A new version of the RDP (Ribosomal Database Project)

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.

The RDP (Ribosomal Database Project) continues

The Ribosomal Database Project (RDP-II), previously described by Maidak et al., continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 7.1 (September 17, 1999) included more than 10 700 small subunit rRNA sequences. More than 850 type strain sequences were identified and added to the prokaryotic alignment, bringing the total number of type sequences to 3324 representing 2460 different species. Availability of an RDP-II mirror site in Japan is also near completion. RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/ ). Analysis services include rRNA probe checking, approx-i-mate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment length polymorphism (T-RFLP) experiments.

Informed consent for clinical trials: a comparative study of standard versus simplified forms

BACKGROUND

A high level of reading skill and comprehension is necessary to understand and complete most consent forms that are required for participation in clinical research studies. This study was conducted to test the hypothesis that a simplified consent form would be less intimidating and more easily understood by individuals with low-to-marginal reading skills.

METHODS

During July 1996, 183 adults (53 patients with cancer or another medical condition and 130 apparently healthy participants) were tested for reading ability and then asked to read either the standard Southwestern Oncology Group (SWOG) consent form (16th grade level) or a simplified form (7th grade level) developed at Louisiana State University Medical Center-Shreveport (LSU). Participants were interviewed to assess their attitudes toward and comprehension of the form read. Then they were given the alternate consent form and asked which one they preferred and why.

RESULTS

Overall, participants preferred the LSU form (62%; 95% confidence interval [CI] = 54.8%-69.2%) over the SWOG form (38%; 95% CI = 30.8%-45.2%) (P = .0033). Nearly all participants thought that the LSU form was easier to read (97%; 95% CI = 93.1%-99.9%) than the SWOG form (75%; 95% CI = 65.1%-85.7%) (P<.0001). However, the degree to which the participants understood the forms was essentially the same for the LSU form (58%; 95% CI = 48.6%-67.0%) and the SWOG form (56%; 95% CI = 43.8%-66.8%).

IMPLICATIONS

These findings raise serious questions regarding the adequacy of the design of written informed consent documents for the substantial proportion of Americans with low-to-marginal literacy skills.

Apoptosis is induced in leishmanial cells by a novel protein kinase inhibitor withaferin A and is facilitated by apoptotic topoisomerase I-DNA complex

Protein kinase C (PKC) is an important constituent of the signaling pathways involved in apoptosis. We report here that like staurosporine, withaferin A is a potent inhibitor of PKC. In Leishmania donovani, the inhibition of PKC by withaferin A causes depolarization of DeltaPsim and generates ROS inside cells. Loss of DeltaPsim leads to the release of cytochrome c into the cytosol and subsequently activates caspase-like proteases and oligonucleosomal DNA cleavage. Moreover, in treated cells, oxidative DNA lesions facilitate the stabilization of topoisomerase I-mediated cleavable complexes, which also contribute to DNA fragmentation. However, withaferin A and staurosporine cannot induce cleavable complex formation in vitro with recombinant topoisomerase I nor with nuclear extracts from control cells. Taken together, our results indicate that inhibition of PKC by withaferin A is a central event for the induction of apoptosis and that the stabilization of topoisomerase I-DNA complex is necessary to amplify apoptotic process.

Observation of extremely long spin relaxation times in an organic nanowire spin valve

Organic semiconductors that are pi-conjugated are emerging as an important platform for 'spintronics', which purports to harness the spin degree of freedom of a charge carrier to store, process and/or communicate information. Here, we report the study of an organic nanowire spin valve device, 50 nm in diameter, consisting of a trilayer of ferromagnetic cobalt, an organic, Alq3, and ferromagnetic nickel. The measured spin relaxation time in the organic is found to be exceptionally long-between a few milliseconds and a second-and it is relatively temperature independent up to 100 K. Our experimental observations strongly suggest that the primary spin relaxation mechanism in the organic is the Elliott-Yafet mode, in which the spin relaxes whenever a carrier scatters and its velocity changes.

DNA breaks at fragile sites generate oncogenic RET/PTC rearrangements in human thyroid cells

Human chromosomal fragile sites are regions of the genome that are prone to DNA breakage, and are classified as common or rare, depending on their frequency in the population. Common fragile sites frequently coincide with the location of genes involved in carcinogenic chromosomal translocations, suggesting their role in cancer formation. However, there has been no direct evidence linking breakage at fragile sites to the formation of a cancer-specific translocation. Here, we studied the involvement of fragile sites in the formation of RET/PTC rearrangements, which are frequently found in papillary thyroid carcinoma (PTC). These rearrangements are commonly associated with radiation exposure; however most of the tumors found in adults are not linked to radiation. In this study, we provide structural and biochemical evidence that the RET, CCDC6, and NCOA4 genes participating in two major types of RET/PTC rearrangements, are located in common fragile sites FRA10C and FRA10G, and undergo DNA breakage after exposure to fragile site-inducing chemicals. Moreover, exposure of human thyroid cells to these chemicals results in the formation of cancer-specific RET/PTC rearrangements. These results provide the direct evidence for the involvement of chromosomal fragile sites in the generation of cancer-specific rearrangements in human cells.

Multiple sequence alignment using simulated annealing

Multiple sequence alignment is a useful technique for studying molecular evolution and analyzing structure-sequence relationships. Dynamic programming of multiple sequence alignment has been widely used to find an optimal alignment. However, dynamic programming does not allow for certain types of gap costs, and it limits the number of sequences that can be aligned due to its high computational complexity. The focus of this paper is to use simulated annealing as the basis for developing an efficient multiple sequence alignment algorithm. An algorithm called Multiple Sequence Alignment using Simulated Annealing (MSASA) has been developed. The computational complexity of MSASA is significantly reduced by replacing the high-temperature phase of the annealing process by a fast heuristic algorithm. This heuristic algorithm facilitates in minimizing the solution set of the low-temperature phase of the annealing process. Compared to the dynamic programming approach, MSASA can (i) use natural gap costs which can generate better solution, (ii) align more sequences and (iii) take less computation time.

Analysis of CAG and CCG repeats in Huntingtin gene among HD patients and normal populations of India

We have analysed the distribution of CAG and adjacent polymorphic CCG repeats in the Huntingtin gene in 28 clinically diagnosed unrelated Huntington's disease (HD) patients and in normal individuals belonging to different ethnic groups of India. The range of expanded CAG repeats in HD patients varied from 41 to 56 repeats, whereas in normal individuals this number varied between 11 and 31 repeats. We identified six CCG alleles from a total of 380 normal chromosomes that were pooled across different ethnic populations of India. There were two predominant alleles: (CCG)7 (72.6%) and (CCG)10 (20%). We report here for the first time one four-repeat CCG allele which has not been found in any population so far. We found 30 haplotypes (two loci CAG-CCG) for 380 normal chromosomes. In the present study, no statistically significant preponderance of expanded HD alleles was found on either (CCG)7 or (CCG)10 backgrounds. Our studies suggest that the overall prevalence of HD in Indian populations may not be as high as in Western populations. Further studies are necessary to identify the origin of HD mutation in these populations.

Determination of gene organization in the human IGHV region on single chromosomes

Organization of the IGHV genes (n=108) on single human chromosomes has been determined by detecting these sequences in single sperm using multiplex PCR amplification followed by microarray detection. A total of 374 single sperm samples from five Caucasian males were studied. Three deletion/insertion polymorphisms (Del I-Del III) with deletion allele frequencies ranging from 0.1 to 0.3 were identified. Del I is a previously reported polymorphism affecting three IGHV genes (IGHV1-8, IGHV3-9, and IGHV2-10). Del II affects a region 2-18 kb containing two pseudogenes IGHV(II)-28.1 and IGHV3-29, and Del III spans approximately 21-53 kb involving genes IGHV4-39, IGHV7-40, IGHV(II)-40-1, and IGHV3-41. Deletion alleles of both Dels II and III were found in a heterozygous state, and therefore, could not be easily detected if haploid samples were not used in the study. Results of the present study indicate that deletions/insertions together with other possible chromosomal rearrangements may play an important role in forming the genetic structure of the IGHV region, and may significantly contribute to antibody diversity. Since these three polymorphisms are located within or next to the 3' half of the IGHV region, they may have an important role in the expressed IGHV gene repertoire during immune response.

Formulation and optimization of sustained release Stavudine microspheres using response surface methodology

The aim of the current study was to formulate and optimize the formulation on the basis of in vitro performance of microsphere. A 3² full factorial design was employed to study the effect of independent variables, polymer-to-drug ratio (X₁) and stirring speed (X₂), on dependent variables, encapsulation efficiency, particle size, and time to 80% drug release. The best batch exhibited a high entrapment efficiency of 70% and mean particle size 290 μm. The drug release was also sustained for more than 12 hours. The study helped in finding the optimum formulation with excellent sustained drug release.

Distribution of ABO and Rh blood groups in Nepalese medical students: a report

The frequencies of ABO and rhesus blood groups vary from one population to another. We studied blood group distribution in 120 Nepalese students; 34% were blood group A, 29% group B, 4% group AB and 32.5% group O. The frequency of Rh-negative blood was 3.33% and Rh-positive 96.66%

Giant current-perpendicular-to-plane magnetoresistance in multilayer graphene as grown on nickel

Strong magnetoresistance effects are often observed in ferromagnet-nonmagnet multilayers, which are exploited in state-of-the-art magnetic field sensing and data storage technologies. In this work we report a novel current-perpendicular-to-plane magnetoresistance effect in multilayer graphene as grown on a catalytic nickel surface by chemical vapor deposition. A negative magnetoresistance effect of ∼10(4)% has been observed, which persists even at room temperature. This effect is correlated with the shape of the 2D peak as well as with the occurrence of D peak in the Raman spectrum of the as-grown multilayer graphene. The observed magnetoresistance is extremely high as compared to other known materials systems for similar temperature and field range and can be qualitatively explained within the framework of "interlayer magnetoresistance" (ILMR).

Attachment of mRNA to the cytoskeletal framework and translational control of gene expression in rat L6 muscle cells

The mRNA of rat L6 muscle cells was distributed between a detergent-insoluble fraction containing the cytoskeletal framework and a detergent-soluble fraction. The majority of cytoskeleton-bound mRNA was translationally active and present as polysomes. The mRNA of the detergent-soluble fraction was not associated with the ribosomes and, thus, considered to be the repressed free population. The binding of mRNA was not mediated through ribosomes or the poly(A) region of mRNA. Cross-linking of RNA and proteins was used to examine whether proteins of the cytoskeletal framework were involved in binding mRNA to this structure. Analysis of the mRNA-protein complexes has shown that a large number of polypeptides of molecular masses between 15 and 220 kilodaltons (kDa) were associated with both cytoskeleton-bound and soluble mRNAs. However, a 165-kDa polypeptide was preferentially associated with cytoskeleton-bound mRNA-protein complexes. This polypeptide was also enriched in the total proteins of the cytoskeleton fraction. We have suggested a receptor-like role for the 165-kDa polypeptide in binding mRNA to the cytoskeletal framework. The mechanism of interaction between the cytoskeleton and mRNA was further examined by using a ghost-monolayer transcription system. The mRNA synthesized by this transcription system was preferentially retained in the detergent-insoluble cytoskeleton component of the ghost-monolayer preparation. To understand the physiological significance of the distribution of mRNA between the translationally active cytoskeleton-bound and repressed soluble fractions we have isolated a cDNA clone for a 1.3-kilobase (kb) mRNA. This mRNA was preferentially repressed in myotubes. Distribution of this mRNA was determined by Northern blot analysis using the recombinant plasmid. This analysis indicates that nearly 90% of this mRNA was not associated with ribosomes. In contrast, only 3% of alpha-actin mRNA was found in the repressed population. However, approximately 25% of the 1.3-kb mRNA was present as repressed free messenger ribonucleoprotein. This behaviour is again different from that of actin. All of the cytoskeleton-bound alpha-actin mRNA was associated with polysomes. Furthermore, most of the small amount of alpha-actin mRNA which was present in the soluble fraction was also associated with polysomes. We have, therefore, concluded from these observations that binding of mRNA to the cytoskeleton framework and translation of mRNA are two separate events. We have suggested that mRNA is transported to the cytoplasm as a cytoskeleton-associated complex and further interaction with ribosomes may stabilize this complex.(ABSTRACT TRUNCATED AT 400 WORDS)

Cytoskeleton-bound mRNA for a 40-kDa polypeptide in rat L6 cells is not always translated

The relationship between attachment of mRNA to the cytoskeletal framework and its translation was examined using the mRNA for a polypeptide of 40 kDa (P-40) which is translated in rat L6 myoblasts but not in the myotubes. In both myoblasts and myotubes this mRNA was found to be associated with the cytoskeletal framework. Furthermore, the stability of the association between P-40 mRNA and the cytoskeletal framework in absence of RNA and protein synthesis was examined by using actinomycin D and NaF to block RNA and protein synthesis, respectively. In absence of RNA synthesis portions of both nontranslated P-40 mRNA and translated actin mRNA of myotubes were released into the soluble fraction. In myoblasts, however, both mRNAs remained associated with the cytoskeletal framework following inhibition of RNA synthesis. Inhibition of protein synthesis, on the other hand, had a more dramatic effect on the association between the cytoskeletal framework and P-40 mRNA in myoblasts but not in myotubes. In contrast, the association between actin mRNA and cytoskeletal framework was unaffected by inhibition of protein synthesis in both myoblasts and myotubes. The results of these studies show that the molecular nature of association between cytoskeletal framework and mRNA may differ among mRNAs and may also depend on whether the cells are dividing or are terminally differentiated. Furthermore, no direct relationship between the translation of mRNA and its attachment to the cytoskeletal framework was observed.

Peroxidase changes in barley induced by ionizing and thermal radiation

Thermal and ionizing (gamma-ray) radiations were used to induce damage to barley seeds (IB65). The activity and isozyme banding patterns of peroxidase were compared. It was found that both physical agents caused damage to barley seeds (as observed from seedling height), but their action on peroxidase activity is not similar. Gamma-Rays enhance peroxidase activity. Thermal radiation, on the other hand, tends to reduce it but fails to alter the number of peroxidase isozymes. It is conjectured that the pathways of damage by thermal and ionizing radiations are not the same.

A general method for tree-comparison based on subtree similarity and its use in a taxonomic database

A number of metrics for comparing the branching structure of trees have been used as important tools in the quantitative analysis of evolutionary trees. Less attention has been paid to developing a general comparison methodology for different leaf-labeled N-trees such as classification trees and various types of dendrograms. In this paper a method for measuring overall similarity based on subtree similarity is proposed. Association coefficients can be used to measure the similarity between each pair of subtrees in two trees, and an algorithm called the 'webbing matrix method' is outlined in order to calculate the overall similarity in this method. In addition, the use of this method for tree searching and tree comparison in a taxonomic database is introduced.

Profile of chronic kidney disease related-mineral bone disorders in newly diagnosed advanced predialysis diabetic kidney disease patients: A hospital based cross-sectional study

AIM

Chronic kidney disease related-mineral bone disorder (CKD-MBD) has been poorly studied in pre-dialysis Indian CKD population. There are limited data on the pattern of these disturbances in diabetic CKD patients. Therefore, a study was conducted to find out the profile of mineral bone disorders in T2DM patients with pre-dialysis CKD.

METHODS

In this cross-sectional design, diabetic patients with newly-diagnosed stage 4 and 5 CKD were evaluated. Serum levels of calcium, phosphorus, intact parathyroid hormone (iPTH), 25 hydroxy vitamin D and total alkaline phosphatase (ALP) were measured in all patients. Bone mineral density (BMD) was measured using dual-energy X-ray absorptiometry (DXA).

RESULTS

A total of 72 eligible patients participated (44 males, 28 females; age 54.2±11.7). Patients with CKD Stage 5 had a lower level of corrected serum calcium and significantly higher level of inorganic phosphorus, total ALP and iPTH as compared to stage 4 patients. Overall, 38.5% were hypocalcemic, 31.43% were hyperphosphatemic. 24.2% of CKD subjects were vitamin D deficient (<10ng/ml) and 41.4% having vitamin D insufficiency (10-20ng/ml). In stage 4, hyperparathyroidism (iPTH>110pg/ml) was detected in nearly 43% of patients. In stage 5, only 32% patients was found to have hyperparathyroidism (iPTH>300pg/ml). There was a good correlation between iPTH and total ALP (r=0.5, p=0.0001) in this cohort. 25 (OH) vitamin D was inversely correlated with ALP (r=-0.39, P=0.001) and showed negative correlation with urine ACR (r=-0.37, P=0.002). As a group, the osteoporotic CKD subjects exhibited higher iPTH (220.1±153.8 vs. 119±108pg/ml, p<0.05) as compared to those who were osteopenic or had normal bone density. There was significant correlation between BMD and iPTH (adjusted r=-0.436; P=0.001). In the multivariate regression model, we found intact PTH to predict BMD even after adjustment of all the confounders.

CONCLUSION

The current study showed that adynamic bone disease is prevalent even in pre-dialysis CKD population. High bone turnover disease may not be the most prevalent type in diabetic CKD. However, it could contribute to the development of osteoporosis in CKD subjects. Serum total ALP can serve as a biochemical marker to identify pattern of bone turnover where intact PTH is not available.

Endometrial balloon ablation as a therapy for intractable uterine bleeding in an adolescent

STUDY OBJECTIVE

To evaluate the use of a minimally invasive global endometrial ablation technique in the management of life-threatening bleeding unresponsive to hormonal treatment.

RESULTS

Immediate cessation of bleeding with recovery of normal hematologic profile.

CONCLUSIONS

Endometrial ablation by global balloon ablation may be considered an alternative to hysterectomy in life-threatening hemorrhage in the adolescent patient who is unresponsive to hormonal therapy.

HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees

MOTIVATION

Numerous database management systems have been developed for processing various taxonomic data bases on biological classification or phylogenetic information. In this paper, we present an integrated system to deal with interacting classifications and phylogenies concerning particular taxonomic groups.

RESULTS

An information-theoretic view (taxon view) has been applied to capture taxonomic concepts as taxonomic data entities. A data model which is suitable for supporting semantically interacting dynamic views of hierarchic classifications and a query method for interacting classifications have been developed. The concept of taxonomic view and the data model can also be expanded to carry phylogenetic information in phylogenetic trees. We have designed a prototype taxonomic database system called HICLAS (HIerarchical CLAssification System) based on the concept of taxon view, and the data models and query methods have been designed and implemented. This system can be effectively used in the taxonomic revisionary process, especially when databases are being constructed by specialists in particular groups, and the system can be used to compare classifications and phylogenetic trees.

AVAILABILITY

Freely available at the WWW URL: http://aims.cps.msu.edu/hiclas/

CONTACT

pramanik@cps.msu.edu; lotus@wipm.whcnc.ac.cn

Alignment of possible secondary structures in multiple RNA sequences using simulated annealing

Multiple sequence alignment has been a useful technique for identifying RNA secondary structures. In this paper, an algorithm for aligning multiple RNA sequences to identify possible secondary structure is presented. In this algorithm, dot matrices generated from intra-sequence comparisons are used to obtain possible common secondary structures. A hit probability for dot matrices is calculated and a score function based on this hit probability is defined. Simulated annealing is applied to optimize the score function. The solution set of multiple sequence alignment is introduced, and the effects on the solution set of increasing the number of alignment gaps and the alignment length are analyzed. Several additional strategies to reduce simulated annealing time are applied. A method is applied to reduce the computation time based on the solution set. Also, an optimized transition rule, double shuffle, which moves two positions in a sequence with each iteration, is applied to increase the rate of convergence. This algorithm was used to find possible common secondary structures in RNA sequences.