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.      

Small Mammal Responses to Fine Woody Debris and Forest Fuel Reduction in Southwest Oregon

Abstract: Despite its importance for wildlife, most forests in the Pacific Northwest contain low volumes of large downed wood compared to fine woody debris (FWD). We used a replicated experiment to compare short-term responses of deer mice (Peromyscus maniculatus) and western red-backed voles (Clethrionomys californicus) among 3 arrangements of FWD: piled, lopped and scattered, and pile burning, a commonly used method of fuel reduction in commercial Douglas fir (Pseudotsuga menziesii) forests in southwest Oregon, USA. We assessed habitat use, density, and survival of mice and voles during 2 consecutive summers (Jun—Aug 1999 and 2000). Both mice and voles used FWD cover disproportionately from its availability, and they differed in their responses to specific FWD arrangements. Mice used piled FWD (proportional use = 37.0%, 90% CI = 33.0–44.0) 43% more than expected (26.0). Number of mice captured (x̄ = 1.9 mice, 90% CI = 1.5–2.5) and index of home range size (x̄ = 4.8 m, 90% CI = 0.7–8.9) at individual FWD piles decreased up to 16% and increased up to 50%, respectively, for each 1-m increase in distance from piles. Voles used all FWD cover classes in proportion to availability, but number of voles captured increased slightly (x̄ = 0.016 voles/m, 90% CI = 0.001–0.031) for each 1-m increase in distance from piles. Piled FWD had no discernable effect on population density and apparent survival of mice, but analyses had low power (0.25, 0.67). Our results suggest that piling FWD would benefit deer mice, whereas lopped and scattered FWD might benefit voles. Thus, a combination of methods to reduce fire risk should be considered to accommodate multiple small mammal species. (JOURNAL OF WILDLIFE MANAGEMENT 72(3):625–632; 2008)     

"Our Beer": Ethnographic Brands in Postsocialist Georgia

Although Georgia is known for its wines, industrial production of beer far outstrips industrial wine production for local markets: wine consumption occurs in ritual contexts in which new wine, typically purchased from peasant producers, is preferred; bottled, aged wines are primarily for exports. Beer, therefore, is a key area in which industrial production for indigenous consumers has been elaborated. Such goods are packaged and presented as being both ecologically "pure" and following "traditional" methods, often referencing "ethnographic" materials about traditional life in brand images, even as they proclaim their reliance on Western technologies.     

Tyrosine phosphorylation of Munc18‐1 inhibits synaptic transmission by preventing SNARE assembly

Tyrosine kinases are important regulators of synaptic strength. Here, we describe a key component of the synaptic vesicle release machinery, Munc18‐1, as a phosphorylation target for neuronal Src family kinases (SFKs). Phosphomimetic Y473D mutation of a SFK phosphorylation site previously identified by brain phospho‐proteomics abolished the stimulatory effect of Munc18‐1 on SNARE complex formation (“SNARE‐templating”) and membrane fusion in vitro. Furthermore, priming but not docking of synaptic vesicles was disrupted in hippocampal munc18‐1‐null neurons expressing Munc18‐1_Y473D. Synaptic transmission was temporarily restored by high‐frequency stimulation, as well as by a Munc18‐1 mutation that results in helix 12 extension, a critical conformational step in vesicle priming. On the other hand, expression of non‐phosphorylatable Munc18‐1 supported normal synaptic transmission. We propose that SFK‐dependent Munc18‐1 phosphorylation may constitute a potent, previously unknown mechanism to shut down synaptic transmission, via direct occlusion of a Synaptobrevin/VAMP2 binding groove and subsequent hindrance of conformational changes in domain 3a responsible for vesicle priming. This would strongly interfere with the essential post‐docking SNARE‐templating role of Munc18‐1, resulting in a largely abolished pool of releasable synaptic vesicles.     

The phylogeny of the Rhinocerotoidea (Mammalia, Perissodactyla)

A new phylogeny of the Superfamily Rhinocerotoidea is proposed, based upon an analysis of shared derived characters of the skull, teeth and skeleton. Hyrachyus is considered the primitive sister-taxon of the three rhinocerotoid families (Amynodontidae, Hyracodontidae, Rhinocerotidae), and the amynodonts appear to be the sister-group of hyracodonts and rhinocerotids. The relationships of primitive hyracodonts and rhinocerotids are clarified. Menoceras and Pleuroceras (new Subfamily Menoceratinae) are removed from the Diceratheriinae, since they appear to be more closely related to higher rhinoceroses than they are to Diceratherium. Of the three major monophyletic groups of higher rhinocerotids (aceratherines, teleoceratines and rhinocerotines), the last two groups are more closely related to each other than either is to aceratherines. Toxotherium and Schizotheroides are tentatively removed from the Rhinocerotoidea and placed in the Lophiodontidae.     

The cost of incubation in relation to clutch-size in the Collared Flycatcher Ficedula albicollis

This study examines the importance of avian incubation costs as determinants of clutch-size variation by performing clutch-size and brood-size manipulations in the same population of Collared Flycatchers Ficedula albicollis during the same breeding season. In 2 5 cases when three or more clutches of the same size were completed on the same day, we moved two eggs on the day after the last egg had been laid from one randomly selected clutch (C) to another (C) and moved two other eggs from this to a third clutch (C⁺). In 20 other cases of simultaneously completed clutches of the same size, we moved two randomly selected young from one brood to a second and from that moved two other young to a third (B, B and B⁺groups). Most females were weighed the day after completion of the clutch and 1–4 days before hatching of the young, and some of them also 10–14 days after hatching of the young. We measured the daily energy expenditure of females incubating manipulated clutches of 4, 6 and 8 eggs by means of the doubly-labelled water (D₂¹⁸O) technique and also recorded their nest attendance. Hatching success of fertilized eggs was reduced in the enlarged clutches compared with control and reduced clutches. Females expired on average 3142.6 ml CO₂ and expended 78.6 kJ per day while incubating, which corresponds to a metabolic intensity of 3.3 times BMR. Daily energy expenditure increased with clutch-size due to higher costs while incubating, and not because of changed activity patterns. There were no significant differences in length of incubation, female mass or mass changes between phases for the C, C and C⁺groups. In both the C and B groups, enlarged broods produced significantly more fledged young than control broods, and those significantly more than reduced broods. Fledgling tarsus-length and mass did not differ significantly between treatments in either the C or B groups. There was no significant difference in breeding success between clutch and brood manipulations. In this season, incubation costs did not entail significant fitness losses, expressed either as fledgling production or female condition. Also, control females could have raised more young to fledging age than they did with no apparent costs.