The interaction of covalently bound heme with the cytochrome c maturation protein CcmE

The heme chaperone CcmE is a novel protein that binds heme covalently via a histidine residue as part of its essential function in the process of cytochrome c biogenesis in many bacteria as well as plant mitochondria. In the continued absence of a structure of the holoform of CcmE, identification of the heme ligands is an important step in understanding the molecular function of this protein and the role of covalent heme binding to CcmE during the maturation of c-type cytochromes. In this work, we present spectroscopic data that provide insight into the ligation of the heme iron in the soluble domain of CcmE from Escherichia coli. Resonance Raman spectra demonstrated that one of the heme axial ligands is a histidine residue and that the other is likely to be Tyr134. In addition, the properties of the heme resonances of the holo-protein as compared with those of a form of CcmE with non-covalently bound heme provide evidence for the modification of one of the heme vinyl side chains by the protein, most likely the 2-vinyl group.     

Sexual reproduction of the reef-building coral Diploria labyrinthiformis (Scleractinia: Faviidae), in the Colombian Caribbean

Sexual reproduction of the coral Diploria labyrinthiformis was studied for the first time. Monthly histological analyses at the Corales del Rosario National Park (Colombian Caribbean) from May 1997 to April 1998 show that D. labyrinthiformis is a hermaphroditic broadcasting species. It presents an annual gametogenic cycle with a 10-11 month period for gonad investment, in which oogenesis begins in August and ends in May-June. Spermiogenesis is short because sperm cysts were only observed in May tissue samples. In histological collected in May, an average of four mature eggs and six spermatic cysts per fertile mesentery were found. The mean diameter of mature eggs was 297 microm (+/- 97 SD) and 90 microm (+/- 33) for spermatic cysts. Rapid maturation of eggs from stage II to stage III coincides with increases in air temperature, high number of solar hours per month, decreases in wind velocity and absence of rainfall. Reproductive effort for D. labyrinthiformis (14.07 mm3/cm2/year) was similar to other Faviidae species. Although gamete release was not observed in the field, the absence of gonads in histological samples in June suggests spawning between May 25 (five days after full moon) and June 24. This event coincides with high air temperature, low number of solar hours per month, low wind velocity, and initiation of the rainy season. The earlier spawning time of this species differs from other species of the same family known for the Caribbean region.     

Local homology recognition and distance measures in linear time using compressed amino acid alphabets

Methods for discovery of local similarities and estimation of evolutionary distance by identifying k-mers (contiguous subsequences of length k) common to two sequences are described. Given unaligned sequences of length L, these methods have O(L) time complexity. The ability of compressed amino acid alphabets to extend these techniques to distantly related proteins was investigated. The performance of these algorithms was evaluated for different alphabets and choices of k using a test set of 1848 pairs of structurally alignable sequences selected from the FSSP database. Distance measures derived from k-mer counting were found to correlate well with percentage identity derived from sequence alignments. Compressed alphabets were seen to improve performance in local similarity discovery, but no evidence was found of improvements when applied to distance estimates. The performance of our local similarity discovery method was compared with the fast Fourier transform (FFT) used in MAFFT, which has O(L log L) time complexity. The method for achieving comparable coverage to FFT is revealed here, and is more than an order of magnitude faster. We suggest using k-mer distance for fast, approximate phylogenetic tree construction, and show that a speed improvement of more than three orders of magnitude can be achieved relative to standard distance methods, which require alignments.     

Antigenic secreted proteins from Haemophilus paragallinarum. A 110-kDa putative RTX protein

Haemophilus paragallinarum is the causal agent of infectious coryza, an economically important disease for the poultry industry. This bacterium secreted proteins of 25-110 kDa during its growth in brain heart infusion, tryptic soy broth, or Luria-Bertani glucose phosphate media, all lacking serum. Some of these proteins were recognized by sera from chickens experimentally infected with H. paragallinarum. A 110-kDa protein was recognized by a serum pool from convalescent-phase pigs naturally infected with Actinobacillus pleuropneumoniae, and also by a rabbit polyclonal serum against Apx I as well as a rabbit serum against Mannheimia haemolytica leukotoxin, suggesting the presence of an RTX-like protein in H. paragallinarum. H. paragallinarum secreted proteins could be important immunogens in the control of infectious coryza.     

Discovery and in vitro evaluation of potent kinase inhibitors: Pyrido[1',2':1,5]pyrazolo[3,4-d]pyrimidines

The discovery, synthesis, potential binding mode, and in vitro kinase profile of several pyrido[1',2':1,5]pyrazolo[3,4-d]pyrimidines as potent kinase inhibitors are discussed.     

Alteration of the sialylation pattern of the murine tooth germ after ethanol exposure

BACKGROUND: Ethanol consumption during pregnancy leads to changes in murine dental morphogenesis, dental size, cellular differentiation, enamel mineralization, and delayed eruption. It has been proposed that glycoproteins play a role during embryonic dental development that may determine the dental morphological pattern and extracellular matrix secretion. O-glycosylation and sialylation appear to actively participate in the differentiation and maturation processes. Because glycosylation may be affected by teratogens that can alter the maturation of several organisms, in this work we describe the main modifications of the sialylation pattern in prenatal day (PD) 18.5 murine tooth germs exposed to ethanol. METHODS: Pregnant female mice were divided into groups that were given 15% or 20% ethanol solutions, or water as a control. The histochemistry of tooth germs from PD 18.5 fetuses was revealed with lectins specific for sialic acid (Neu5Ac), such as Sambucus nigra (SNA), Maackia amurensis (MAA), and Machrobrachium rosenbergii (MRL), and for sialylated-O-glycosidically linked glycans, such as Amaranthus leucocarpus (ALL). RESULTS: The basement membrane, preameloblasts, inner-enamel epithelium, preodontoblasts, and subodontoblastic cells of the test groups showed changes in labeling according to the 4 lectins used. Intranuclear staining was observed with SNA (specific for Neu5Acalpha2,6Gal/GalNAc) in the control group, but this was reduced in the test groups. The nuclei of dental papillary cells under the experimental conditions were stained with MAA (Neu5Acalpha2,3Gal). CONCLUSIONS: Dental development involves different types of sialylated O-glycosidically linked glycans that are likely to regulate cell-to-cell and cell-to-matrix interactions. Our results suggest that ethanol consumption during pregnancy alters the sialylation pattern during murine dental morphogenesis.     

Die experimentelle Beeinflussung des Puffmusters von Riesenchromosomen

By treating larvae and prepupae of Ch. thummi with 2 mg/ml oxytetracycline (OTC) about 30 puffs not present in normal development are induced in the salivary gland chromosomes. Already existing puffs become enlarged (cf. Fig. 4). A considerable number of induced puffs appeared in heterozygous condition (cf. Fig. 1a-c). The species Ch. strenzkei does not react in any way to the same treatment. Other inhibitors of protein synthesis such as cycloheximide and chloramphenicole do not influence the puffing pattern in both species. — Animals which had been treated with OTC for 2 hrs show the first signs of puffing. Fully developed OTC-induced puffs are detectable 20 hrs after treatment. At this time the Balbiani rings and the nucleolus are mostly regressed. — Both the induced puffing pattern and the number of heterozygous puffs depend on the genetic constitution of the animals. Animals derived from different locations can be shown to possess different specific spectra of induced puffs. The induced puffing pattern of animals bred from single egg masses is reduced, and heterozygous puffs are rare or absent. — OTC-induced puffs show a strong uptake of tritiated uridine (cf. Fig. 2). Heterozygous puffs are labelled only in the puffed half of the band (cf. Fig. 3).