Comparative genomics reveals multiple pathways to mutualism for tick-borne pathogens

Accelerated pipeline for DNA and amino acid sequences clustering

Whole Proteome Clustering of 2,307 Proteobacterial Genomes Reveals Conserved Proteins and Significant Annotation Issues

We clustered 8.76 M protein sequences deduced from 2,307 completely sequenced Proteobacterial genomes resulting in 707,311 clusters of one or more sequences of which 224,442 ranged in size from 2 to 2,894 sequences. To our knowledge this is the first study of this scale. We were surprised to find that no single cluster contained a representative sequence from all the organisms in the study. Given the minimal genome concept, we expected to find a shared set of proteins. To determine why the clusters did not have universal representation we chose four essential proteins, the chaperonin GroEL, DNA dependent RNA polymerase subunits beta and beta′ (RpoB/RpoB′), and DNA polymerase I (PolA), representing fundamental cellular functions, and examined their cluster distribution. We found these proteins to be remarkably conserved with certain caveats. Although the groEL gene was universally conserved in all the organisms in the study, the protein was not represented in all the deduced proteomes. The genes for RpoB and RpoB′ were missing from two genomes and merged in 88, and the sequences were sufficiently divergent that they formed separate clusters for 18 RpoB proteins (seven clusters) and 14 RpoB′ proteins (three clusters). For PolA, 52 organisms lacked an identifiable sequence, and seven sequences were sufficiently divergent that they formed five separate clusters. Interestingly, organisms lacking an identifiable PolA and those with divergent RpoB/RpoB′ were predominantly endosymbionts. Furthermore, we present a range of examples of annotation issues that caused the deduced proteins to be incorrectly represented in the proteome. These annotation issues made our task of determining protein conservation more difficult than expected and also represent a significant obstacle for high-throughput analyses

Kairo, Ägypten. Die Goldblechbeschläge aus dem Grab des Tutanchamun

Apart from the ongoing restauration of the gold sheet appliqués from the tomb of Tutankhamun, several important studies could be accomplished as part of the joint German-Egyptian project. The iconographical analysis which is nearly completed deals with both traditional Egyptian and ‘international’ motifs depicted on the gold sheets and how they were integrated in the context of Egyptian art at the end of the 18th dynasty. Furthermore, various technical aspects concerning the backings of the gold sheets which consist of different layers of leather, textile, gesso and resins were investigated. In addition, the composition of the gold was examined by portable XRF-analysis resulting in the identification of six different material groups which broadly overlap with groups formed on grounds of iconographical results

Purification of Tropomyosin Br-3 and 5NM1 and Characterization of Their Interactions with Actin

Tropomyosins were first identified in neuronal systems in 1973. Although numerous isoforms were found and described since then, many aspects of their function and interactions remained unknown. Tropomyosin isoforms show different sorting pattern in neurogenesis. As one example, TM5NM1/2 is present in developing axons, but it is replaced by TMBr-3 in mature neurons, suggesting that these tropomyosin isoforms contribute differently to the establishment of the functional features of the neuronal actin networks. We developed a method for the efficient purification of TMBr-3 and TM5NM1 as recombinant proteins using bacterial expression system and investigated their interactions with actin. We found that both isoforms bind actin filaments, however, the binding of TM5NM1 was much stronger than that of TMBr-3. TMBr-3 and TM5NM1 modestly affected actin assembly kinetics, in an opposite manner. Consistently with the higher affinity of TM5NM1 it inhibited actin filament disassembly more efficiently than TMBr-3. Similarly to other previously studied tropomyosins TM5NM1 inhibited the Arp2/3 complex-mediated actin assembly. Notably, TMBr-3 did not influence the Arp2/3 complex-mediated polymerization. This is a unique feature of TMBr-3, since so far it is the only known tropomyosin supporting the activity of the Arp2/3 complex, indicating that TMBr-3 may colocalize and work simultaneously with Arp2/3 complex in neuronal cells

Nursery location and potassium enrichment in Aleppo pine stock 1. Effect on nursery culture, growth, allometry and seedling quality

There is a need for a better understanding of the primary role of macronutrients in Aleppo pine stock quality and for producing larger nutrient-loaded stock, which may be challenging for inland nurseries. The influence of nursery location and fertilization on nursery culture, growth, allometry and seedling quality of Aleppo pine was studied in seedlings cultivated over the 2006 growing year. Fertilization treatments considered how a K enrichment performed over common programs currently being practiced and divided into three levels of K/N ratio: 0.63-0.89 (normal), 1.81-1.89 (high), and 2.25-2.53 (very high). Results showed that fertilization had a minor effect on seedling growth and allometry in comparison with location, which was the governing factor. However, fertilizing treatments significantly affected final seedling attributes, which has its origin on the early treatment differences that were kept up to the end of culture. Higher nutrient supply treatments produced the highest nutrient concentration in seedlings but they were associated with lower fertilization efficiencies. Fertilizer efficiency was approximately twofold in the coastal nursery for the three macronutrients, although concentration was higher in the inland nursery due to lower seedling growth. It is concluded that warmer regions are more suitable for producing large stock more efficiently. © Institute of Chartered Foresters, 2011. All rights reserved.This work was supported by the projects 'Improvement of reforestation in the province of Valencia through the definition of seedling quality standards' (20020995) and 'Establishment of protocols for seedling quality testing in nursery and field' (20080682), directed by the Polytechnic University of Valencia and the Valencian Regional Government (Generalitat Valenciana).Campo García, ADD.; Hermoso De Mena, J.; Ceacero, CJ.; Navarro Cerrillo, RM. (2011). Nursery location and potassium enrichment in Aleppo pine stock 1. Effect on nursery culture, growth, allometry and seedling quality. Forestry. 84(3):221-233. https://doi.org/10.1093/forestry/cpr008S22123384

Identification of Anaplasma marginale Type IV Secretion System Effector Proteins

Anaplasma marginale, an obligate intracellular alphaproteobacterium in the order Rickettsiales, is a tick-borne pathogen and the leading cause of anaplasmosis in cattle worldwide. Complete genome sequencing of A. marginale revealed that it has a type IV secretion system (T4SS). The T4SS is one of seven known types of secretion systems utilized by bacteria, with the type III and IV secretion systems particularly prevalent among pathogenic Gram-negative bacteria. The T4SS is predicted to play an important role in the invasion and pathogenesis of A. marginale by translocating effector proteins across its membrane into eukaryotic target cells. However, T4SS effector proteins have not been identified and tested in the laboratory until now.Published copyLockwood, S., D. E. Voth, K. A. Brayton, P. A. Beare, W. C. Brown, R. A. Heinzen, and S. L. Broschat, Identification of Anaplasma marginale type IV secretion system effector proteins, PLoS ONE, Vol. 6, No. 11, e7724, Nov. 2011. DOI: 10.1371/journal.pone.0027724

What Kind of Seed Dormancy Might Palms Have?

Palm diaspores are reported to have various kinds of dormancy. However, (1) the embryo is underdeveloped; (2) the endocarp is water permeable; and (3) the diaspores take a long time to germinate. Thus, we conclude that the diaspores of the majority of palm species have morphophysiological dormancy (MPD). The ones that do not have MPD are morphologically dormant

Physical Fruit Traits in Moroccan Almond Seedlings: Quality Aspects and Post-Harvest Uses

The physical traits of local almond populations from Morocco were studied to characterize their genetic resources and to evaluate the possibility of their commercial valorization. Nut weight ranged between 1.15 and 7.39 g, and kernel weight between 0.54 and 1.85 g, but most accessions were characterized by small kernels, pronounced wrinkles, and double kernels. Although the physical quality of the kernels of these populations was low, they show the possibility of some specialized uses, which could improve their marketable value. The genotypes with favorable values could be incorporated into an almond breeding program as parents to increase the kernel quality.Publishe