Taphonomy and compositional fidelity of Quaternary fossil assemblages of terrestrial gastropods from carbonate-rich environments of the Canary Islands

Quaternary aeolian deposits of the Canary Islands contain well‐preserved terrestrial gastropods, providing a suitable setting for assessing the taphonomy and compositional fidelity of their fossil record over ~13 kyr. Nine beds (12, 513 shells) have been analysed in terms of multivariate taphonomic and palaeoecological variables, taxonomic composition, and the stratigraphic and palaeontological context. Shells are affected by carbonate coatings, colour loss and fragmentation. Shell preservation is size‐specific: juveniles are less fragmented and show colour preservation more commonly than adults. In palaeosols, the adult shell density correlates negatively with the proportion of fragmented adults, negatively with the proportion of juveniles, and positively with the proportion of adults with coatings. High bioturbation intensity in palaeosols is associated with low shell fragmentation and high proportion of shells with coatings. These relationships imply that high adult density in palaeosols was driven by an increase in shell production rate (related to a decrease in predation rates on adults and a decrease in juvenile mortality) and a decrease in shell destruction rate (related to an increase in durability enhanced by carbonate precipitation). In dunes, the relationships between taphonomic alteration, shell density and bioturbation are insignificant. However, dune assemblages are characterized by a lower frequency of shells with coatings and higher rates of colour loss, indicating lower shell durability in dunes than in palaeosols. Additionally, non‐random differences in the coating proportion among palaeosols imply substantial temporal variation in the rate of carbonate crust formation, reflecting long‐term changes in bioturbation intensity that covaries positively with shell preservation. Dunes and palaeosols do not differ in species abundances despite differences in the degree of shell alteration, suggesting that both weakly and strongly altered assemblages offer data with a high compositional fidelity. Carbonate‐rich terrestrial deposits originating in arid conditions can enhance the preservation of gastropods and result in fossil assemblages that are suitable for palaeoecological and palaeoenvironmental studies of terrestrial ecosystems.     

Efficacy of neem and diatomaceous earth against cowpea aphids and their deleterious effect on predating Coccinelidae

Philippine vegetable farmers commonly use synthetic insecticides to control insect pests on yardlong beans ( Vigna unguiculata ssp. sesquipedalis ). An important pest on yardlong beans is the cowpea aphid, Aphis craccivora Koch. Overuse of chemical insecticides and the adverse consequences for farmer health and for the environment have been reported. The natural enemies of A. craccivora , such as the coccinelidae beetle, Menochilus sexmaculatus (Fabr.), do not provide economic control on their own. In the present study the efficacy of the biological insecticide neem (both commercial and homemade) alone, and in combination with diatomaceous earth against A. craccivora was evaluated. The same insecticides were also examined to investigate their deleterious effect on M. sexmaculatus . The efficacies of different treatments with biological insecticides were compared with the use of the synthetic insecticide Hostathion (triazophos). Experiments were conducted under Philippine lowland conditions during the dry season when the occurrence of pest problems in yardlong beans is very great. Commercial neem, NeemAzal-T/S (Trifolio-M GmbH, Lahnau, Germany), significantly reduced the number of A. craccivora . NeemAzal-T/S and diatomaceous earth in combination produced the best control of A. craccivora and were less toxic to M. sexmaculatus than treatment with Hostathion (triazophos). Aqueous homemade neem solution did not control the A. craccivora populations.     

The weak interdomain coupling observed in the 70 kDa subunit of human replication protein A is unaffected by ssDNA binding

Replication protein A (RPA) is a heterotrimeric, multi-functional protein that binds single-stranded DNA (ssDNA) and is essential for eukaryotic DNA metabolism. Using heteronuclear NMR methods we have investigated the domain interactions and ssDNA binding of a fragment from the 70 kDa subunit of human RPA (hRPA70). This fragment contains an N-terminal domain (NTD), which is important for hRPA70–protein interactions, connected to a ssDNA-binding domain (SSB1) by a flexible linker (hRPA70_1–326). Correlation analysis of the amide ¹H and ¹⁵N chemical shifts was used to compare the structure of the NTD and SSB1 in hRPA70_1–326 with two smaller fragments that corresponded to the individual domains. High correlation coefficients verified that the NTD and SSB1 maintained their structures in hRPA70_1–326, indicating weak interdomain coupling. Weak interdomain coupling was also suggested by a comparison of the transverse relaxation rates for hRPA70_1–326 and one of the smaller hRPA70 fragments containing the NTD and the flexible linker (hRPA70_1–168). We also examined the structure of hRPA70_1–326 after addition of three different ssDNA substrates. Each of these substrates induced specific amide ¹H and/or ¹⁵N chemical shift changes in both the NTD and SSB1. The NTD and SSB1 have similar topologies, leading to the possibility that ssDNA binding induced the chemical shift changes observed for the NTD. To test this hypothesis we monitored the amide ¹H and ¹⁵N chemical shift changes of hRPA70_1–168 after addition of ssDNA. The same amide ¹H and ¹⁵N chemical shift changes were observed for the NTD in hRPA70_1–168 and hRPA70_1–326. The NTD residues with the largest amide ¹H and/or ¹⁵N chemical shift changes were localized to a basic cleft that is important for hRPA70–protein interactions. Based on this relationship, and other available data, we propose a model where binding between the NTD and ssDNA interferes with hRPA70–protein interactions.     

The solution structure of bacteriophage lambda protein W, a small morphogenetic protein possessing a novel fold

Protein W (gpW) from bacteriophage lambda is required for the stabilization of DNA within the phage head and for attachment of tails onto the head during morphogenesis. Although comprised of only 68 residues, it likely interacts with at least two other proteins in the mature phage and with DNA. Thus, gpW is an intriguing subject for detailed structural studies. We have determined its solution structure using NMR spectroscopy and have found it to possesses a novel fold consisting of two alpha-helices and a single two-stranded beta-sheet arranged around a well-packed hydrophobic core. The 14 C-terminal residues of gpW, which are essential for function, are unstructured in solution.     

Chemical shift changes provide evidence for overlapping single-stranded DNA- and XPA-binding sites on the 70 kDa subunit of human replication protein A

Replication protein A (RPA) is a heterotrimeric single-stranded DNA- (ssDNA) binding protein that can form a complex with the xeroderma pigmentosum group A protein (XPA). This complex can preferentially recognize UV-damaged DNA over undamaged DNA and has been implicated in the stabilization of open complex formation during nucleotide excision repair. In this report, nuclear magnetic resonance (NMR) spectroscopy was used to investigate the interaction between a fragment of the 70 kDa subunit of human RPA, residues 1–326 (hRPA70_1–326), and a fragment of the human XPA protein, residues 98–219 (XPA-MBD). Intensity changes were observed for amide resonances in the ¹H–¹⁵N correlation spectrum of uniformly ¹⁵N-labeled hRPA70_1–326 after the addition of unlabeled XPA-MBD. The intensity changes observed were restricted to an ssDNA-binding domain that is between residues 183 and 296 of the hRPA70_1–326 fragment. The hRPA70_1–326 residues with the largest resonance intensity reductions were mapped onto the structure of the ssDNA-binding domain to identify the binding surface with XPA-MBD. The XPA-MBD-binding surface showed significant overlap with an ssDNA-binding surface that was previously identified using NMR spectroscopy and X-ray crystallography. Overlapping XPA-MBD- and ssDNA-binding sites on hRPA70_1–326 suggests that a competitive binding mechanism mediates the formation of the RPA–XPA complex. To determine whether a ternary complex could form between hRPA70_1–326, XPA-MBD and ssDNA, a ¹H–¹⁵N correlation spectrum was acquired for uniformly ¹⁵N-labeled hRPA70_1–326 after the simultaneous addition of unlabeled XPA-MBD and ssDNA. In this experiment, the same chemical shift perturbations were observed for hRPA70_1–326 in the presence of XPA-MBD and ssDNA as was previously observed in the presence of ssDNA alone. The ability of ssDNA to compete with XPA-MBD for an overlapping binding site on hRPA70_1–326 suggests that any complex formation between RPA and XPA that involves the interaction between XPA-MBD and hRPA70_1–326 may be modulated by ssDNA.     

Identification of a novel archaebacterial thioredoxin: determination of function through structure

As part of a high-throughput, structural proteomic project we have used NMR spectroscopy to determine the solution structure and ascertain the function of a previously unknown, conserved protein (MtH895) from the thermophilic archeon Methanobacterium thermoautotrophicum. Our findings indicate that MtH895 contains a central four-stranded beta-sheet core surrounded by two helices on one side and a third on the other. It has an overall fold superficially similar to that of a glutaredoxin. However, detailed analysis of its three-dimensional structure along with molecular docking simulations of its interaction with T7 DNA polymerase (a thioredoxin-specific substrate) and comparisons with other known members of the thioredoxin/glutaredoxin family of proteins strongly suggest that MtH895 is more akin to a thioredoxin. Furthermore, measurement of the pK(a) values of its active site thiols along with direct measurements of the thioredoxin/glutaredoxin activity has confirmed that MtH895 is, indeed, a thioredoxin and exhibits no glutaredoxin activity. We have also identified a group of previously unknown proteins from several other archaebacteria that have significant (34-44%) sequence identity with MtH895. These proteins have unusual active site -CXXC- motifs not found in any known thioredoxin or glutaredoxin. On the basis of the results presented here, we predict that these small proteins are all members of a new class of truncated thioredoxins.