Phylogenetic diversification of immunoglobulin genes and the antibody repertoire

Immunoglobulins are encoded by a large multigene system that undergoes somatic rearrangement and additional genetic change during the development of immunoglobulin-producing cells. Inducible antibody and antibody-like responses are found in all vertebrates. However, immunoglobulin possessing disulfide-bonded heavy and light chains and domain-type organization has been described only in representatives of the jawed vertebrates. High degrees of nucleotide and predicted amino acid sequence identity are evident when the segmental elements that constitute the immunoglobulin gene loci in phylogenetically divergent vertebrates are compared. However, the organization of gene loci and the manner in which the independent elements recombine (and diversify) vary markedly among different taxa. One striking pattern of gene organization is the "cluster type" that appears to be restricted to the chondrichthyes (cartilaginous fishes) and limits segmental rearrangement to closely linked elements. This type of gene organization is associated with both heavy- and light-chain gene loci. In some cases, the clusters are "joined" or "partially joined" in the germ line, in effect predetermining or partially predetermining, respectively, the encoded specificities (the assumption being that these are expressed) of the individual loci. By relating the sequences of transcribed gene products to their respective germ-line genes, it is evident that, in some cases, joined-type genes are expressed. This raises a question about the existence and/or nature of allelic exclusion in these species. The extensive variation in gene organization found throughout the vertebrate species may relate directly to the role of intersegmental (V<==>D<==>J) distances in the commitment of the individual antibody-producing cell to a particular genetic specificity. Thus, the evolution of this locus, perhaps more so than that of others, may reflect the interrelationships between genetic organization and function.      

Carbon flux and diversity of nematodes and termites in Cameroon forest soils

Theoretically, there are three principal ways in which ecosystem processes might respond to reductions in species richness. These theories are reviewed, and then considered in the context of a study of the diversity of soil nematodes and termites in near-primary forest sites at Mbalmayo, Cameroon, and the contribution made by these two taxa to carbon fluxes (CO₂ and CH₄) from the forest floor. Nematode abundances average 2.04 × 10⁶ m^-2, and termites between 2933 and 6957 m^-2. The site is the most species-rich yet investigated for both groups anywhere in the world, so that a very large number of species contribute to carbon fluxes. We speculate about how much redundancy might be built into the functioning of both assemblages, and point out the enormous difficulties of resolving such questions, and of producing such detailed species-inventories.     

Termite assemblages, forest disturbance and greenhouse gas fluxes in Sabah, East Malaysia

A synthesis is presented of sampling work conducted under a UK government-funded Darwin Initiative grant undertaken predominantly within the Danum Valley Conservation Area (DVCA), Sabah, East Malaysia. The project concerned the assemblage structure, gas physiology and landscape gas fluxes of termites in pristine and two ages of secondary, dipterocarp forest. The DVCA termite fauna is typical of the Sunda region, dominated by Termes-group soil-feeders and Nasutitermitinae. Selective logging appears to have relatively little effect on termite assemblages, although soil-feeding termites may be moderately affected by this level of disturbance. Species composition changes, but to a small extent when considered against the background level of compositional differences within the Sunda region. Physiologically the assemblage is very like others that have been studied, although there are some species that do not fit on the expected body size-metabolic rate curve. As elsewhere, soil-feeders and soil-wood interface-feeders tend to produce more methane. As with the termite assemblage characteristics, gross gas and energy fluxes do not differ significantly between logged and unlogged sites. Although gross methane fluxes are high, all the soils at DVCA were methane sinks, suggesting that methane oxidation by methanotrophic bacteria was a more important process than methane production by gut archaea. This implies that methane production by termites in South-East Asia is not contributing significantly to the observed increase in levels of methane production worldwide. Biomass density, species richness, clade complement and energy flow were much lower at DVCA than at a directly comparable site in southern Cameroon. This is probably due to the different biogeographical histories of the areas.     

What can we learn from noncoding regions of similarity between genomes?

Background  

In addition to known protein-coding genes, large amounts of apparently non-coding sequence are conserved between the human and mouse genomes. It seems reasonable to assume that these conserved regions are more likely to contain functional elements than less-conserved portions of the genome.     

The gene for juvenile hyaline fibromatosis maps to chromosome 4q21

Juvenile hyaline fibromatosis (JHF) is an autosomal recessive condition characterized by multiple subcutaneous nodular tumors, gingival fibromatosis, flexion contractures of the joints, and an accumulation of hyaline in the dermis. We performed a genomewide linkage search in two families with JHF from the same region of the Indian state of Gujarat and identified a region of homozygosity on chromosome 4q21. Dense microsatellite analyses within this interval in five families with JHF who were from diverse origins demonstrate that all are compatible with linkage to chromosome 4q21 (multipoint LOD score 5.5). Meiotic recombinants place the gene for JHF within a 7-cM interval bounded by D4S2393 and D4S395.     

Molecular phylogenetic profiling of prokaryotic communities in guts of termites with different feeding habits

Termites are an important group of terrestrial insects that harbor an abundant gut microbiota, many of which contribute to digestion, termite nutrition and gas (CH(4), CO(2) and H(2)) emission. With 2200 described species, termites also provide a good model to study relationships between host diet and gut microbial community structure and function. We examined the relationship between diet and gut prokaryotic community profiles in 24 taxonomically and nutritionally diverse species of termites by using nucleic acid probes targeting 16S-like ribosomal RNAs. The relative abundance of domain-specific 16S-like rRNAs recovered from gut extracts varied considerably (ranges: Archaea (0-3%); Bacteria (15-118%)). Although Bacteria were always detectable and the most abundant, differences in domain-level profiles were correlated with termite diet, as evidenced by higher relative abundances of Archaea in guts of soil-feeding termites, compared to those of wood-feeding species in the same family. The oligonucleotide probes also readily distinguished gut communities of wood-feeding taxa in the family Termitidae (higher termites) from those of other wood-feeding termite families (lower termites). The relative abundances of 16S-like archaeal rRNA in guts were positively correlated with rates of methane emission by live termites, and were consistent with previous work linking high relative rates of methanogenesis with the soil (humus)-feeding habit. Probes for methanogenic Archaea detected members of only two families (Methanobacteriaceae and Methanosarcinaceae) in termite guts, and these typically accounted for 60% of the all archaeal probe signal. In four species of termites, Methanosarcinaceae were dominant, a novel observation for animal gut microbial communities, but no clear relationship was apparent between methanogen family profiles and termite diet or taxonomy.     

Use of gas chromatograms of essential leaf oils to compare clones of Eucalyptus camaldulensis

Using a gentle vacuum technique essential oils were distilled from the leaves of six clones (29 different trees) of Eucalyptus camaldulensis which had previously been propagated by CSIRO, from four seed lots collected from an area of southern Australia bounded approximately by latitude 26 degrees S and longitude 142 degrees E. Inspection of the analyses of the oils together with principal components analysis (PCA) of the gas chromatograms shows that corresponding profiles (for those clones studied in groups of two, three, four and 20), as indicated by the scores of the principal components, are almost independent of environmental and seasonal conditions.