A mixed-age classed ‘pelycosaur’ aggregation from South Africa: earliest evidence of parental care in amniotes?

Living species of mammals, crocodiles and most species of birds exhibit parental care, but evidence of this behaviour is extremely rare in the fossil record. Here, we present a new specimen of varanopid 'pelycosaur' from the Middle Permian of South Africa. The specimen is an aggregation, consisting of five articulated individuals preserved in undisturbed, close, lifelike, dorsal-up, subparallel positions, indicating burial in 'life position'. Two size classes are represented. One is 50% larger than the others, is well ossified, has fused neurocentral sutures and is distinguished by a coat of dermal ossifications that covers the neck and shoulder regions. We regard this individual to be an adult. The remaining four skeletons are considered to be juveniles as they are approximately the same size, are poorly ossified, have open neurocentral sutures and lack dermal ossifications. Aggregates of juvenile amniotes are usually siblings. Extant analogues of adult and juvenile groupings suggest that the adult is one of the parents, leading us to regard the aggregation as a family group. The Late Middle Permian age of the varanopid family predates the previously known oldest fossil evidence of parental care in terrestrial vertebrates by 140 Myr.     

Preservation of T cell proliferation restricted by protective HLA alleles is critical for immune control of HIV-1 infection

HIV-1-infected persons with HLA-B27 and -B57 alleles commonly remain healthy for decades without antiretroviral therapy. Properties of CD8+ T cells restricted by these alleles considered to confer disease protection in these individuals are elusive but important to understand and potentially elicit by vaccination. To address this, we compared CD8+ T cell function induced by HIV-1 immunogens and natural infection using polychromatic flow cytometry. HIV-1-specific CD8+ T cells from all four uninfected immunized and 21 infected subjects secreted IFN-gamma and TNF-alpha. However, CD8+ T cells induced by vaccination and primary infection, but not chronic infection, proliferated to their cognate epitopes. Notably, B27- and B57-restricted CD8+ T cells from nonprogressors exhibited greater expansion than those restricted by other alleles. Hence, CD8+ T cells restricted by certain protective alleles can resist replicative defects, which permits expansion and antiviral effector activities. Our findings suggest that the capacity to maintain CD8+ T cell proliferation, regardless of MHC-restriction, may serve as an important correlate of disease protection in the event of infection following vaccination.     

Temperature and plant nutrient effects on the development, survival and reproduction of Cinara sp. nov., an invasive pest of cypress trees in Africa

Cinara sp. nov., previously identified as Cinara cupressi (Buckton) (Homoptera: Aphididae), is an important alien aphid pest of cypresses and junipers, and invaded Africa in the late 1980s. The work reported here was carried out as part of a larger programme aimed at the classical biological control of the aphid in Africa. Basic life history attributes including life table statistics of the aphid were quantified in order to facilitate the development of efficient aphid culturing methods and essential baseline information necessary for the culturing of potential parasitoid biological agents prior to selection for introduction to Africa. Developmental rates and fecundity were studied under four constant temperatures (10 °C, 15 °C, 20 °C, and 25 °C). The effects of several plant nutrients (nitrogen, potassium and phosphorus) supplied at different dose levels on life history attributes of Cinara sp. nov. were also studied.Unlike most other aphids, the apterous morph of Cinara sp. nov. developed through only three instars, and the alate four instars. The aphid is highly aggregative and exploits a wide range of feeding sites from young green branches to woody stems. The developmental period of Cinara sp. nov. ranged from 9.3 days at 25 °C to 22.3 days at 10 °C and the developmental threshold was 0.61 °C. Reproduction was delayed, because of the longer duration of development, and nymph production decreased with decreasing temperature. The intrinsic rate of increase ranged between 0.117 at 25 °C and 0.060 at 10 °C. Aphid size increased significantly as temperature was lowered. Wing formation was not induced when apterae were reared for up to three generations at each constant temperature but continuous crowding in the supply cultures held at 21 °C resulted in a high number of alates being formed. No appreciable effects of the different plant nutrients, supplied either singly or in combination, on the duration of instars or overall survival could be detected.     

Siderophore uptake in bacteria and the battle for iron with the host; a bird’s eye view

Siderophores are biosynthetically produced and secreted by many bacteria, yeasts, fungi and plants, to scavenge for ferric iron (Fe³⁺). They are selective iron-chelators that have an extremely high affinity for binding this trivalent metal ion. The ferric ion is poorly soluble but it is the form of iron that is predominantly found in oxygenated environments. Siderophore uptake in bacteria has been extensively studied and over the last decade, detailed structural information for many of the proteins that are involved in their transport has become available. Specifically, numerous crystal structures for outer membrane siderophore transporters, as well as for soluble periplasmic siderophore-binding proteins, have been reported. Moreover, unique siderophore-binding proteins have recently been serendipitously discovered in humans, and the structures of some of their siderophore-complexes have been characterized. The binding pockets for different ferric-siderophores in these proteins have been described in great molecular detail. In addition to highlighting this structural information, in this review paper we will also briefly discuss the relevant chemical properties of iron, and provide a perspective on our current understanding of the human and bacterial iron uptake pathways. Potential clinical uses of siderophores will also be discussed. The emerging overall picture is that iron metabolism plays an extremely important role during bacterial infections. Because levels of free ferric iron in biological systems are always extremely low, there is serious competition for iron and for ferric-siderophores between pathogenic bacteria and the human or animal host.     

Targeting of the Arf-like GTPase Arl3p to the Golgi requires N-terminal acetylation and the membrane protein Sys1p

The GTPase Arl3p is required to recruit a second GTPase, Arl1p, to the Golgi in Saccharomyces cerevisiae. Arl1p binds to the GRIP domain, which is present in a number of long coiled-coil proteins or 'golgins'. Here we show that Arl3p is not myristoylated like most members of the Arf family, but is instead amino-terminally acetylated by the NatC complex. Targeting of Arl3p also requires a Golgi membrane protein Sys1p. The human homologues of Arl3p (Arf-related protein 1 (ARFRP1)) and Sys1p (hSys1) can be isolated in a complex after chemical cross-linking. This suggests that the targeting of ARFRP1/Arl3p to the Golgi is mediated by a direct interaction between its acetylated N terminus and Sys1p/hSys1.     

Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis

Since the initial sequencing of the human genome, many projects are underway to understand the effects of genetic variation between individuals. Predicting and understanding the downstream effects of genetic variation using computational methods are becoming increasingly important for single nucleotide polymorphism (SNP) selection in genetics studies and understanding the molecular basis of disease. According to the NIH, there are now more than four million validated SNPs in the human genome. The volume of known genetic variations lends itself well to an informatics approach. Bioinformaticians have become very good at functional inference methods derived from functional and structural genomics. This review will present a broad overview of the tools and resources available to collect and understand functional variation from the perspective of structure, expression, evolution and phenotype. Additionally, public resources available for SNP identification and characterisation are summarised.     

Structural characterization of proteins using residue environments

A primary challenge for structural genomics is the automated functional characterization of protein structures. We have developed a sequence-independent method called S-BLEST (Structure-Based Local Environment Search Tool) for the annotation of previously uncharacterized protein structures. S-BLEST encodes the local environment of an amino acid as a vector of structural property values. It has been applied to all amino acids in a nonredundant database of protein structures to generate a searchable structural resource. Given a query amino acid from an experimentally determined or modeled structure, S-BLEST quickly identifies similar amino acid environments using a K-nearest neighbor search. In addition, the method gives an estimation of the statistical significance of each result. We validated S-BLEST on X-ray crystal structures from the ASTRAL 40 nonredundant dataset. We then applied it to 86 crystallographically determined proteins in the protein data bank (PDB) with unknown function and with no significant sequence neighbors in the PDB. S-BLEST was able to associate 20 proteins with at least one local structural neighbor and identify the amino acid environments that are most similar between those neighbors.     

Influence of dietary conjugated linoleic acid (CLA) on lipid and fatty acid composition in liver and flesh of Atlantic salmon (Salmo salar)

The aim of the present study was to determine the effects of conjugated linoleic acid (CLA) on lipid and fatty acid metabolism in Atlantic salmon. The overall objective being to test the hypotheses that CLA has beneficial effects in salmon including growth enhancement, improved flesh quality through decreased adiposity and lipid deposition thereby minimising detrimental effects of feeding high fat diets, and increased nutritional quality through increased levels of beneficial fatty acids including n-3 highly unsaturated fatty acids (HUFA) and CLA itself. Salmon smolts were fed diets containing two levels of fish oil (low, approximately 18% and high, approximately 34%) containing three levels of CLA (a 1:1 mixture of 9-cis,trans-11 and trans-10,cis-12. at 0, 1 and 2% of diet) for 3 months and the effects on growth performance, liver and muscle (flesh) lipid contents and class compositions, and fatty acid compositions determined. The diets were also specifically formulated to investigate whether the effects of CLA, if any, were more dependent upon absolute content of CLA in the diet (as percentage of total diet) or the relative level of CLA to other fatty acids. Dietary CLA in salmon smolts had no effect on growth parameters or biometric parameters. However, there was a clear trend of increased total lipid and triacylglycerol contents in both liver and flesh in fish fed CLA, particularly in fish fed the high oil diets. Finally, CLA was incorporated into tissue lipids, with levels in flesh being 2-fold higher than in liver, but importantly, incorporation in liver was at the expense of saturated and monounsaturated fatty acids whereas in flesh it was at the expense of n-3HUFA.     

Effects of nonylphenol on hepatic testosterone metabolism and the expression of acute phase proteins in winter flounder (Pleuronectes americanus): comparison to the effects of Saint John's Wort

4-Nonylphenol (4-NP), a major by-product of alkylphenol ethoxylates, is used in several industries and as a consequence is quite common in rivers, estuaries and other aquatic environments that receive sewage discharges or are near offshore oil platforms. 4-NP is an environmental estrogen that also binds human and rodent Pregnane X-receptor (PXR), the orphan nuclear receptor that controls the expression of several detoxication genes in mammals, including several CYP3A and CYP2B family members. These P450s preferentially hydroxylate testosterone in the 6beta- and 16beta-positions, respectively. In this study, the effects of 4-NP on testosterone metabolism and hepatic CYP3A induction were compared to the effects of St. John's Wort (SJW), a well established mammalian PXR agonist, in winter flounder. Male winter flounder (Pleuronectes americanus) were injected with 100 mg/kg/day 4-NP or 500 mg/kg/day SJW or both (S and N) every 24 h. Forty-eight hours after the initial injections, flounder were euthanized. Western blots and testosterone 6beta-hydroxylation indicated that CYP3A was increased 50% by 4-NP, but was not affected by SJW. Testosterone 16beta-hydroxylase activity was also significantly increased in flounder treated with 4-NP (2.8 x), but not with SJW. This is not consistent with our hypothesis that both SJW and 4-NP would induce CYP3A. Subtractive hybridization was performed between control and 4-NP treated hepatic mRNA samples to isolate differentially expressed genes. Subtractive hybridization indicated that several acute phase proteins were altered by 4-NP. Quantitative real-time PCR (Q-PCR) confirmed 4-NP altered the expression of complement components C8b, cathepsin L, C-type lectin domain, FK506 binding protein 2 precursor (FKBP2) and an EST (expressed sequence tag). SJW and 4-NP treated flounder demonstrated similar induction profiles for the EST, cathepsin L and FKBP2, suggesting that SJW was at a sufficient dose to alter gene expression but not induce P450s. In conclusion, testosterone hydroxylase activity and Western blots indicate that SJW did not activate detoxication pathways in a similar manner to 4-NP.