and NADP+ to proton translocation across a membrane. The enzyme comprises three components; dI binds NAD(H), dIII binds NADP(H), and dII spans the membrane. The 1,4,5,6-tetrahydro analogue of NADH (designated H2NADH) bound to isolated dI from Rhodospirillum rubrum transhydrogenase with similar affinity to the physiological nucleotide. Binding of either NADH or H2NADH led to closure of the dI mobile loop. The 1,4,5,6-tetrahydro analogue of NADPH (H2NADPH) bound very tightly to isolated R. rubrum dIII, but the rate constant for dissociation was greater than that for NADPH. The replacement of NADP+ on dIII either with H2NADPH or with NADPH caused a similar set of chemical shift alterations, signifying an equivalent conformational change. Despite similar binding properties to the natural nucleotides, neither H2NADH nor H2NADPH could serve as a hydride donor in transhydrogenation reactions. Mixtures of dI and dIII form dI2dIII1 complexes. The nucleotide charge distribution of complexes loaded either with H2NADH and NADP+ or with NAD+ and H2NADPH should more closely mimic the ground states for forward and reverse hydride transfer, respectively, than previously studied dead-end species. Crystal structures of such complexes at 2.6 and 2.3 A resolution are described. A transition state for hydride transfer between dihydronicotinamide and nicotinamide derivatives determined in ab initio quantum mechanical calculations resembles the organization of nucleotides in the transhydrogenase active site in the crystal structure. Molecular dynamics simulations of the enzyme indicate that the (dihydro)nicotinamide rings remain close to a ground state for hydride transfer throughout a 1.4 ns trajectory.     

Expression of polypeptide GalNAc-transferases in stratified epithelia and squamous cell carcinomas: immunohistological evaluation using monoclonal antibodies to three members of the GalNAc-transferase family

Mucin-type O-glycosylation is initiated by a large family of UDP- GalNAc: polypeptide N -acetyl-galactosaminyltransferases (GalNAc- transferases). Individual GalNAc-transferases appear to have different functions and Northern analysis indicates that they are differently expressed in different organs. This suggests that O-glycosylation may vary with the repertoire of GalNAc-transferases expressed in a given cell. In order to study the repertoire of GalNAc-transferases in situ in tissues and changes in tumors, we have generated a panel of monoclonal antibodies (MAbs) with well defined specificity for human GalNAc-T1, -T2, and -T3. Application of this panel of novel antibodies revealed that GalNAc- transferases are differentially expressed in different cell lines, in spermatozoa, and in oral mucosa and carcinomas. For example, GalNAc-T1 and -T2 but not -T3 were highly expressed in WI38 cells, and GalNAc-T3 but not GalNAc-T1 or -T2 was expressed in spermatozoa. The expression patterns in normal oral mucosa were found to vary with cell differentiation, and for GalNAc-T2 and -T3 this was reflected in oral squamous cell carcinomas. The expression pattern of GalNAc-T1 was on the other hand changed in tumors to either total loss or expression in cytological poorly differentiated tumor cells, where the normal undifferentiated cells lacked expression. These results demonstrate that the repertoire of GalNAc-transferases is different in different cell types and vary with cellular differentiation, and malignant transformation. The implication of this is not yet fully understood, but it suggests that specific changes in sites of O-glycosylation of proteins may occur as a result of changes in the repertoire of GalNAc-transferases.      

Intraspecific abundance–occupancy relationships: case studies of six bird species in Britain

Although acknowledged to be common, intraspecific relationships between local abundance and site occupancy have been examined in detail for few species. Here we report such analyses for six widespread species of breeding birds in Britain, using data from the Common Birds Census. These exhibit a range of temporal trends, including different combinations of increase and decrease in abundance and occupancy. Overall, two species have a statistically significant positive abundance–occupancy relationship on farmland but no relationship in woodland (collared dove, tree sparrow), one a significant positive relationship on farmland and in woodland (magpie), two a significant positive relationship on farmland and a negative one in woodland (redstart, song thrush), and one a significant negative abundance–occupancy relationship on farmland but no relationship in woodland (sparrowhawk). The population dynamics associated with these patterns are used to discern their underlying mechanisms.