The PYRIN domain: a member of the death domain-fold superfamily

PYRIN domains were identified recently as putative protein-protein interaction domains at the N-termini of several proteins thought to function in apoptotic and inflammatory signaling pathways. The approximately 95 residue PYRIN domains have no statistically significant sequence homology to proteins with known three-dimensional structure. Using secondary structure prediction and potential-based fold recognition methods, however, the PYRIN domain is predicted to be a member of the six-helix bundle death domain-fold superfamily that includes death domains (DDs), death effector domains (DEDs), and caspase recruitment domains (CARDs). Members of the death domain-fold superfamily are well established mediators of protein-protein interactions found in many proteins involved in apoptosis and inflammation, indicating further that the PYRIN domains serve a similar function. An homology model of the PYRIN domain of CARD7/DEFCAP/NAC/NALP1, a member of the Apaf-1/Ced-4 family of proteins, was constructed using the three-dimensional structures of the FADD and p75 neurotrophin receptor DDs, and of the Apaf-1 and caspase-9 CARDs, as templates. Validation of the model using a variety of computational techniques indicates that the fold prediction is consistent with the sequence. Comparison of a circular dichroism spectrum of the PYRIN domain of CARD7/DEFCAP/NAC/NALP1 with spectra of several proteins known to adopt the death domain-fold provides experimental support for the structure prediction.     

Genetic variation and structure of fisher (Martes pennanti) populations across North America

Fishers are mid-sized forest carnivores indigenous to North America that experienced sharp population declines from the early 1800s through to the mid-1900s. To evaluate levels of genetic variation within and subdivision among northern fisher populations 459 individuals were genotyped using 13 microsatellite loci. Genetic diversity was found to be slightly lower in re-introduced populations than in adjacent indigenous populations. Furthermore, fisher populations revealed much more genetic structuring than two closely related mustelids. Further investigation is needed to determine if fishers are more philopatric than martens and wolverines or if barriers to dispersal explain the levels of structure identified in this study.     

Independent origins and horizontal transfer of bacterial symbionts of aphids

Many insect groups have obligate associations with primary endosymbionts: mutualistic bacteria that are maternally transmitted and derived from an ancient infection. Often, the same insects are hosts to 'secondary' bacterial symbionts which are maternally transmitted but relatively labile within host lineages. To explore the dynamics of secondary symbiont associations in aphids, we characterized bacteria infecting 15 species of macrosiphine aphids using DNA sequencing, diagnostic polymerase chain reaction (PCR), diagnostic restriction digests, phylogenetic analyses, and electron microscopy to examine aphids from nature and from laboratory colonies. Three types of bacteria besides Buchnera were found repeatedly; all three fall within the Enterobacteriaceae. The R-type has a 16S rDNA less than 0.1% different from that of the secondary symbiont previously reported from Acyrthosiphon pisum and is related to Serratia species. The T-type includes a symbiont previously reported from a whitefly; the U-type comprises a new cluster near the T-type. The T-type was found in every one of 40 Uroleucon ambrosiae clones collected throughout the United States. In contrast, A. pisum individuals were infected by any combination of the three symbiont types. Secondary symbionts were maternally transmitted for 11 months within laboratory-reared A. pisum clones and were present in sexually produced eggs. PCR screens for a bacteriophage, APSE-1, indicated its presence in both A. pisum and U. ambrosiae containing secondary symbionts. Electron microscopy of R-type and T-type bacteria in A. pisum and in U. ambrosiae revealed rod-shaped organisms that attain extremely high densities within a few bacteriocytes.     

热带季节雨林林窗边缘不同热力作用面热力效应的季节变化特征

通过对热带季节雨林雾凉季和湿热季昼间林窗区域不同热力作用面的热力效应初步分析,指出在西双版纳,不论是雾凉季还是湿热季,热带季节雨林林窗边缘壁面均具有不可忽视的热力作用,且由于受林缘树木的影响,热力效应较强的东侧,北侧林缘壁面最大区域出现位置高于次生林林窗,而强度小于次生林林窗,显示了林窗边缘壁面的热力效应除与太阳高度角,太阳辐射的时间长短和强度有关之外,林窗边缘树木高度也是不可忽视的因子,其结果可为进一步研究林窗小气候形成机制提供研究基础,为研究林窗更新及生物多样性问题提供科学参考。     

Structure and Conformational Heterogeneity of a Weak Toxin from the Cobra Naja kaouthiaVenom

Resonances in the two-dimensional ¹H NMR spectra of a weak toxin (WTX) from the venom of cobra Naja kaouthiafor all 65 amino acid residues were assigned. The amino acid sequence of WTX, determined by the sequential assignment of spin systems, was found to be similar to that of the CM-9a toxin from the N. kaouthiavenom. Unlike CM-9a, WTX contains an additional Trp36 residue; Lys50 and Tyr52 are interchanged; and there is a Thr residue in place of Arg2. For some residues of WTX, the presence of two components of approximately equal intensities in the spectra was shown, which is explained by the conformational heterogeneity of the polypeptide owing to the cis–transisomerization of the peptide bond Arg32–Pro33. The data (contacts of the nuclear Overhauser effect, constants of spin–spin coupling of protons, and rates of exchange of amide protons for deuterium of the solvent) made it possible to determine the secondary structure of two forms of WTX, which is characterized by the presence of two antiparallel -sheets, one of which consists of two strands (regions 1–5 and 13–17) and the other, of three strands (regions 23–28, 38–43, and 55–59).     

Improved paclitaxel accumulation in cell suspension cultures of Taxus chinensis by brassinolide

When brassinolide was added at 17 ng l^–1 to Taxus chinensis cell suspension cultures, the paclitaxel content was increased by over 100% to 580 g g^–1 dry weight. Brassinolide may therefore be a novel regulator of paclitaxel biosynthesis.     

Primate Population Densities and Sizes in Atlantic Forest Remnants of Northern Espírito Santo,Brazil

We surveyed primates in seven fragments of Atlantic forest ranging from 210 to 24,250 ha in Espírito Santo, southeastern Brazil. The objective was to assess their population densities and fragment-specific population sizes in order to discuss the survival of primates in this highly fragmented landscape. We used line-transect sampling for censusing primates and estimated densities via DISTANCE program. Alouatta fusca, Cebus apella, Callicebus personatus, and Callithrix geoffroyi live in the study area. Although variable, primate numbers were higher in larger than in smaller fragments, the likely reasons being the lack of space and food resources (fruits) and higher impact of mesopredators (small cats) in small fragments. The estimated densities are within the range reported for other Atlantic forest sites, except for brown howlers (Alouatta fusca), which were extremely rare. Estimates of population sizes were on the order of several hundreds to thousands of individuals/species in the large-sized fragments (ca. 20,000 ha), while comparable estimates for the other areas indicate <500 individuals/species in the medium-sized reserves (ca. 2,000 ha), and <50 individuals/species in the small fragments (ca. 200 ha). These estimates suggest that only Atlantic forest fragments 20,000 ha can harbor primate populations large enough to escape extinction in the long term. Given that <20% of all protected areas remaining in the Atlantic forest are 20,000 ha, management measures are urgently needed to improve primate conservation in this biome.     

Differential expression of cell-wall-related genes during the formation of tracheary elements in the Zinnia mesophyll cell system

Plants, animals and some fungi undergo processes of cell specialization such that specific groups of cells are adapted to carry out particular functions. One of the more remarkable examples of cellular development in higher plants is the formation of water-conducting cells that are capable of supporting a column of water from the roots to tens of metres in the air for some trees. The Zinnia mesophyll cell system is a remarkable tool with which to study this entire developmental pathway in vitro. We have recently applied an RNA fingerprinting technology, to allow the detection of DNA fragments derived from RNA using cDNA synthesis and subsequent PCR-amplified fragment length polymorphisms (cDNA-AFLP), to systematically characterize hundreds of the genes involved in the process of tracheary element formation. Building hoops of secondary wall material is the key structural event in forming functional tracheary elements and we have identified over 50 partial sequences related to cell walls out of 600 differentially expressed cDNA fragments. The Zinnia system is an engine of gene discovery which is allowing us to identify and characterize candidate genes involved in cell wall biosynthesis and assembly.     

Use of Terrestrial Invertebrates as Indicators of the Ecological Sustainability of Forest Management under the Montreal Process

Twelve nations involved in boreal or temperate forest management are committed to reporting on indicators under the Montreal Process as a mechanism for assessing progress towards sustainable forest management. For fauna, invertebrates are often considered too poorly known and diverse to include in sustainability indicator reporting. The alternative view, that no monitoring of sustainability can be considered adequate without inclusion of some invertebrate species, is espoused in this paper. The microhabitats of soil and litter, foliage and canopy, bark and branch, dead standing trees and coarse woody debris are highlighted as relevant in the context of determining the impacts of forest management on invertebrates and for selecting representative species. It is argued that a selection of those species from each of the key microhabitats that are restricted to later stages of succession should be monitored. This could be complemented by a selection of easily monitored species from a range of functional groups as a means of endeavouring to pick up adverse impacts not foreseen on the basis of present knowledge. In the longer term, habitat indices (developed from predictive models of fauna habitat) should be used to monitor the occurrence of indicator species across the broader landscape, rather than at specific sites where monitoring of species takes place. Most countries would be in a position to select indicator species and commence monitoring for some key microhabitats (e.g. soil and litter). However, further research is needed in many countries before indicator species can be selected for other key microhabitats (e.g. coarse woody debris).