Structural genomics and signaling domains.

Many novel signal transduction domains are being identified in the wake of genome sequencing projects and improved sensitivity in homology-detection techniques. The functions of these domains are being discovered by hypothesis-driven experiments and structural genomics approaches. This article reviews the recent highlights of research on modular signaling domains, and the relative contributions and limitations of the various approaches being used.     

Assessing re-introductions of the African Wild dog (Lycaon pictus) in the Limpopo Valley Conservancy, South Africa, using the stochastic simulation program VORTEX

The African wild dog (Lycaon pictus) is one of Africa's most endangered species and therefore classified as endangered by IUCN. Earlier distributions included most of Africa but currently the African wild dog only has populations larger than 300 individuals in three countries (Botswana, Tanzania and South Africa). In 1998, a plan was launched in South Africa to manage sub-populations of the African wild dog in several small, geographically isolated, conservation areas. This management program involved the reintroduction of wild dogs into suitable conservation areas and periodic translocations among them. We used the stochastic population simulation model VORTEX to evaluate the Limpopo Valley Conservancy in the north of South Africa, as a possible reintroduction site for African wild dogs. The simulations showed that the size of the initial population released only had a small effect on the population dynamics. However, when individuals were supplemented and harvested over a longer period the probability of persistence increased. Number of females breeding, male mortality, and carrying capacity were key factors in the population dynamics, but according to VORTEX the severity of natural catastrophes had the greatest influence on the extinction risk and inbreeding. We suggest that the reintroduction program may be successful, if areas are properly secured, the dogs are held in a boma before release, wild animals or at least a mix of wild and captive animals are used for the release and the animals are vaccinated against rabies. It is, however, essential to continue monitoring followed by modelling efforts to re-evaluate the success of the reintroduction program.     

Coordinate Regulation of TPL-2 and NF-κB Signaling in Macrophages by NF-κB1 p105

The role of IκB kinase (IKK)-induced proteolysis of NF-κB1 p105 in innate immune signaling was investigated using macrophages from Nfkb1(SSAA/SSAA) mice, in which the IKK target serines on p105 are mutated to alanines. We found that the IKK/p105 signaling pathway was essential for TPL-2 kinase activation of extracellular signal-regulated kinase (ERK) mitogen-activate protein (MAP) kinase and modulated the activation of NF-κB. The Nfkb1(SSAA) mutation prevented the agonist-induced release of TPL-2 from its inhibitor p105, which blocked activation of ERK by lipopolysaccharide (LPS), tumor necrosis factor (TNF), CpG, tripalmitoyl-Cys-Ser-Lys (Pam(3)CSK), poly(I · C), flagellin, and R848. The Nfkb1(SSAA) mutation also prevented LPS-induced processing of p105 to p50 and reduced p50 levels, in addition to decreasing the nuclear translocation of RelA and cRel. Reduced p50 in Nfkb1(SSAA/SSAA) macrophages significantly decreased LPS induction of the IκBζ-regulated Il6 and Csf2 genes. LPS upregulation of Il12a and Il12b mRNAs was also impaired although specific blockade of TPL-2 signaling increased expression of these genes at late time points. Activation of TPL-2/ERK signaling by IKK-induced p105 proteolysis, therefore, induced a negative feedback loop to downregulate NF-κB-dependent expression of the proinflammatory cytokine interleukin-12 (IL-12). Unexpectedly, TPL-2 promoted soluble TNF production independently of IKK-induced p105 phosphorylation and its ability to activate ERK, which has important implications for the development of anti-inflammatory drugs targeting TPL-2.     

A sort of revolution: Systematics and physical anthropology in the 20th century

During the first four decades of the 20th century, a system of ideas about the evolution and systematics of humans and other primates coalesced around the work of George Gaylord Simpson and W. E. Le Gros Clark. Buttressed by the “new physical anthropology” of the 1950s, that system provided an authoritative model—a disciplinary matrix or paradigm—for the practice of that aspect of biological anthropology. The Simpson-Le Gros Clark synthesis began to unravel in the 1960s and collapsed in the 1970s under the onslaught of cladistic systematics. The cladistic “revolution” resembles a paradigm shift of the sort proposed by Thomas Kuhn because it was driven, not by new biological discoveries or theories, but by a change in aesthetics.     

Single-gene deletions that restore mating competence to diploid yeast

Using the Saccharomyces cerevisiae MATa/MATalpha ORF deletion collection, homozygous deletion strains were identified that undergo mating with MATa or MATalpha haploids. Seven homozygous deletions were identified that confer enhanced mating. Three of these, lacking CTF8, CTF18, and DCC1, mate at a low frequency with either MATa or MATalpha haploids. The products of these genes form a complex involved in sister chromatid cohesion. Each of these strains also exhibits increased chromosome loss rates, and mating likely occurs due to loss of one copy of chromosome III, which bears the MAT locus. Three other homozygous diploid deletion strains, ylr193cDelta/ylr193cDelta, yor305wDelta/yor305wDelta, and ypr170cDelta/ypr170cDelta, mate at very low frequencies with haploids of either or both mating types. However, an ist3Delta/ist3Delta strain mates only with MATa haploids. It is shown that IST3, previously linked to splicing, is required for efficient processing of the MATa1 message, particularly the first intron. As a result, the ist3Delta/ist3Delta strain expresses unbalanced ratios of Matalpha to Mata proteins and therefore mates with MATa haploids. Accordingly, mating in this diploid can be repressed by introduction of a MATa1 cDNA. In summary, this study underscores and elaborates upon predicted pathways by which mutations restore mating function to yeast diploids and identifies new mutants warranting further study.     

Functional incorporation of chimeric b subunits into F1Fo ATP synthase

F(1)F(o) ATP synthases function by a rotary mechanism. The enzyme's peripheral stalk serves as the stator that holds the F(1) sector and its catalytic sites against the movement of the rotor. In Escherichia coli, the peripheral stalk is a homodimer of identical b subunits, but photosynthetic bacteria have open reading frames for two different b-like subunits thought to form heterodimeric b/b' peripheral stalks. Chimeric b subunit genes have been constructed by substituting sequence from the Thermosynechococcus elongatus b and b' genes in the E. coli uncF gene, encoding the b subunit. The recombinant genes were expressed alone and in combination in the E. coli deletion strain KM2 (Deltab). Although not all of the chimeric subunits were incorporated into F(1)F(o) ATP synthase complexes, plasmids expressing either chimeric b(E39-I86) or b'(E39-I86) were capable of functionally complementing strain KM2 (Deltab). Strains expressing these subunits grew better than cells with smaller chimeric segments, such as those expressing the b'(E39-D53) or b(L54-I86) subunit, indicating intragenic suppression. In general, the chimeric subunits modeled on the T. elongatus b subunit proved to be more stable than the b' subunit in vitro. Coexpression of the b(E39-I86) and b'(E39-I86) subunits in strain KM2 (Deltab) yielded F(1)F(o) complexes containing heterodimeric peripheral stalks composed of both subunits.     

Subcellular fractions and the refringent granules of the spermatozoa of Ascaris suum (Nematoda)

Summary Six subcellular fractions were isolated by differential centrifugation of the homogenate of spermatozoa of Ascaris suum. The cellular constituents of pelleted fractions, as identified by electron microscopy, were membranes and membranous organelles (fraction A1), microsomal (A2), cytoplasmic (A3), large refringent granules (B1), small refringent granules (B2) and a detergent-soluble fraction (B3).Polypeptide analysis by SDS-PAGE showed that the 18,400-dalton band, one of the major spermatozoan proteins, is detectable in all of the fractions. However, the cytoplasmic (A1) and refringent-granule (B1) fractions contained the highest level.The isolated refringent granules consisted of 2–6 % lipid while the nonlipid fraction formed an insoluble matrix with a fibrillar network morphology. This fibrillar matrix contained three polypeptides of small molecular weight (7,000–14,000) in addition to the 18,400-dalton polypeptide. These small polypeptides (7,000–14,000 MW) are detectable only in fractions of the refringent granules and are therefore called the refringent-granule proteins (RGP). These RGP are sensitive to tryptic hydrolysis and have solubility properties similar to the protein, ascaridine.Adult Ascaris suum were generously provided by Wilson and Company, Cedar Rapids, Iowa. This study was supported by postdoctoral fellowship 5F32AI05646 from NIH. The assistance of Mr. Douglas Wood is gratefully acknowledged     

Consistent centennial-scale change in European sub-Arctic peatland vegetation toward Sphagnum dominance—Implications for carbon sink capacity

Climate warming is leading to permafrost thaw in northern peatlands, and current predictions suggest that thawing will drive greater surface wetness and an increase in methane emissions. Hydrology largely drives peatland vegetation composition, which is a key element in peatland functioning and thus in carbon dynamics. These processes are expected to change. Peatland carbon accumulation is determined by the balance between plant production and peat decomposition. But both processes are expected to accelerate in northern peatlands due to warming, leading to uncertainty in future peatland carbon budgets. Here, we compile a dataset of vegetation changes and apparent carbon accumulation data reconstructed from 33 peat cores collected from 16 sub-arctic peatlands in Fennoscandia and European Russia. The data cover the past two millennia that has undergone prominent changes in climate and a notable increase in annual temperatures toward present times. We show a pattern where European sub-Arctic peatland microhabitats have undergone a habitat change where currently drier habitats dominated by Sphagnum mosses replaced wetter sedge-dominated vegetation and these new habitats have remained relatively stable over the recent decades. Our results suggest an alternative future pathway where sub-arctic peatlands may at least partly sustain dry vegetation and enhance the carbon sink capacity of northern peatlands.