Multipoint estimation of identity-by-descent probabilities at arbitrary positions among marker loci on general pedigrees

OBJECTIVES: To describe, implement, and test an efficient algorithm to obtain multipoint identity-by-descent (IBD) probabilities at arbitrary positions among marker loci for general pedigrees. Unlike existing programs, our algorithm can analyze data sets with large numbers of people and markers. The algorithm has been implemented in the SimWalk2 computer package. METHODS: Using a rigorous testing regimen containing five pedigrees of various sizes with realistic marker data, we compared several widely used IBD computation programs: Allegro, Aspex, GeneHunter, MapMaker/Sibs, Mendel, Sage, SimWalk2, and Solar. RESULTS: The testing revealed a few discrepancies, particularly on consanguineous pedigrees, but overall excellent results in the deterministic multipoint packages. SimWalk2 was also found to be in good agreement with the deterministic multipoint programs, usually matching to two decimal places the kinship coefficient that ranges from 0 to 1. However, the packages based on single-point IBD estimation, while consistent with each other, often showed poor results, disagreeing with the multipoint kinship results by as much as 0.5. CONCLUSIONS: Our testing has clearly shown that multipoint IBD estimation is much better than single-point estimation. In addition, our testing has validated our algorithm for estimating IBD probabilities at arbitrary positions on general pedigrees.     

Three-dimensional finite element analysis of the composite and compomer onlays in primary molars

Resin onlay restoration is an esthetic alternative technique used for restoring extensively damaged primary molars. Understanding the behavior of materials under repeated functional stress and how the stress is transmitted to the remaining tooth structure is important. The aim of this study was to compare stresses in primary molars restored with indirect composite and compomer onlay. 3D frame models of the right mandibular and maxillary primary molars and the alveolar bone were created using computerized tomography images of a six-year-old girl. The enamel and dentine layers above the cement layer were unified to generate onlay restoration, and composite and compomer were used as restorative materials. The vertical occlusal load (100?N) was applied to the teeth in the occlusal contact areas. The von Mises stress distributions and normal stress distributions of the y-axis (parallel to the long axis of tooth) were evaluated. The occlusal stress is transmitted to the cervical part of healthy teeth by spreading it through the enamel layer. The composite and compomer restorative materials exhibited similar stress distribution patterns. An indirect technique creates a structure similar to the original morphological form, and it allows restorations to distribute high occlusal stresses and to minimize possible breakages.     

Microstructural changes of basal ganglia in migraine with restless legs syndrome: findings from a neuroimaging study

Sleep and Biological Rhythms - In this study, it is planned to investigate the integrity of the basal ganglia structures in migraineurs with restless legs syndrome (RLS) to explore this...     

Association between osteoporosis and polymorphisms of the bone Gla protein, estrogen receptor 1, collagen 1-A1 and calcitonin receptor genes in Turkish postmenopausal women

In this study, we have investigated the association between osteoporosis and osteocalcin (BGLAP) − 298 C>T, estrogen receptor 1 (ER1) 397 T>C, collagen type1 alpha 1 (Col1A1) 2046 G>T and calcitonin receptor (CALCR) 1340 T>C polymorphisms. Genomic DNA was obtained from 266 persons (158 osteoporotic and 108 healthy controls). Genomic DNA was extracted from EDTA-preserved peripheral venous blood of patients and controls by a salting-out method and analyzed by PCR-RFLP. As a result, there was no statistically significant difference in the genotype and allele frequencies of patients and controls for BGLAP − 298 C>T, Col1A1 2046 G>T, ER1 397 T>C and CALCR 1340 T>C polymorphisms. However, ER1 CC genotype compared with TT + TC genotypes was found to increase the two fold the risk of osteoporosis [p = 0.039, OR = 2.156, 95% CI (1.083–4.293)] and CALCR CC genotype compared with TT + TC genotypes was found to have protective effect against osteoporosis [p = 0.045, OR = 0.471, 95% CI (0.237–0.9372)]. In the combined genotype analysis, ER1/CALCR TCCC combined genotype was estimated to have protective effect against osteoporosis [p = 0.0125, OR = 0.323, 95% CI (0.1383–0.755)] whereas BGLAP/Col1A1 CCTT and ER1/CALCR CCTT combined genotypes were estimated as risk factors for osteoporosis in Turkish population (p = 0.027, p = 0.009 respectively).     

Evaluation of an automated system for the detection of carbapenem resistant Acinetobacter baumannii and assessment of metallo-β-lactamase production using two different phenotyping methods

We tested 200 clinical Acinetobacter baumannii isolates against imipenem and meropenem using the methods of broth microdilution, disk diffusion, agar dilution, MicroScan/WalkAway automated system. Very major errors were mostly obtained between MicroScan/WA system and disk diffusion test. MicroScan/WA system generated unacceptable errors. Combined disk and modified Hodge tests used for detection of metallo-β-lactamase production were practical and useful.     

Reduction in co-trimoxazole resistance inEscherichia coli isolates from urinary tract infections between 1995 and 2005: a multicenter study in Ankara, Turkey

Co-trimoxazole resistance inEscherichia coli isolates from urinary tract infections (UTI) was assessed in 382 strains from 1995 and 510 strains from 2005. The strains were collected from five microbiology laboratories in Ankara, Turkey. Documentation on patient gender, age and outpatient/inpatient status was collected in 2005, but not in 1995. The resistance percentages were 751% in 1995 and 55.5% in 2005. This reduction in resistance percentage was statistically significant, overall in all except two of the participating laboratories. The resistance percentage in 2005 was 61.1% for children (n=208) and 51.2% for adults (n=258), 53.7% for females (n=380) and 60.8% for males (n=130), and 55.3% for outpatients (n=400) and 56.4% for inpatients (n=110). The reduction in resistance is believed to be a consequence of reduced usage. Although decreased, the level of co-trimoxazole resistance remains high, and continued avoidance of its use for empiric treatment of UTI in Turkey appears to be an appropriate strategy.     

Investigation of antibiotic resistance profile and TEM-type β-lactamase gene carriage of ampicillin-resistantEscherichia coli strains isolated from drinking water

Fifty-five ampicillin-resistant (Amp^r)Escherichia coli strains were isolated from 51 drinking water points in Rize region containing abundant fresh water sources in Turkey during the years 2000 to 2002 and from January to February 2004. The large number of organisms (nearly 57%) exhibited resistance to three or more antibiotics commonly used in human and veterinary medicine. These strains displayed a multiresistant phenotype. Nearly half of the strains (27%) expressed resistance to ceftazidime, but these strains were not an extended-spectrum β-lactamase-producer according to the results of double-disk synergy test. All isolates were then screened for the carriage of TEM-type β-lactamase gene (bla _TEM) by polymerase chain reaction. TEM-type β-lactamase genes were found in six (11%) isolates. Sequence analysis showed TEM-1 type genes. However, isoelectric focusing analysis did not confirm the production of TEM-1 type β-lactamase except for one strain. Conjugation experiments showed that resistance to ampicillin, tetracycline or trimethoprim/sulfamethoxazole was transferable in six (11%) isolates. Emergence of transferable antibiotic resistance andbla _TEM-1 gene inE. coli strains from public drinking waters possesses a significant public health risk.     

Evaluating the Effect of Three Water Management Techniques on Tomato Crop

The effects of three water management techniques were evaluated on subsurface drip irrigated tomatoes. The three techniques were the intermittent flow (3 pulses), the dual-lateral drip system (two lateral lines per row, at 15 and 25cm below soil surface), and the physical barrier (buried at 30 cm below soil surface). Field experiments were established for two successive seasons. Water movement in soil was monitored using continuously logging capacitance probes up to 60 cm depth. The results showed that the dual lateral technique positively increased the yield up to 50%, water use efficiency up to 54%, while the intermittent application improved some of the quality measures (fruit size, TSS, and Vitamin C), not the quantity of the yield that decreased in one season, and not affected in the other. The physical barrier has no significant effect on any of the important growth measures. The soil water patterns showed that the dual lateral method lead to uniform wetting pattern with depth up to 45 cm, the physical barrier appeared to increase lateral and upward water movement, while the intermittent application kept the wetting pattern at higher moisture level for longer time. The cost analysis showed also that the economic treatments were the dual lateral followed by the intermittent technique, while the physical barrier is not economical. The study recommends researching the effect of the dual lateral method on the root growth and performance. The intermittent application may be recommended to improve tomato quality but not quantity. The physical barrier is not recommended unless in high permeable soils.     

Domoic acid production by Pseudo-nitzschia calliantha Lundholm, Moestrup et Hasle (bacillariophyta) isolated from the Black Sea

A species of Pseudo-nitzschia isolated from Sevastopol Bay, Black Sea, was examined for its toxicity. The species was identified as P. calliantha Lundholm, Moestrup et Hasle based on SEM and TEM examination. Domoic acid (DA) was detected in batch culture throughout the growth cycle of P. calliantha. The production of DA by this diatom species was confirmed by fluorenylmethoxycarbonyl (FMOC) derivatization and HPLC-fluorescence method. The cellular DA level was higher in the early exponential phase, with the maximum value of 0.95 pg DA cell⁻¹. In the stationary phase, the cellular DA levels declined. This is the first record of a DA producing diatom isolated from the Black Sea.     

Influence of two different green algal diets on specific dynamic action and incorporation of carbon into biochemical fractions in the copepod Acartia tonsa

Previous studies have shown that the two green algae Tetraselmissp. (Prasinophyceae) and Dunaliella tertiolecta (Chlorophyceae)induce high and low egg production rates in Acartia tonsa. Theprimary goal of the present study was to investigate if thisis attributable to differences in the specific dynamic action(SDA) of the two diets. Secondly, we wanted to investigate ifany qualitative differences in the incorporation of nutritionalconstituents from the two diets are influencing SDA. The functionalresponse of ingestion was very different with the two diets.Ingestion of T. impellucida was relatively high even at lowfood concentrations with a maximum of 19 µg C ind^-1 day^-1.The functional response was more clearly sigmoidal on D. tertiolectawith a maximum of 7.3 µg C ind^-1 day^-1. The higher ingestionrate of T. impellucida also induced higher respiration rates.Maximum respiration rates were 3.0 nl O₂ ind^-1 min^-1 on T. impellucidaand 1.5 nl O₂ ind^-1 min^-1 onD. tertiolecta. This created significantlydifferent SDA coefficients: 0.19 on T. impellucida and 0.06on D. tertiolecta, which implies that the magnitude of SDA isstrongly influenced by the composition of the diet. The incorporationof carbon into lipids was significantly higher on D. tertiolecta.However, because of lack of longer chain fatty acids in D. tertiolectathe copepods did not benefit from this. Thus, the proportionof carbon allocated to egg lipids was much lower than when feedingon T. impellucida. Acartia tonsa incorporated relatively morecarbon into proteins when feeding on T. impellucida than onD. tertiolecta. Since protein synthesis is energetically verydemanding this is probably the reason for the higher SDA coefficientin those feeding on T. impellucida.