The relation between the neutrality index for mitochondrial genes and the distribution of mutational effects on fitness

We explore factors affecting patterns of polymorphism and divergence (as captured by the neutrality index) at mammalian mitochondrial loci. To do this, we develop a population genetic model that incorporates a fraction of neutral amino acid sites, mutational bias, and a probability distribution of selection coefficients against new nonsynonymous mutations. We confirm, by reanalyzing publicly available datasets, that the mitochondrial cyt-b gene shows a broad range of neutrality indices across mammalian taxa, and explore the biological factors that can explain this observation. We find that observed patterns of differences in the neutrality index, polymorphism, and divergence are not caused by differences in mutational bias. They can, however, be explained by a combination of a small fraction of neutral amino acid sites, weak selection acting on most amino acid mutations, and differences in effective population size among taxa.     

Costs and Benefits of Sociality Differ Between Female Guanacos Living in Contrasting Ecological Conditions

According to current theory, anti‐predator benefits promote group formation in open‐dwelling ungulates. An inverse relationship between vigilance effort and group size has been documented frequently and thought to reflect the consequent decrease in perceived predation risk as group size increases. In contrast, competition costs are supposed to set the upper limit to the number of individuals that can forage together. As anti‐predator behavior is no longer functional in the absence of predation and competition costs might be affected by resource distribution, the net benefit of aggregation will depend on the particular combination of predation risk and habitat structure experienced by the individual. To test this hypothesis, group‐size effects on female time allocation and within‐group aggression rate were compared between two guanaco populations exposed to contrasting levels of puma predation. Habitat structure within both sites consisted of mosaics of shrublands and grasslands, and group‐size effects were also compared between these habitat types. Females under predation risk showed a strong reduction in vigilance as the number of adults in the group increased, whereas females from the predator‐free population showed overall low levels of vigilance, regardless of group size. These results emphasize the anti‐predator significance of the group‐size effect on female vigilance, as well as guanaco plasticity to adjust time allocation to local conditions. On the other hand, within‐group aggression rate increased with the number of adults in the group. Aggression rate was almost null within groups located in grasslands but was significantly higher in shrublands, regardless of predation risk, suggesting that the more heterogeneous distribution of shrubs increases the interference competition level. These results strengthen the notion of predation pressure and habitat structure as major determinants of the balance between costs and benefits of group living, and highlight the potential of individual behavioral patterns to make qualitative predictions about group‐size variation within territorial ungulates.     

Genetic differentiation and history of populations of the Italian treefrog Hyla intermedia: lack of concordance between mitochondrial and nuclear markers

The genetic differentiation among 33 populations of the Italian treefrog, Hyla intermedia (Anura: Hylidae), was investigated using both biparentally (23 allozyme loci) and maternally (partial mitochondrial cytochrome b gene) inherited markers. Two main population groups were evidenced by both markers, located north and south of the northern Apennines. However, the pattern of differentiation between these two groups was much less pronounced at allozymes than at mtDNA, leading to gene flow estimates that were 25 times lower at mitochondrial than at nuclear level. Also, the mtDNA divergence between the two groups was particularly marked for two cospecific lineages of anuran amphibians (the P-distance being on average 9.04%), while their average genetic distance at allozymes was comparatively low (D _NEI = 0.07). This contrasting pattern of nuclear versus mitochondrial genetic variation is discussed in the context of: (1) marker specific selection, (2) secondary contact and sex-biased gene flow and (3) ancestral polymorphism and colonization from north to south. Finally we emphasize how, for population genetic studies, the use of multiple markers having distinct evolutionary properties can help unravel the existence of more complex evolutionary histories.     

Does Wet Prairie Vegetation Retain More Nitrogen with or withoutPhalaris arundinaceainvasion?

Elevated nitrogen (N) levels accelerate expansion of Phalaris arundinacea L. (reed canary grass), a highly aggressive invader that displaces native vegetation and forms monotypes. Hence, Phalaris is commonly presumed to have high nutrient uptake that contributes to higher N retention in a wetland. We compared the capability of wet prairie vegetation with and without invading Phalaris under low-N and high-N treatments to (1) accumulate N in plant tissues, (2) retain N in soil and (3) remove N from water flowing through mesocosms. With high-N treatment, above-ground biomass increased by > 90% (P < 0.0004; yrs. 1–2) and percent total N in above-ground tissues increased by > 46% (P = 0.0005; yrs. 1–2). Consequently, there was ~3 times as much total N accumulation in above-ground tissue (calculated from biomass and percent total N in tissues) with high-N treatment vs. low-N treatment (P < 0.0001; yrs. 1–2). Without invading Phalaris, wet prairie vegetation produced over 49% more above-ground biomass (P ￡ 0.022; yrs. 1–2) and accumulated over 38% more N in its above-ground tissues (P = 0.009; yrs. 1–2), compared to invaded mesocosms. The high-N treatment increased concentrations of soil ammonium (NH4–N) up to 157% (P = 0.0001) and soil nitrate (NO3–N) up to 549% (P < 0.001). After N treatments began, we found no differences in total N or NO3–N in soils (P > 0.05) or in concentrations of NH4–N or NO3–N released in the discharged water (P > 0.1) from wet prairie mesocosms with and without invading Phalaris. Soil NH4–N did not differ between the wet prairie mesocosms with and without Phalaris invasions on five dates (P > 0.05); the one exception was in August 2004 (27% greater with invasion; P = 0.02). Our results from wet prairie mesocosms do not support the presumption that Phalaris retains more N than native plant assemblages.     

NMR studies of prebiotic polypeptides

Several polypeptides prepared by means of pyrocondensation have been the subject of structural investigations. Attention has been focused on the constitutional characterization of homo-and co-polymers containing Asp and Glu residues, whose role is essential for the formation of the so-called proteinoids. Contrary to the literature data based on chemical degradation, nmr studies show conclusively that in thermal poly-aspartic acid only β-peptide linkages are present. This result casts serious doubt on the role thermal condensation might have played in prebiotic polypeptide syntheses.     

IL-23 and IL-17 in tuberculosis

Tuberculosis is a chronic disease requiring the constant expression of cellular immunity to limit bacterial growth. The constant expression of immunity also results in chronic inflammation, which requires regulation. While IFN-gamma-producing CD4+ T helper cells (Th1) are required for control of bacterial growth they also initiate and maintain a mononuclear inflammatory response. Other T cell subsets are induced by Mycobacterium tuberculosis (Mtb) infection including those able to produce IL-17 (Th17). IL-17 is a potent inflammatory cytokine capable of inducing chemokine expression and recruitment of cells to parenchymal tissue. Both the IL-17 and the Th17 response to Mtb are largely dependent upon IL-23. Although both Th17 and Th1 cells are induced following primary infection with Mtb, the protective response is significantly altered in the absence of Th1 cells but not in the absence of Th17. In contrast, in vaccinated animals the absence of memory Th17 cells results in loss of both the accelerated memory Th1 response and protection. Th1 and Th17 responses cross-regulate each other during mycobacterial infection and this may be important for immunopathologic consequences not only in tuberculosis but also other mycobacterial infections.     

Involvement of ERK1/2 and p38 in Mg2+ accumulation in liver cells

Activation of PKC signaling induces Mg²⁺ accumulation in liver cells. To test the hypothesis that PKC induces Mg²⁺ accumulation via MAPKs activation, hepatocytes were incubated in the presence of PD98059 and SB202190 as specific inhibitors of ERK1/2 and p38, respectively, and stimulated for Mg²⁺ accumulation by addition of PMA or OAG. Accumulation of Mg²⁺ within the cells was measured by atomic absorbance spectrophotometry in the acid extract of cell pellet. The presence of either inhibitor completely abolished Mg²⁺ accumulation irrespective of the dose of agonist utilized while having no discernible effect on β -adrenoceptor mediated Mg²⁺ extrusion. A partial inhibition on α ₁-adrenoceptor mediated Mg²⁺ extrusion was observed only in cells treated with PD98059. To confirm the inhibitory effect of PD98509 and SB202190, total and basolateral liver plasma membrane vesicles were purified in the presence of either MAPK inhibitor during the isolation procedure. Consistent with the data obtained in intact cells, liver plasma membrane vesicles purified in the presence of PD98509 or SB202190 lost the ability to accumulate Mg²⁺in exchange for intra-vesicular entrapped Na⁺ while retaining the ability to extrude entrapped Mg²⁺ in exchange for extra-vesicular Na⁺. These data indicate that ERK1/2 and p38 are involved in mediating Mg²⁺ accumulation in liver cells following activation of PKC signaling. The absence of a detectable effect of either inhibitor on β -adrenoceptor induced, Na⁺-dependent Mg²⁺ extrusion in intact cells and in purified plasma membrane vesicles further support the hypothesis that Mg²⁺ extrusion and accumulation occur through distinct and differently regulated transport mechanisms.     

Methylenetetrahydrofolate reductase gene C677T polymorphism,homocysteine, vitamin B12, and DNA damage in coronary artery disease

Elevated levels of plasma homocysteine (Hcy), a risk factor for coronary artery disease (CAD), can result from genetic errors, e.g., the methylenetetrahydrofolate reductase (MTHFR) polymorphism, or nutritional deficiencies, e.g., in vitamin B12 and folate. The mechanism by which Hcy induces atherosclerosis is not fully understood. Recently, Hcy has also been observed to induce DNA damage. In this study, we have investigated whether DNA damage is related to the C677T variant in the MTHFR gene and to plasma levels of Hcy, B12, and folate in patients with CAD. Patients ( n=46) with angiographically proven CAD were studied by using the micronucleus (MN) test, an accepted method for evaluating genetic instability. TT patients had plasma Hcy levels higher than those with the CT or CC genotypes (27.8+/-5.2 vs 13.7+/-2.2 and 12.9+/-1.9 micro mol/l, respectively; P=0.02). Patients with multi-vessel disease had higher plasma Hcy levels (11.6+/-1.2, 22.0+/-4.7, 19.3+/-3.9 micromol/l for one-, two- and three-vessel disease, respectively; P=0.05). The MN index increased with the number of affected vessels (8.4+/-0.7, 11.1+/-2.0, 14.2+/-1.7 for one-, two-, and three-vessels disease, respectively; P=0.02) and was significantly higher in subjects with the TT genotype compared with the CC or CT genotypes (15.7+/-2.4 vs 8.9+/-1.7 and 9.9+/-0.8; P=0.02). The MN index was also correlated negatively with plasma B12 concentration ( r=-0.343; P=0.019) and positively with plasma Hcy ( r=0.429, P=0.005). These data indicate that the MN index is associated with the severity of CAD and is related to the MTHFR polymorphism, suggesting an interesting link between coronary atherosclerosis and genetic instability in humans.     

Implementing quality by design for biotech products: Are regulators on track?

Quality by design (QbD) is an innovative approach to drug development that has started to be implemented into the regulatory framework, but currently mainly for chemical drugs. The recent marketing authorization of the first monoclonal antibody developed using extensive QbD concepts in the European Union paves the way for future further regulatory approvals of complex products employing this cutting-edge technological concept. In this paper, we report and comment on insights and lessons learnt from the non-public discussions in the European Medicines Agency''s Biologicals Working Party and Committee for Medicinal Products for Human Use on the key issues during evaluation related to the implementation of an extensive QbD approach for biotechnology-derived medicinal products. Sharing these insights could prove useful for future developments in QbD for biotech products in general and monoclonal antibodies in particular.     

The Primordial Growth Disorder 3-M Syndrome Connects Ubiquitination to the Cytoskeletal Adaptor OBSL1

3-M syndrome is an autosomal-recessive primordial growth disorder characterized by significant intrauterine and postnatal growth restriction. Mutations in the CUL7 gene are known to cause 3-M syndrome. In 3-M syndrome patients that do not carry CUL7 mutations, we performed high-density genome-wide SNP mapping to identify a second locus at 2q35-q36.1. Further haplotype analysis revealed a 1.29 Mb interval in which the underlying gene is located and we subsequently discovered seven distinct null mutations from 10 families within the gene OBSL1. OBSL1 is a putative cytoskeletal adaptor protein that localizes to the nuclear envelope. We were also able to demonstrate that loss of OBSL1 leads to downregulation of CUL7, implying a role for OBSL1 in the maintenance of CUL7 protein levels and suggesting that both proteins are involved within the same molecular pathway.