Population genetic structure of savannah elephants in Kenya: conservation and management implications

We investigated population genetic structure and regional differentiation among African savannah elephants in Kenya using mitochondrial and microsatellite markers. We observed mitochondrial DNA (mtDNA) nucleotide diversity of 1.68% and microsatellite variation in terms of average number of alleles, expected and observed heterozygosities in the total study population of 10.20, 0.75, and 0.69, respectively. Hierarchical analysis of molecular variance of mtDNA variation revealed significant differentiation among the 3 geographical regions studied (F(CT) = 0.264; P < 0.05) and a relatively lower differentiation among populations within regions (F(SC) = 0.218; P < 0.0001). Microsatellite variation significantly differentiated among populations within regions (F(SC) = 0.019; P < 0.0001) but not at the regional levels (F(CT) = 0.000; P > 0.500). We attribute the high differentiation at the mitochondrial genome to the matrilineal social structure of elephant populations, female natal philopatry, and probably ancient vicariance. Lack of significant regional differentiation at the nuclear loci vis-a-vis strong differences at mtDNA loci between regions is likely the effect of subsequent homogenization through male-mediated gene flow. Our results depicting 3 broad regional mtDNA groups and the observed population genetic differentiation as well as connectivity patterns should be incorporated in the planning of future management activities such as translocations.     

Processing of an antigenic sequence from IgG constant domains for presentation by MHC class II

Targeting of T cell epitopes to APC enhances T cell responses. We used an APC-specific Ab (anti-IgD) and substituted either of 18 loops connecting beta strands in human IgG constant H (C(H)) domains with a characterized T cell peptide epitope. All Ab-epitope fusion molecules were secreted from producing cells except IgG-loop 2(BC)C(H)1, and comparing levels, a hierarchy appeared with fusions involving C(H)2 > or = C(H)1 > C(H)3. Within each domain, fusion at loop 6(FG) showed best secretion, while low secretion correlated with the substitution of native loops that contain conserved amino acids buried within the folded molecule. Comparing the APC-specific rAb molecules for their ability to induce T cell activation in vitro, the six mutants with epitope in C(H)2 were the most effective, with loop 4C(H)2 ranking on top. The C(H)1 mutants were more resistant to processing, and the loop 6C(H)1 mutant only induced detectable activation. The efficiency of the C(H)3 mutants varied, with loop 6C(H)3 being the least effective and equal to loop 6 C(H)1. Considering both rAb secretion level and T cell activation efficiency, a total of eight loops may carry T cell epitopes to APC for processing and presentation to T cells, namely, all in C(H)2 in addition to loop 6 in C(H)1 and C(H)3. Comparing loop 4C(H)2 with loop 6C(H)1 mutants after injection of Ab in BALB/c mice, the former was by far the most efficient and induced specific T cell activation at concentrations at least 100-fold lower than loop 6C(H)1.     

Endocrine and behavioral changes in male African elephants: linking hormone changes to sexual state and reproductive tactics

Hormones play a crucial role in mediating genetic and environmental effects into morphological and behavioral phenotypes. In systems with alternative reproductive tactics (ART) shifts between tactics are hypothesized to be under proximate hormonal control. Most studies of the underlying endocrine changes behind ART have focused on fish and amphibians rather than mammals and few have investigated the potential interaction between different endocrine axes in regulating shifts between conditional dependent tactics. Using a combination of endocrine and behavioral data from male African elephants we expand on our previously published analysis and show that the initial increase in androgens predates the behavioral shifts associated with reproductively active periods, supporting the role of androgens in activating sexually active periods in males. A strong interactive effect between androgens and glucocorticoids was found to determine the presence or absence of temporal gland secretion and urine dribbling, signals associated with the competitive reproductive tactic of musth, with elevated glucocorticoids levels suppressing the occurrence of musth signals. In addition external environmental conditions affected hormone levels. The presence of receptive females resulted in elevated androgens in dominant musth males but increased glucocorticoids in subordinate non-musth males. The presented data on hormones, behavior and reproductive tactics strongly support an underlying endocrine mechanism for mediating the translation of intrinsic as well as extrinsic local conditions into the conditional dependent reproductive tactics in male elephants via interactions between the hypothalamic-pituitary-gonadal and -adrenal axes.     

Acclimation of subsurface microbial communities to mercury

We studied the acclimation to mercury of bacterial communities of different depths from contaminated and noncontaminated floodplain soils. The level of mercury tolerance of the bacterial communities from the contaminated site was higher than those of the reference site. Furthermore, the level of mercury tolerance and functional versatility of bacterial communities in contaminated soils initially were higher for surface soil, compared with the deeper soils. However, following new mercury exposure, no differences between bacterial communities were observed, which indicates a high adaptive potential of the subsurface communities, possibly due to differences in the availability of mercury. IncP-1 trfA genes were detected in extracted community DNA from all soil depths of the contaminated site, and this finding was correlated to the isolation of four different mercury-resistance plasmids, all belonging to the IncP-1beta group. The abundance of merA and IncP-1 plasmid carrying populations increased, after new mercury exposure, which could be the result of selection as well as horizontal gene exchange. The data in this study suggest a role for IncP-1 plasmids in the acclimation to mercury of surface as well as subsurface soil microbial communities.     

Protein oxidation in the leaves and roots of cucumber plants (Cucumis sativus L.), mutant MSC16 and wild type

Reactive oxygen species (ROS) may cause irreversible carbonylation of proteins, resulting in structural and/or functional modifications. Carbonylated proteins were analyzed and compared in tissue extracts or purified mitochondria isolated from the leaves and roots of wild-type (WT) or MSC16 mutant cucumber plants. For analysis of the oxidized protein formation and degradation, several techniques were applied: Western blotting, quantitative, spectrophotometric assay of carbonyl concentration and protease activity measurements. Oxidized proteins were tagged with 2,4-dinitrophenylhydrazine (DNPH) and detected with anti-DNP antibodies. Western blots of 1D gels indicated that, in the leaves of both WT and MSC16 plants, certain oxidized proteins have chloroplastic origin. In MSC16 plants, protein oxidation is probably higher in chloroplasts than in mitochondria. Carbonyl concentration is similar in MSC16 and WT leaf extracts, but this may be the result of twice as high protease activity observed in MSC16 leaf extracts and indicates that chloroplastic proteases may effectively remove the oxidized proteins from chloroplasts. In mitochondria of both WT and MSC16 leaves, the levels of oxidized proteins and protease activity are similar. In MSC16 root extracts, the carbonyl concentration is lower and protease activity is similar as compared to WT plants. Nevertheless, in MSC16 root mitochondria, the 30% lower carbonyl concentration, lower band abundance for oxidized proteins and over 50% higher protease activity indicate that mitochondrial proteases are involved in degradation of the oxidatively damaged proteins. In matrix and membrane subfractions, the levels of oxidized proteins are similar in leaf mitochondria or lower in root mitochondria from MSC16 as compared to WT plants. The results show that the oxidized protein degradation network in MSC16 cucumber mutants is well developed, thus becoming a survival factor for plants with mitochondrial dysfunctions.     

Sequential muscle biopsies during a 6-h tracer infusion do not affect human mixed muscle protein synthesis and muscle phenylalanine kinetics

Stable isotope tracer experiments of human muscle amino acid and protein kinetics often involve a sequential design, with the same subject studied at baseline and during an intervention. However, prolonged fasting and sequential muscle biopsies from the same area could theoretically affect muscle protein metabolism. The purpose of this study was to determine if sequential muscle biopsies and extended fasting significantly affect parameters of muscle protein and amino acid kinetics in six human subjects. After a 12-h overnight fast, a primed continuous infusion of L-[ring-(2)H(5)]phenylalanine was started. After 120 min, we took the first of a series of five hourly muscle biopsies from the same vastus lateralis to measure mixed muscle protein fractional synthetic rate. Furthermore, between 150-180, 210-240, and 330-360 min, we measured leg phenylalanine kinetics using the two-pool and the three-pool arteriovenous balance models. Tracer enrichments were at steady state, and muscle protein FSR and phenylalanine kinetics did not change throughout the experiment (P=not significant). We conclude that a 6-h tracer infusion during extended fasting (up to 18 h) with five sequential muscle biopsies from the same muscle do not affect basal mixed muscle protein synthesis and muscle phenylalanine kinetics in human subjects. Thus, when using a sequential study design over this period of time, it is unnecessary to include a saline only control group to account for these variables.     

Effect of environment on multi-element grain composition of pigeonpea cultivars under farmers’ conditions

Pigeonpea (Cajanus cajan L. Millsp.) is often intercropped with maize (Zea mays L.) in eastern and southern Africa. The studies aimed at determining how different genotypes of pigeonpea responded in terms of grain element composition under farmers’ cropping conditions. Approx. 78 farmers participated. They came from four study sites in Tanzania (Babati and Gairo) and Malawi (Nyambi and Ntonda) that differed in terms of tradition for using pigeonpea as well as in environmental conditions. The individual grain weight of the pigeonpea crops from Malawi were 21% (P < 0.05) higher than those from Tanzania. However, only B, Cu, Mo, N, Ni, P and S were affected by grain weight (P < 0.05). Weak (r ² < 0.10) negative correlations existed between grain yield and the grains’ proportion of Ca, Mg, P, and Zn. The proportion of every element, with the exception of Cr, in the grain differed between sites (P < 0.05) but not between varieties (P > 0.05). The amounts of K, Mg, S and Fe accumulated per grain were slightly lower (P < 0.11) in ICEAP00040 compared to the more traditional varieties. Variations in DTPA-exchangeable Zn and Fe in the soil were not reflected in grain concentrations but grain P had a curvi-linear relation (r ² = 0.44) to the soil NaHCO₃^–-exchangeable P indicating P deficiency for several soils. The P and Zn content were correlated (r ² > 0.41) as the only two grain elements. Unique fingerprinting by multivariate statistics was possible for each site when using the element proportion of the grain dry matter with or without soil characteristics. In all cases, different elements contributed with varying weight to the discrimination between the sites. However, it was not possible to distinguish between the varieties when considering all four environments. Reducing the models to include Fe, K, Mg, P, S and Zn only, did however allow some distinction between the two genotypes, which indicates that genotypic variability is expressed in a fairly limited number of elements. In the cases of Gairo and Nyambi, it was possible to distinguish between varieties. In the case of Gairo, the models distinguished between ICEAP00068 and the others, i.e. ICEAP00040 and Babati White where ICEAP00068 was associated with a higher proportion of Fe, P, S, and Zn in the grain. In the case of Nyambi, the models distinguished between ICEAP00040 and ICP9145 where ICEAP00040 was associated with a lower proportion of Ca, Cu, Fe, Mn, Ni, P, S, and Zn and a higher proportion of Cr and Na in the grain. It is thus possible in some cases to separate varieties based on multi-element grain content across a relatively narrow environmental gradient but not generally across all environments. These findings should be included in breeding programmes focusing on the improvement of the nutritional value of our food crops.     

Direct crystallographic observation of an acyl-enzyme intermediate in the elastase-catalyzed hydrolysis of a peptidyl ester substrate: Exploiting the “glass transition” in protein dynamics

The crystal structure of the acyl complex of porcine pancreatic elastase with its peptidyl ester substrate N-acetyl-ala-ala-ala-methyl ester (Ac(Ala)₃OMe) has been determined at 2.5 Å resolution. The complex was stabilized by exploiting the “glass transition” in protein dynamics that occurs at around −53 °C (220 K). Substrate was flowed into the crystal in a cryoprotective solvent above this temperature, and then the crystal was rapidly cooled to a temperature below the transition to trap the species that formed. The use of a flow cell makes the experiment a kinetic one and means that the species prior to the rate determining transition state has a chance to accumulate. The resulting crystal structure shows an acyl-enzyme intermediate in which the leaving group is absent and the carbonyl carbon of the C-terminal alanine residue is covalently bound to the gamma oxygen of the active site serine. The ester carbonyl shows no significant distortion from planarity, with the carbonyl oxygen forming one hydrogen bond with the oxyanion hole. The tripeptide is bound in an extended antiparallel β-sheet with main chain residues of the enzyme. The geometry and interactions of this acyl-enzyme suggest that it represents a productive intermediate. To test this hypothesis, the same crystal was then warmed above the glass transition temperature and a second data set was collected. The resulting electron density map shows no sign of the substrate, indicating hydrolysis of the intermediate followed by product release. This experiment provides direct evidence for the importance of dynamic properties in catalysis and also provides a blueprint for the stabilization of other short-lived species for direct crystallographic observation.     

Identification of Salmonella enterica serovar Typhimurium genes important for survival in the swine gastric environment

Since the stomach is a first line of defense for the host against ingested microorganisms, an ex vivo swine stomach contents (SSC) assay was developed to search for genes important for Salmonella enterica serovar Typhimurium survival in the hostile gastric environment. Initial characterization of the SSC assay (pH 3.87) using previously identified, acid-sensitive serovar Typhimurium mutants revealed a 10-fold decrease in survival for a phoP mutant following 20 min of challenge and no survival for mutants of rpoS or fur. To identify additional genes, a signature-tagged mutagenesis bank was constructed and screened in the SSC assay. Nineteen mutants were identified and individually analyzed in the SSC and acid tolerance response assays; 13 mutants exhibited a 10-fold or greater sensitivity in the SSC assay compared to the wild-type strain, but only 3 mutants displayed a 10-fold or greater decrease in survival following pH 3.0 acidic challenge. Further examination determined that the lethal effects of the SSC are pH dependent but that low pH is not the sole killing mechanism(s). Gas chromatography analysis of the SSC revealed lactic acid levels of 126 mM. Upon investigating the effects of lactic acid on serovar Typhimurium survival in a synthetic gastric fluid, not only was a concentration- and time-dependent lethal effect observed, but the phoP, rpoS, fur, and pnp genes were identified as involved in protection against lactic acid exposure. These studies indicate a role in gastric survival for several serovar Typhimurium genes and imply that the stomach environment is defined by more than low pH.     

The influence of 1-aminocyclopentane-1-carboxylic acid at position 2 or 3 of AVP and its analogues on their pharmacological properties.

This study describes the synthesis and some pharmacological properties of eight new analogues of arginine vasopressin (AVP) substituted at position 2 or 3 with cycloleucine (1-aminocyclopentane-1-carboxylic acid, Apc). All new peptides were tested for their pressor, antidiuretic and uterotonic in vitro potency. The Apc3 modification resulted in an almost complete loss of potency in all three tests, which is interpreted as a loss of interaction with all three neurohypophyseal hormone receptors. On the other hand, the Apc2 modification resulted in compounds having differently modified activities (high antidiuretic potency, low and graded pressor activity and either no activity or low oxytocin antagonizing activity in the uterotonic in vitro test) thus selectively altering the interaction with the receptors similar to that of 1-aminocyclohexane-1-carboxylic acid (Acc). The results obtained may be helpful for designing new analogues of arginine vasopressin.