Reconstruction of metabolic pathways for the cattle genome

<p>Abstract</p> <p>Background</p> <p>Metabolic reconstruction of microbial, plant and animal genomes is a necessary step toward understanding the evolutionary origins of metabolism and species-specific adaptive traits. The aims of this study were to reconstruct conserved metabolic pathways in the cattle genome and to identify metabolic pathways with missing genes and proteins. The MetaCyc database and PathwayTools software suite were chosen for this work because they are widely used and easy to implement.</p> <p>Results</p> <p>An amalgamated cattle genome database was created using the NCBI and Ensembl cattle genome databases (based on build 3.1) as data sources. PathwayTools was used to create a cattle-specific pathway genome database, which was followed by comprehensive manual curation for the reconstruction of metabolic pathways. The curated database, CattleCyc 1.0, consists of 217 metabolic pathways. A total of 64 mammalian-specific metabolic pathways were modified from the reference pathways in MetaCyc, and two pathways previously identified but missing from MetaCyc were added. Comparative analysis of metabolic pathways revealed the absence of mammalian genes for 22 metabolic enzymes whose activity was reported in the literature. We also identified six human metabolic protein-coding genes for which the cattle ortholog is missing from the sequence assembly.</p> <p>Conclusion</p> <p>CattleCyc is a powerful tool for understanding the biology of ruminants and other cetartiodactyl species. In addition, the approach used to develop CattleCyc provides a framework for the metabolic reconstruction of other newly sequenced mammalian genomes. It is clear that metabolic pathway analysis strongly reflects the quality of the underlying genome annotations. Thus, having well-annotated genomes from many mammalian species hosted in BioCyc will facilitate the comparative analysis of metabolic pathways among different species and a systems approach to comparative physiology.</p

Recurrence characteristics in European patients with ocular toxoplasmosis

BACKGROUND: The risk of function loss after each episode of ocular toxoplasmosis (OT) supports efforts to improve our understanding of the disease. Patients and methods: 139 patients with OT were contacted retrospectively and requested to complete a questionnaire addressing course and activity of their disease. This information was compared with that retrieved from their medical records. Sixty-three patients completed the questionnaire and were included in the study. They were allocated according to their median age to one of two groups (group 1: or=20.9 years). RESULTS: The mean reported age at the time of first ocular manifestation was 23.9 (median 20.9, range 0 to 70.5; SD 12.9) years. The clinical diagnosis was made 3.5 years later (p = 0.0008). The follow-up time was 6.5 (median 5.0; range 0.5 to 49.9; SD 7.6) years. The recurrence rate was higher in patients below 20.9 years (66%; n = 35) than in older patients (39%; n = 28; chi(2) test, p<0.05). Patients reporting only one episode were older at first manifestation (29.6 (median 25.6; range 10.6 to 70.5; SD 14.3) years; n = 29) than those reporting two episodes (17.9 (median 19.5; range 5.9 to 33.9; SD 7.8) years; n = 15 (p<0.05)). The proportion of patients who developed a recurrence was 54-63% after each episode without a tendency to enlarge, and the interval between successive episodes remained stable between 1.0 and 1.7 years for the first three recurrences. CONCLUSION: Younger OT patients carry a higher risk of developing a recurrence than older ones. After each episode, two-thirds of all OT patients will develop another one

[Diagnostics and treatment of ocular toxoplasmosis : Results of a survey].

BACKGROUND Ocular toxoplasmosis (OT) is the most common infectious cause of posterior uveitis. This survey aimed to evaluate the current diagnostic and therapeutic approach to OT in Germany. MATERIAL AND METHODS A detailed questionnaire with specific patient examples was sent in July 2021 to the members of the Uveitis Section of the German Ophthalmological Society (DOG) and the Retinological Society (RG). RESULTS The questionnaire was answered by 53 (29 RG and 24 DOG) ophthalmologists. Of the respondents 16 (30%) work in private practice, 18 (34%) in a clinical facility and 19 (36%) in university hospital, 9 (17%) colleagues see < 50, 28 (53%) 50-200 and 16 (30%) more than 200 uveitis patients per year. The clinical results are still the gold standard (87%) for the diagnosis of OT and in cases of first manifestation 60% are supported by serological antibody investigations, while 10 out of 53 (19%) ophthalmologists rely on the clinical presentation only. An IgM test is requested by 25 (47%) respondents, 6 expected an increase in IgG titer (11%) and 1 the detection of specific IgA antibodies (2%). The majority (n = 28, 53%) of ophthalmologists would aim at confirming the diagnosis by an anterior chamber puncture, from which 20 (38%) prefer PCR, 3 (6%) determination of Goldmann-Witmer coefficients (GW) and 5 (9%) a combination of both methods. Clindamycin was most frequently used for treatment (n = 21, 40%), followed by pyrimethamine/sulfadiazine (n = 17, 32%) and trimethoprime + sulfamethoxazole (TMP/SMX) (n = 10, 19%); the latter was also used (n = 40, 75%) for secondary prophylaxis. CONCLUSION The results show that apart from the clinical results as the gold standard for the diagnosis, there is no uniform approach to diagnosis and treatment of OT. The high request rate for serum IgM antibodies indicates a widespread uncertainty about the importance of serological findings. This should be viewed critically, given the continued high seroprevalence in Germany

Secondary intraocular lenses in eyes with aphakia or dislocated IOL: impact of suture fixation on early and late complications

BACKGROUND: Secondary intraocular lens (IOL) implantation is exposed to an increased risk of complications, including endophthalmitis and retinal detachment. The present analysis compares the outcomes and complications experienced in our own series of patients. PATIENTS AND METHODS: We retrospectively reviewed a consecutive series of secondary posterior chamber IOL implantations performed in a single centre, two surgeon setting over a period of 8 years and with a follow up-time of at least 4 months. RESULTS: Between 1997 and 2005, 75 patients received a sulcus-supported secondary IOL without suture fixation, whereas suture fixation was required in 137 instances. Visual acuity improved in both groups (group 1: from 0.36 +/- 0.39 (0.01-1.2) to 0.73 +/- 0.33 (0.02-1.0; p = 0.18); group 2: from 0.33 +/- 0.34 (0.02-1.0) to 0.46 +/- 0.33 (0.01-1.0; p = 0.006), but more pronounced in eyes not requiring suture fixation (p = 0.012). IOL placement was more likely to be combined with endophacoemulsification in the not suture-fixed IOLs (12.7 vs. 5.3 %). In contrast, retinal tears (10.6 vs. 8.6 %, respectively) and retinal detachment (5.3 vs. 2.2 %, respectively) were equally distributed. In the early postoperative phase, IOP was lower in suture-fixed eyes, which showed a higher incidence of minor intraocular haemorrhages and cystoid macular edema (5.3 vs. 8.0 %); late complications up to 5 years postoperatively were equally distributed. CONCLUSION: A preoperatively less complicated anterior segment situation and a lower incidence of postoperative macular edema may account for a better visual outcome after placement of a sulcus supported IOLs without suturing. If required, suture fixation may be performed without exposing the eye to an increased risk of late postoperative complications