Bioinformatic Mining of Type I Microsatellites from Expressed Sequence Tags of Channel Catfish (<Emphasis Type="Italic">Ictalurus punctatus</Emphasis>)

Gene-derived markers are pivotal to the analysis of genome structure, organization, and evolution and necessary for comparative genomics. However, gene-derived markers are relatively difficult to develop. This project utilized the genomic resources of channel catfish expressed sequence tags (ESTs) to identify simple sequence repeats (SSRs), or microsatellites. It took the advantage of ESTs for the establishment of gene identities, and of microsatellites for the acquisition of high polymorphism. When microsatellites are tagged to genes, the microsatellites can then be used as gene markers. A bioinformatic analysis of 43,033 ESTs identified 4855 ESTs containing microsatellites. Cluster analysis indicated that 1312 of these ESTs fell into 569 contigs, and the remaining 3534 ESTs were singletons. A total of 4103 unique microsatellite-containing genes were identified. The dinucleotide CA/TG and GA/TC pairs were the most abundant microsatellites. AT-rich microsatellite types were predominant among trinucleotide and tetranucleotide microsatellites, consistent with our earlier estimation that the catfish genome is highly AT-rich. Our preliminary results indicated that the majority of the identified microsatellites were polymorphic and, therefore, useful for genetic linkage mapping of catfish. Mapping of these gene-derived markers is under way, which will set the foundation for comparative genome analysis in catfish.     

Meiotic state of bovine oocytes is regulated by interactions between cAMP,cumulus, and granulosa

Bovine oocytes are arrested at the prophase of first meiotic cell cycle. Meiosis resumes in oocytes of pre-ovulatory follicles upon LH surge. However, oocytes from secondary follicles spontaneously resume meiosis in the absence of hormones if removed from the follicle and cultured in vitro. The nature of meiotic arrestor in bovine follicles is poorly understood. In this study we investigated the role of cell-cell interactions between granulosa and cumulus cells and the oocyte in mediating maintenance of meiotic arrest by cAMP. We sorted oocytes as granulosa-cumulus oocyte complexes (GCOC) if surrounded with cumulus cells attached to a large granulosa investment or cumulus oocytes complexes (COC) if surrounded with cumulus cells only and investigated the role cAMP in maintenance of meiotic arrest in these oocytes under various conditions. In hormone- and serum-free medium both GCOC and COC enclosed oocytes resumed meiosis. When [cAMP](i) was elevated with addition of invasive adenylate cyclase (iAC) GCOC enclosed oocytes were maintained in the prophase with intact germinal vesicle (GV) while COC enclosed oocytes underwent GV breakdown (GVBD). iAC elevated [cAMP](i) in both types of oocytes to the same level. If oocytes were liberated from the cumulus and granulosa cells, they re-initiated meiosis in serum and hormone free medium, but remained in the GV stage if iAC was added to the medium. Untreated GCOC and COC enclosed oocytes extruded first polar body at the same frequency in hormone-supplemented media. GCOC and COC enclosed oocytes but not denuded oocytes (DO) cultured without somatic cells acquired developmental competence if cultured in hormone-containing medium. It is concluded that maintenance of meiotic arrest is regulated by the interplay of [cAMP](i), and cumulus and granulosa cells.     

Flavonoid glycosides from Centaurea pseudoscabiosa subsp. pseudoscabiosa from Turkey

Three flavonoid glycosides were isolated and characterized, together with a further 13 substances belonging to various classes of compounds, in particular two phenolic acids, a coumarin, a sugar and nine flavonoids from the flowered aerial parts of Centaurea pseudoscabiosa subsp. pseudoscabiosa Boiss. et Buhse (Asteraceae). Some considerations about their evolutionary meaning are provided.     

Benzofurans and another constituent from seeds of Styrax officinalis

The benzofuran constituents of the seeds of Styrax officinalis were investigated. From the hexane extract, two new constituents named 5-(3"benzoyloxypropyl)-7-methoxy-2-(3',4'-methylenedioxyphenyl)-benzofuran (5) and 4-[3"-(1c-methylbutanoyloxy)propyl]-2-methoxy-(3',4'-methylenedioxyphenyl)-1a, 5b-dihydrobenzo-[3,4]-cyclobutaoxirene (6) were isolated together with four known compounds, 5-[3"-(1c-methylbutanoyloxy)propyl]-7-methoxy-2-(3',4'-dimethoxyphenyl)-benzofuran (4), 5-[3"-(1c-methylbutanoyloxy)propyl]-7- methoxy-2-(3',4'-methylenedioxyphenyl)-benzofuran (3), 5-(3"-acetoxypropyl)-7-methoxy2-(3',4'-methylenedioxphenyl)-benzofuran (2) and 5-(3"-hydroxypropyl)-7-methoxy-2-(3',4'-met hylenedioxyphenyl)-benzofuran (1). Although the compounds 1, 2, and 3 have been isolated previously from the seeds of Styrax obassia, this is the first record of their isolation from seeds of Styrax officinalis. The structures of the isolated compounds were established by 1D- and 2D-NMR (HMBC, HMQC, COSY), FABMS and high-resolution ESI FTMS.     

Analysis of essential oil of Coridothymus capitatus (L.) and its antibacterial and antifungal activity

The water-distilled essential oil the leaves of Coridothymus capitatus were analyzed by GC/MS and also analyzed by direct thermal desorption GC/MS. Comparison was made between two analyses techniques. The essential oil consisted mainly of monoterpenes 98.9%, while oxygenated hydrocarbons were identified as 55.6 % and non-oxygenated hydrocarbons as 43.6%. As major components were found carvacrol (35.6%), p-cymene (21.0%), thymol (18.6%), gamma-terpinene (12.3%), alpha-terpinene (3.2%), beta-myrcene (3.0%) and alpha-thujene (1.3%) by hydrodistillation and by the GC/MS method. The direct thermal desorption GC/MS analysis also showed the same major components, namely carvacrol (51.6%), thymol (21.7%), p-cymene (9.7%) gamma-terpinene (8.2%), alpha-terpinene (1.64%). The essential oil of C. capitatus showed strong activity against S. aureus, P. vulgaris, P. aeruginosa, E. coli, K. pneumonia, B.     

Investigation of C5a receptor gene 450 C/T polymorphism in Turkish patients with familial Mediterranean fever

Familial Mediterranean fever (FMF) is a genetic disorder with acute inflammatory serosal attacks due to MEFV gene mutations which resides in chromosome 16. Lack of a C5a inhibitor activity in the peritoneum has previously been proposed in part to contribute in propagation of the serosal inflammation in FMF attacks. The aim of this study is to investigate C5a receptor (C5aR) gene polymorphism in patients with FMF and its relation to the main features of the disease. A polymorphism in the coding region of C5aR gene leading to C to T transition at nucleotide position 450 has been investigated in 85 non-related Turkish FMF patients and 160 non-related healthy controls by using PCR-RFLP. The frequencies of C5aR gene 450 CT genotype and T allele were not significantly different between Turkish FMF patients and healthy subjects (14.12 and 8.24% for FMF vs. 10 and 5% for controls, respectively). C5aR gene 450 CT genotype tended to associate with the presence Henoch-Schonlein purpura (OR: 1.25, 95% CI: 0.917–1.704, P = 0.017) but with no other clinical findings of the disease. C5aR polymorphism might be searched in populations having high prevalence of FMF.     

Ordovician chitinozoans and acritarchs from southern and southeastern Turkey

Revision of the lithostratigraphy of Ordovician deposits in southern and southeastern Turkey led to a re-evaluation of the age assignments of formations identified in the subsurface and at outcrop. Previous datings were based on macrofauna (mainly trilobites and graptolites). The present paper focuses exclusively on organic-walled microfossils (chitinozoans and acritarchs), which provide numerous chronostratigraphical improvements, especially in successions barren or poor in macrofossils. Close to 200 samples were collected in the Taurus chain (i.e. from Kemer, Seydisehir, Ovacik, Kozan, to Sariz regions in southern Turkey) and in the Border Folds (Mardin and Hakkari regions), usually regarded as part of the Arabian Plate in palaeogeographical reconstructions. Many samples are productive and yield chitinozoans and/or acritarchs of extremely variable preservation, depending on their geographical and geological location. In the Taurus chain, the material is “coalified” and frequently fragmented whereas, in the Border Folds, maturation of the organic matter is much lower and preservation of the microfossils is good to excellent. Several Ordovician chitinozoan biozones (northern Gondwana zonation) as well as diagnostic acritarch assemblages are identified in southern and southeastern Turkey. These Ordovician formations are assigned here to the new global stages of the Ordovician chronostratigraphical scale. The Seydisehir (upper part), Sobova, and Kilgen Lake (lower part) formations are referred to the Darriwilian. The Kilgen Lake (upper part), Sort Tepe, and Bedinan formations are attributed to the Sandbian and to the Katian, and the Halevikdere Formation (glacio-marine part) is assigned to the Hirnantian. Reworking of Early Ordovician acritarchs is documented in pre-glacial and in glacial Late Ordovician deposits. They indicate that active erosive processes occurred during the Middle and Late Ordovician sedimentation. The organic-walled microfossils recorded in the Ordovician of south and southeastern Turkey belong to the northern Gondwana realm. Interestingly however, some Baltoscandian influences are noted in the Border Folds during Early Late Ordovician.