Genetic analysis of the exed region in mouse

The extraembryonic ectoderm development (exed) mutant phenotype was described in mice homozygous for the c(6H) deletion, a radiation-induced deletion in the tyrosinase region of mouse Chromosome 7. These mutants fail to gastrulate and die around embryonic day 8.0. Several genes including, for example, embryonic ectoderm development (eed), are deleted in the c(6H) mutants; however, the portion of the chromosome responsible for the more severe exed phenotype is localized to a 20-kb region called the "exed-critical region." To understand the genetics behind the exed phenotype, we analyzed this region in two ways. First, to determine whether the 20-kb exed-critical region alone causes the mutant phenotype, we removed it from a wild-type chromosome. The resulting mice homozygous for this deletion were viable and fertile, indicating that the 20-kb exed-critical region by itself is not sufficient to cause the phenotype when deleted. We then sequenced the 20-kb exed-critical region and no expressed exons were found. Several short matches to GenBank Expressed Sequence Tag (EST) databases were identified; however, none of these ESTs mapped to the region. Taken together, these results indicate that the exed phenotype may either be a position effect on a distal gene caused by the c(6H) breakpoint or the result of composite effects of nullizygosity of multiple genes in the deletion homozygotes.     

Dispersal, Environmental Correlation, and Spatial Synchrony in Population Dynamics

Many species exhibit widespread spatial synchrony in population fluctuations. This pattern is of great ecological interest and can be a source of concern when the species is rare or endangered. Both dispersal and spatial correlations in the environment have been implicated as possible causes of this pattern, but these two factors have rarely been studied in combination. We develop a spatially structured population model, simple enough to obtain analytic solutions for the population correlation, that incorporates both dispersal and environmental correlation. We ask whether these two synchronizing factors contribute additively to the total spatial population covariance. We find that there is always an interaction between these two factors and that this interaction is small only when one or both of the environmental correlation and the dispersal rate are small. The interaction is opposite in sign to the environmental correlation; so, in the normal case of positive environmental correlation across sites, the population synchrony will be lower than predicted by simply adding the effects of dispersal and environmental correlation. We also find that population synchrony declines as the strength of population regulation increases. These results indicate that dispersal and environmental correlation need to be considered in combination as explanations for observed patterns of population synchrony.     

Identification of a Sequence Motif That Confers SecB Dependence on a SecB-Independent Secretory Protein In Vivo

SecB is a cytosolic chaperone which facilitates the transport of a subset of proteins, including membrane proteins such as PhoE and LamB and some periplasmic proteins such as maltose-binding protein, in Escherichia coli. However, not all proteins require SecB for transport, and proteins such as ribose-binding protein are exported efficiently even in SecB-null strains. The characteristics which confer SecB dependence on some proteins but not others have not been defined. To determine the sequence characteristics that are responsible for the SecB requirement, we have inserted a systematic series of short, polymeric sequences into the SecB-independent protein alkaline phosphatase (PhoA). The extent to which these simple sequences convert alkaline phosphatase into a SecB-requiring protein was evaluated in vivo. Using this approach we have examined the roles of the polarity and charge of the sequence, as well as its location within the mature region, in conferring SecB dependence. We find that an insert with as few as 10 residues, of which 3 are basic, confers SecB dependence and that the mutant protein is efficiently exported in the presence of SecB. Remarkably, the basic motifs caused the protein to be translocated in a strict membrane potential-dependent fashion, indicating that the membrane potential is not a barrier to, but rather a requirement for, translocation of the motif. The alkaline phosphatase mutants most sensitive to the loss of SecB are those most sensitive to inhibition of SecA via azide treatment, consistent with the necessity for formation of a preprotein-SecB-SecA complex. Furthermore, the impact of the basic motif depends on location within the mature protein and parallels the accessibility of the location to the secretion apparatus.     

An adrenaline (and gold?) rush for the GPCR community.

G-Protein-coupled receptors are one of the largest protein families found in metazoans. Using several novel strategies, the first atomic resolution structures of a receptor that is activated by a diffusible ligand have been determined.     

Age validation and variation in growth,mortality and population structure of Liza argentea and Myxus elongatus (Mugilidae) in two temperate Australian estuaries

This study investigated variation in the rates of growth and mortality, and age and fork‐length (L_F) compositions of two exploited species of Mugilidae, Liza argentea and Myxus elongatus, in two south‐east Australian estuaries (Lake Macquarie and St Georges Basin). An ageing protocol was developed by counting opaque growth zones on sectioned otoliths which was validated by periodically examining the otoliths of captive‐reared young‐of‐the‐year fishes, and marginal increment analysis of wild fishes. The maximum recorded age was 17 years for L. argentea and 12 years for M. elongatus, which is greater than generally observed in other species of mugilids. Growth models of each species significantly differed between sexes and, except for male L. argentea, between estuaries. Fishes from Lake Macquarie generally had a greater mean L_F at age than those from St Georges Basin and females of both species generally attained a greater maximum L_F and age than males. Gillnet catches of L. argentea were of similar L_F and age compositions in both estuaries, whereas the age composition of catches of M. elongatus in Lake Macquarie contained a greater proportion of younger fish. Estimates of total, natural and fishing mortality were greater for M. elongatus than L. argentea across both estuaries, and estimates of total mortality were greatest for both species in Lake Macquarie. The data indicate that neither species has been overfished in these estuaries.     

Mass balance and life cycle assessment of biodiesel from microalgae incorporated with nutrient recycling options and technology uncertainties

This article presents mass balances and a detailed life cycle assessment (LCA) for energy and greenhouse gases (GHGs) of a simulated microalgae biodiesel production system. Key parameters of the system include biomass productivity of 16 and 25 g m^?2 day^?1 and lipid content of algae of 40% and 25% for low and normal nitrogen conditions respectively. Based on an oil extraction efficiency from wet biomass of 73.6% and methane yields from anaerobically digested lipid‐extracted biomass of 0.31 to 0.34 l per gram of volatile solids, the mass balance shows that recycling growth media and recovering nutrients from residual biomass through anaerobic digestion can reduce the total demand for nitrogen by 66% and phosphorus by 90%. Freshwater requirements can be reduced by 89% by recirculating growth media, and carbon requirements reduced by 40% by recycling CO₂ from biogas combustion, for normal nitrogen conditions. A variety of technology options for each step of the production process and allocation methods for coproducts used outside the production system are evaluated using LCA. Extensive sensitivity and scenario analysis is also performed to provide better understanding of uncertainty associated with results. The best performing scenario consists of normal nitrogen cultivation conditions, bioflocculation and dissolved air flotation for harvesting, centrifugation for dewatering, wet extraction with hexane, transesterification for biodiesel production, and anaerobic digestion of biomass residual, which generates biogas used in a combined heat and power unit for energy recovery. This combination of technologies and operating conditions results in life cycle energy requirements and GHG emissions of 1.02 MJ and 71 g CO₂‐equivalent per MJ of biodiesel, with cultivation and oil extraction dominating energy use and emissions. Thus, even under optimistic conditions, the near‐term performance of this biofuel pathway does not achieve the significant reductions in life cycle GHG emissions hoped for from second‐generation biofuel feedstocks.     

SiRNA-Induced Mutation in HIV-1 Polypurine Tract Region and Its Influence on Viral Fitness

Converting single-stranded viral RNA into double stranded DNA for integration is an essential step in HIV-1 replication. Initial polymerization of minus-strand DNA is primed from a host derived tRNA, whereas subsequent plus-strand synthesis requires viral primers derived from the 3′ and central polypurine tracts (3′ and cPPTs). The 5′ and 3′ termini of these conserved RNA sequence elements are precisely cleaved by RT-associated RNase H to generate specific primers that are used to initiate plus-strand DNA synthesis. In this study, siRNA wad used to produce a replicative HIV-1 variant contained G(-1)A and T(-16)A substitutions within/adjacent to the 3′PPT sequence. Introducing either or both mutations into the 3′PPT region or only the G(-1)A substitution in the cPPT region of NL4-3 produced infectious virus with decreased fitness relative to the wild-type virus. In contrast, introducing the T(-16)A or both mutations into the cPPT rendered the virus(es) incapable of replication, most likely due to the F185L integrase mutation produced by this nucleotide substitution. Finally, the effects of G(-1)A and T(-16)A mutations on cleavage of the 3′PPT were examined using an in vitro RNase H cleavage assay. Substrate containing both mutations was mis-cleaved to a greater extent than either wild-type substrate or substrate containing the T(-16)A mutation alone, which is consistent with the observed effects of the equivalent nucleotide substitutions on the replication fitness of NL4-3 virus. In conclusion, siRNA targeting of the HIV-1 3′PPT region can substantially suppress virus replication, and this selective pressure can be used to generate infectious virus containing mutations within or near the HIV-1 PPT. Moreover, in-depth analysis of the resistance mutations demonstrates that although virus containing a G(-1)A mutation within the 3′PPT is capable of replication, this nucleotide substitution shifts the 3′-terminal cleavage site in the 3′PPT by one nucleotide (nt) and significantly reduces viral fitness.     

The effect of physiological concentrations of sex hormones,insulin, and glucagon on growth of breast and prostate cells supplemented with unmodified human serum

The majority of cell culture studies have assessed the effect of hormones on cancer cell growth using media supplemented with charcoal-treated fetal bovine serum (CTS). We aimed to determine whether using a system more reflective of the human condition by changing the charcoal-treated serum to an untreated pooled human serum (PHS) resulted in the same hormone responses in breast and prostate cell lines. MCF-7 breast cancer, MCF-10A non-transformed breast, and LNCaP prostate cancer cell lines supplemented with PHS were treated with high and low physiological concentrations of six hormones (17β-estradiol, dehydroepiandosterone (DHEA), dihydrotestosterone (DHT), testosterone, insulin, and glucagon). Cell growth was measured after 72 h of incubation. All hormones stimulated growth of MCF-7 cells (p < 0.05). MCF-10A cell growth was inhibited by DHEA, DHT, and testosterone (p < 0.05), unaffected by 17β-estradiol and glucagon, and stimulated by insulin (p < 0.05). LNCaP cell growth was stimulated by the highest concentration of DHEA and DHT (p < 0.05) and inhibited by the highest concentration of 17β-estradiol (p < 0.05), while insulin and testosterone, had no effect. Overall, PHS lowered the magnitude of the effect of hormones on cell growth in comparison to CTS. Due to the presence of all serum constituents, our model represents a more appropriate physiological environment for determining the effect of hormones on cancer cell growth. Further studies are required to determine the mechanisms by which added hormones interact with the constituents of untreated human serum.