COMPAM :visualization of combining pairwise alignments for multiple genomes

COMPAM is a tool for visualizing relationships among multiple whole genomes by combining all pairwise genome alignments. It displays shared conserved regions (blocks) and where these blocks occur (edges) as block relation graphs which can be explored interactively. An unannotated genome, e.g. can then be explored using information from well-annotated genomes, COG-based genome annotation and genes. COMPAM can run either as a stand-alone application or through an applet that is provided as service to PLATCOM, a toolset for whole genome comparative analysis, where a wide variety of genomes can be easily selected. Features provided by COMPAM include the ability to export genome relationship information into file formats that can be used by other existing tools. AVAILABILITY: http://bio.informatics.indiana.edu/projects/compam/     

Inferring functional information from domain co-evolution

MOTIVATION: Co-evolution is a powerful mechanism for understanding protein function. Prior work in this area has shown that co-evolving proteins are more likely to share the same function than those that do not because of functional constraints. Many of the efforts founded on this observation, however, are at the level of entire sequences, implicitly assuming that the complete protein sequence follows a single evolutionary trajectory. Since it is well known that a domain can exist in various contexts, this assumption is not valid for numerous multi-domain proteins. Motivated by these observations, we introduce a novel technique called Coevolutionary-Matrix that captures co-evolution between regions of two proteins. Instead of using existing domain information, the method exploits residue-level conservation to identify co-evolving regions that might correspond to domains. RESULTS: We show that the Coevolutionary-Matrix method can detect greater number of known functional associations for the Escherichia coli proteins when compared with earlier implementations of phylogenetic profiles. Furthermore, co-evolving regions of proteins detected by our method enable us to make hypotheses about their specific functions, many of which are supported by existing biochemical studies.     

Sex determination using the scapula in medieval skeletons from East Anatolia

Sex determination from skeletal human remains by discriminant function analysis is one of the methods utilized in the forensic and osteoarcheological sciences. The purpose of the present study is to establish metric standards for sex determination for medieval Anatolian populations using scapular measurements. The database for this research consisted of 93 adult skeletal remains (47 males and 46 females) from the Dilkaya medieval collection. Four measurements were taken: maximum scapular height, maximum scapular breadth, glenoid cavity height, glenoid cavity breadth, and subjected to discriminant function analysis. All measurements demonstrated some degree of sexual dimorphism, with the highest accuracy of sex determination (94.8%) obtained using maximum scapular breadth. Overall accuracies of the functions ranged from 82.9% to 95.0%, with a higher accuracy rate obtained for female skeletons than for males. Population specific discriminant formulas were developed using combinations of measurements, which can be used in ancient Anatolian populations.     

Use of natural dye-casein complexes: effect of proteolytic treatment

The activity of proteolytic enzymes is commonly measured using casein as a substrate. A modified caseinolysis assay was developed with natural dyes such as juglone, lawsone, berberine, and quercetin for Subtilisin carlsberg, protease type XVI, and trypsin, respectively. The pH dependence and incubation time were determined. K(m), V(max), and k(cat)/K(m) values were also determined for these enzymes. Lawsone was found to be a better substrate than the others.     

Influence of citric acid amendments on the availability of weathered PCBs to plant and earthworm species

A series of small and large pot trials were conducted to assess the phytoextraction potential of several plant species for weathered polychlorinated biphenyls (PCBs) in soil (105 microg/g Arochlor 1268). In addition, the effect of citric acid on PCB bioavailability to both plants and earthworms was assessed. Under small pot conditions (one plant, 400 g soil), three cucurbits (Cucurbita pepo ssp pepo [zucchini] and ssp ovifera [nonzucchini summer squash], Cucumis sativus, cucumber) accumulated up to 270 microg PCB/g in the roots and 14 microg/g in the stems, resulting in 0.10% contaminant removal from soil. Periodic 1 mM subsurface amendments of citric acid increased the stem and leaf PCB concentration by 330 and 600%, respectively, and resulted in up to a 65% increase in the total amount of contaminant removed from soil. Although citric acid at 10 mM more than doubled the amount of PCB desorbed in abiotic batch slurries, contaminant accumulation by two earthworm species (Eisenia foetida and Lumbricus terrestris) was unaffected by citric acid at 1 and 10 mM and ranged from 11-15 microg/g. Two large pot trials were conducted in which cucurbits (C. pepo ssp pepo and ssp ovifera, C. sativus) and white lupin (Lupinus albus) were grown in 70 kg of PCB-contaminated soil White lupin was the poorest accumulator of PCBs, with approximately 20 microg/g in the roots and 1 microg/g in the stems. Both C. pepo ssp ovifera (summer squash) and C. sativus (cucumber) accumulated approximately 65-100 microg/g in the roots and 6-10 microg/g in the stems. C. pepo ssp pepo (zucchini) accumulated significantly greater levels of PCB than all other species, with 430 microg/g in the roots and 22 microg/g in the stems. The mechanism by which C. pepo spp pepo extracts and translocates weathered PCBs is unknown, but confirms earlier findings on the phytoextraction of other weathered persistent organic pollutants such as chlordane, p,p'-DDE, and polycyclic aromatic hydrocarbons.     

CAPS-microsatellites: use of CAPS method to convert non-polymorphic microsatellites into useful markers

Microsatellites found in expressed sequence tags (ESTs) have several advantages in comparison to conventional microsatellites developed from genomic DNA. Advantages of EST-microsatellites include better transferability between the species and lower development cost of primer pairs. However, in many cases the amplified products of genomic DNA are larger than their expected sizes based on ESTs and these markers have low level of polymorphism. In the present study we report on a new approach as a modest modification of the cleavage amplified polymorphic sequence (CAPS) called CAPS-microsatellites. Using a total of 20 EST-microsatellite primer pairs on four Capsicum species and two Gossypium species we observed that all 20 monomorphic EST-microsatellites could be converted into polymorphic markers among the species used. Further analyses using a total of 37 F₂ individuals obtained from two Capsicum annuum L. lines indicated that CAPS-microsatellite markers usually segregated as co-dominant fashions, discriminating the homozygous from heterozygous genotypes and could be used in genetic analyses of plant species.     

TAP1 and TAP2 gene polymorphisms in childhood cystic echinococcosis

The incidence of cystic echinococcosis (CE) due to Echinococcus granulosus is as high as 2000–2500 patients per year in Turkey. Whether genetic characteristics of the Turkish population cause a tendency to the disease is currently unknown. We aimed at studying the role of TAP gene polymorphisms in Turkish children with cystic echinococcosis. For an overview of allelic distribution of TAP1 and TAP2 genes, genotypes of 85 patients with CE and 100 controls were studied. To determine the genotype–phenotype correlation, 81 of the patients whose clinical data were available were analyzed. For TAP1-637, Asp/Gly heterozygosity was significantly more prevalent in CE patients than in controls (20 vs. 4%, odds ratio 6.0), while Gly/Gly homozygosity was less frequent (5 vs. 14%). For TAP2-379, Ile/Val heterozygosity was significantly more prevalent in CE patients than in controls (14 vs. 1%, odds ratio 16.27), while Ile/Ile homozygosity was less frequent (13 vs. 25%). TAP1-637 and TAP2-379 polymorphisms may have a role in causing genetic tendency for CE in children. The data may reflect the genetic properties of the Turkish population or may reveal the minor role of TAP gene polymorphisms in CE.     

Effects of Extremely Low-Frequency Magnetic Field on Caspase Activities and Oxidative Stress Values in Rat Brain

This study was aimed to investigate the effect of extremely low-frequency magnetic field (ELF-MF) on apoptosis and oxidative stress values in the brain of rat. Rats were exposed to 100 and 500 µT ELF-MF, which are the safety standards of public and occupational exposure for 2 h/day for 10 months. Brain tissues were immunohistochemically stained for the active (cleaved) caspase-3 in order to measure the apoptotic index by a semi-quantitative scoring system. In addition, the levels of catalase (CAT), malondialdehyde (MDA), myeloperoxidase (MPO), total antioxidative capacity (TAC), total oxidant status (TOS), and oxidative stress index (OSI) were measured in rat brain. Final score of apoptosis and MPO activity were not significantly different between the groups. CAT activity decreased in both exposure groups (p?<?0.05), while TAC was found to be lower in ELF 500 group than those in ELF-100 and sham groups (p?<?0.05). MDA, TOS, and OSI values were found to be higher in ELF-500 group than those in ELF-100 and sham groups (p?<?0.05). In conclusion, apoptosis was not changed by long-term ELF-MF exposure, while both 100 and 500 µT ELF-MF exposure induced toxic effect in the rat brain by increasing oxidative stress and diminishing antioxidant defense system.     

Effect of Endemic Fluorosis on Hematological Parameters

Although so many studies exist on effect of fluoride on hematological parameters in experimental animals, a few studies have been conducted to investigate the effects of chronic fluorosis on hematological parameters in humans’ subjects with endemic fluorosis. So we aimed to determine the hematological parameters in patients with endemic fluorosis. The study group consisted of 60 patients with endemic fluorosis (27 females, 33 males, and mean age 33.4?±?9.6 years). An age-, gender-, and body mass index-matched control group was composed of 34 healthy volunteers (11 females, 23 males with a mean age 32.6?±?5.6 years). Urine fluoride levels of fluorosis patients were significantly higher than control subjects as expected (0.42?±?0.09 vs 1.92?±?0.14 mg/l, respectively; P?<?0.001). There were no statistically significant differences between the fluorosis group and control group with respect to hematological parameters (complete blood count and ferritin). We concluded that chronic fluorosis has no effect on hematological parameters in patients with endemic fluorosis.     

Advanced Age, Female Gender and Delay in Pacemaker Implantation May Cause TdP in Patients With Complete Atrioventricular Block

Aim

We aimed to report the clinical features related to torsades de pointes (TdP) in patients with complete AV block (CAVB).

Methods

Patients with CAVB who were admitted to our instituition between January 2007 and January 2010 were retrospectively evaluated in terms of the occurence of TdP. The clinical features were compared in patients with and without TdP using the software of SPSS.

Results

Sixty-four patients were determined to have CAVB. Three of them had documented episodes of TdP. All three patients experiencing TdP were females, whereas 48% of the patients with CAVB were females. The mean age of patients with TdP was significantly greater than the mean age of the other patients (85 ±3 vs. 78±7.6, respectively; p<0.05). In our archives, bradycardia exposure time could be determined in only 49 patients without TdP. Among them, just 10 patients had been exposed to bradycardia over 48 hours, whereas all of the 3 patients with TdP had been exposed to bradycardia over 48 hours (p<0.05). Additionally, in two patients with TdP, we demonstrated that QT and QTc prolongation increases as the duration of bradycardia is extended. Furthermore, all patients with TdP had notched T waves in the ECG on the occurrence day of TdP, whereas they did not have any notched T wave in their ECG on the admission day.

Conclusion

Among the patients with CAVB, elderly females are more susceptible to development of TdP. Delay in institution of physiological heart rate leads to further QT prolongation and thereby to TdP. Besides QT prolongation, the finding of T wave notching on ECG may also have a predictive value for TdP.