Bilayer Charge Asymmetry and Oil Residues Destabilize Membranes upon Poration

Transmembrane asymmetry is ubiquitous in cells, particularly with respect to lipids, where charged lipids are mainly restricted to one monolayer. We investigate the influence of anionic lipid asymmetry on the stability of giant unilamellar vesicles (GUVs), minimal plasma membrane models. To quantify asymmetry, we apply the fluorescence quenching assay, which is often difficult to reproduce, and caution in handling the quencher is generally underestimated. We first optimize this assay and then apply it to GUVs prepared with the inverted emulsion transfer protocol by using increasing fractions of anionic lipids restricted to one leaflet. This protocol is found to produce highly asymmetric bilayers but with ∼20% interleaflet mixing. To probe the stability of asymmetric versus symmetric membranes, we expose the GUVs to porating electric pulses and monitor the fraction of destabilized vesicles. The pulses open macropores, and the GUVs either completely recover or exhibit leakage or bursting/collapse. Residual oil destabilizes porated membranes, and destabilization is even more pronounced in asymmetrically charged membranes. This is corroborated by the measured pore edge tension, which is also found to decrease with increasing charge asymmetry. Using GUVs with imposed transmembrane pH asymmetry, we confirm that poration-triggered destabilization does not depend on the approach used to generate membrane asymmetry.

Elucidating the Morphology of the Endoplasmic Reticulum: Puzzles and Perspectives

Artificial or synthetic organelles are a key challenge for bottom-up synthetic biology. So far, synthetic organelles have typically been based on spherical membrane compartments, used to spatially confine selected chemical reactions. In vivo, these compartments are often far from being spherical and can exhibit rather complex architectures. A particularly fascinating example is provided by the endoplasmic reticulum (ER), which extends throughout the whole cell by forming a continuous network of membrane nanotubes connected by three-way junctions. The nanotubes have a typical diameter of between 50 and 100 nm. In spite of much experimental progress, several fundamental aspects of the ER morphology remain elusive. A long-standing puzzle is the straight appearance of the tubules in the light microscope, which form irregular polygons with contact angles close to 120°. Another puzzling aspect is the nanoscopic shapes of the tubules and junctions, for which very different images have been obtained by electron microcopy and structured illumination microscopy. Furthermore, both the formation and maintenance of the reticular networks require GTP and GTP-hydrolyzing membrane proteins. In fact, the networks are destroyed by the fragmentation of nanotubes when the supply of GTP is interrupted. Here, it is argued that all of these puzzling observations are intimately related to each other and to the dimerization of two membrane proteins anchored to the same membrane. So far, the functional significance of this dimerization process remained elusive and, thus, seemed to waste a lot of GTP. However, this process can generate an effective membrane tension that stabilizes the irregular polygonal geometry of the reticular networks and prevents the fragmentation of their tubules, thereby maintaining the integrity of the ER. By incorporating the GTP-hydrolyzing membrane proteins into giant unilamellar vesicles, the effective membrane tension will become accessible to systematic experimental studies.

Biomimetic asymmetric bacterial membranes incorporating lipopolysaccharides

Gram-negative bacteria are equipped with a cell wall that contains a complex matrix of lipids, proteins, and glycans, which form a rigid layer protecting bacteria from the environment. Major components of this outer membrane are the high-molecular weight and amphiphilic lipopolysaccharides (LPSs). They form the extracellular part of a heterobilayer with phospholipids. Understanding LPS properties within the outer membrane is therefore important to develop new antimicrobial strategies. Model systems, such as giant unilamellar vesicles (GUVs), provide a suitable platform for exploring membrane properties and interactions. However, LPS molecules contain large polysaccharide parts that confer high water solubility, which makes LPS incorporation in artificial membranes difficult; this hindrance is exacerbated for LPS with long polysaccharide chains, i.e., the smooth LPS. Here, a novel emulsification step of the inverted emulsion method is introduced to incorporate LPS in the outer or the inner leaflet of GUVs, exclusively. We developed an approach to determine the LPS content on individual GUVs and quantify membrane asymmetry. The asymmetric membranes with outer leaflet LPS show incorporations of 1-16 mol % smooth LPS (corresponding to 16-79 wt %), while vesicles with inner leaflet LPS reach coverages of 2-7 mol % smooth LPS (28-60 wt %). Diffusion coefficient measurements in the obtained GUVs showed that increasing LPS concentrations in the membranes resulted in decreased diffusivity.

Binding of His-tagged fluorophores to lipid bilayers of giant vesicles

His-tagged molecules can be attached to lipid bilayers via certain anchor lipids, a method that has been widely used for the biofunctionalization of membranes and vesicles. To observe the membrane-bound molecules, it is useful to consider His-tagged molecules that are fluorescent as well. Here, we study two such molecules, green fluorescence protein (GFP) and green-fluorescent fluorescein isothiocyanate (FITC), both of which are tagged with a chain of six histidines (6H) that bind to the anchor lipids within the bilayers. The His-tag 6H is much smaller than the GFP molecule but somewhat larger than the FITC dye. The lipid bilayers form giant unilamellar vesicles (GUVs), the behavior of which can be directly observed in the optical microscope. We apply and compare three well-established preparation methods for GUVs: electroformation on platinum wire, polyvinyl alcohol (PVA) hydrogel swelling, and electroformation on indium tin oxide (ITO) glass. Microfluidics is used to expose the GUVs to a constant fluorophore concentration in the exterior solution. The brightness of membrane-bound 6H-GFP exceeds the brightness of membrane-bound 6H-FITC, in contrast to the quantum yields of the two fluorophores in solution. In fact, 6H-FITC is observed to be strongly quenched by the anchor lipids which bind the fluorophores via Ni²⁺ ions. For both 6H-GFP and 6H-FITC, the membrane fluorescence is measured as a function of the fluorophores' molar concentration. The theoretical analysis of these data leads to the equilibrium dissociation constants K_d = 37.5 nM for 6H-GFP and K_d = 18.5 nM for 6H-FITC. We also observe a strong pH-dependence of the membrane fluorescence.

Exposure of Aggregation-Prone Segments is the Requirement for Amyloid Fibril Formation

Arranging into well-organized fibrillar aggregate, commonly known as amyloid fibril is an inherent property of any polypeptide chain. Amyloid fibrils are associated with a number of severe human pathologies like the Alzheimer's disease, Parkinson's disease, type2 diabetes and many more. Recent studies suggest that most of the fibrils are inert and extremely stable, thus could be used for the bionanotechnological applications. As the native state is protected by evolution from aggregation under physiological condition, understanding the structure of aggregation precursor state (APS) will be of extreme importance to decode mechanism of its formation and prevention. This review article includes the recent studies of identification and characterization of possible conformations of proteins which can act as APS. The literature regarding the research in this field revealed that any conformation ranging from native-like state to completely unfolded state could be an APS. The structural characteristics of the APS depend on the protein and on its surrounding environment. From this review of literatures, we conclude that exposure of aggregation-prone segments is the requirement for amyloid fibril formation and the amyloid state seems to be the most stable known physical state of the proteins. This means all conformations of proteins with exposed aggregation-prone segments can promote intermolecular interactions and channel to amyloid fibril pathway to acquire their minimum energy state.

Cell Permeable Imidazole-Desferrioxamine Conjugates: Synthesis and In Vitro Evaluation

Desferrioxamine (DFO), a clinically approved iron chelator used for iron overload, is unable to chelate labile plasma iron (LPI) because of its limited cell permeability. Herein, alkyl chain modified imidazolium cations with varied hydrophobicities have been conjugated with DFO. The iron binding abilities and the antioxidant properties of the conjugates were found to be similar to DFO. The degree of cellular internalization was much higher in the octyl-imidazolium-DFO conjugate (IV) compared with DFO, and IV was able to chelate LPI in vitro. This opens up a new avenue in using N-alkyl imidazolium salts as a delivery vector for hydrophilic cell-impermeable drugs.

Giant magnetoresistance switching in multilayer graphene grown on cobalt

Magnetic multilayer devices, showing large magnetoresistance (MR) effects, have revolutionized magnetic sensing and data storage sectors over the last few decades. Two-dimensional van der Waals layered materials are relatively new entrants in this area, and these materials can give rise to large MR effects with diverse physical origins. Here we report observation of giant MR switching (∼10 orders of magnitude) in multilayered graphene grown on cobalt (Co) substrates, which persists even at room temperature. The origin of this effect is linked with weak interlayer coupling of the graphene stacks, which gives rise to an 'interlayer MR' effect. This effect is found to be robust against some degree of inhomogeneity in the graphene stack, making it an attractive platform for the emerging area of flexible magnetic sensorics.

Spontaneous Fluctuations Can Guide Drug Design Strategies for Structurally Disordered Proteins

Structure-based "rational" drug design strategies fail for diseases associated with intrinsically disordered proteins (IDPs). However, structural disorder allows large-amplitude spontaneous intramolecular dynamics in a protein. We demonstrate a method that exploits this dynamics to provide quantitative information about the degree of interaction of an IDP with other molecules. A candidate ligand molecule may not bind strongly, but even momentary interactions can be expected to perturb the fluctuations. We measure the amplitude and frequency of the equilibrium fluctuations of fluorescently labeled small oligomers of hIAPP (an IDP associated with type II diabetes) in a physiological solution, using nanosecond fluorescence cross-correlation spectroscopy. We show that the interterminal distance fluctuates at a characteristic time scale of 134 ± 10 ns, and 6.4 ± 0.2% of the population is in the "closed" (quenched) state at equilibrium. These fluctuations are affected in a dose-dependent manner by a series of small molecules known to reduce the toxicity of various amyloid peptides. The degree of interaction increases in the following order: resveratrol < epicatechin ∼ quercetin < Congo red < epigallocatechin 3-gallate. Such ordering can provide a direction for exploring the chemical space for finding stronger-binding ligands. We test the biological relevance of these measurements by measuring the effect of these molecules on the affinity of hIAPP for lipid vesicles and cell membranes. We find that the ability of a molecule to modulate intramolecular fluctuations correlates well with its ability to lower membrane affinity. We conclude that structural disorder may provide new avenues for rational drug design for IDPs.

Aggressive Angioimmunoblastic T Cell Lymphomas (AITL) with Soft Tissue Extranodal Mass Varied Histopathological Patterns with Peripheral Blood, Bone Marrow, and Splenic Involvement and Review of Literature

Angioimmunoblastic T cell lymphoma (AITL) is a peripheral T cell non-Hodgkin lymphoma with an aggressive fatal course and it has varied clinical presentation with an uncommon presentation when they present as soft tissue masses or when there is spill in the peripheral blood or there are composite lymphomas that are rare presentations. Common presentations include lymphadenopathy, fever and systemic symptoms, hemolytic anemias, skin rashes, and rheumatoid arthritis. The classical histopathology is absence of follicles in lymph nodes with presence of high endothelial venules and the tumor cells of small to medium-sized lymphocytes with pale cytoplasm mixed with reactive T cells. On immunohistochemistry, the cells are positive for CD3, CD4, CD10, BCL2, and CXCL13. In this observational study, the clinicopathologic presentation and the immunohistochemical profile of five cases who initially presented with a soft tissue mass which is an extremely rare presentation of this rare type of non-Hodgkin lymphoma that was diagnosed at our center with peripheral blood and bone marrow involvement and the clinicopathologic presentation, immunohistochemical profile, and response to treatment on follow-up are correlated with the literature review. One case had a fulminant and aggressive course and was fatal within 2 months of diagnosis. The rest of the four cases are on regular chemotherapy and follow-up. Our five cases had presented with soft tissue masses, two in the axillary regio,n two in the hand, and one in the scapular region with an extranodal presentation, and there was associated lymphadenopathy which developed subsequently with classic histomorphology and immunohistochemical findings. The age range was 46-54 years and all five cases were males. Three cases were with anemia (hemoglobin range 6.5-8.0 mg/dl) and all five cases were having peripheral blood plasmacytosis. Histopathology was classic with paracortical involvement with polymorphous population of cells with neoplastic lymphocytes of small and large sizes with numerous arborizing blood vessels which correspond to high endothelial venules. Microscopically, three architectural patterns; pattern I was seen in three cases (60%) and then pattern II and III in one case each (20% each). Immunohistochemistry revealed CD4+, CD8-, CXCL13+, CD10+, BCL6+, CD19, CD20, CD1a, Tdt, CD21, and CD23+ in follicular dendritic cells. AITL is a rare and aggressive non-Hodgkin lymphoma with varied clinical presentation with classic histomorphology with various patterns which may cause diagnostic dilemma and immunophenotypic findings, and prompt and early diagnosis is mandatory for institution of therapy.

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.

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).

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.

COMPARATIVE ASSESSMENT OF TOTAL PHENOLIC CONTENT IN SELECTED MEDICINAL PLANTS

This study was to compare the total phenolic (TP) content in extracts from eleven plant materials collected at different geographical locations in Kenya, Nigeria, and USA. These plants have been selected because the majority of them are highly pigmented, from yellow to purple, and would therefore have economic value in industries for producing antioxidants and surfactants. Two of them were collected from the industrial and domestic waste outlets. Each analysis was achieved using the Folin-Ciocalteau technique. The order of decreasing phenolic acid content as gallic acid concentration (mg/g dry weight) was Prunus africana (55.14) > Acacia tortilis (42.11) > Khaya grandifoliola (17.54) > Curcuma longa (17.23) > Vernonia amygdalina (14.9)> Russelia equisetiformis (14.03) > Calendula officinalis (7.96) >Phragmites australis (control) (7.09) > Rauwolfia vomitoria (6.69) > Phragmites australis (industrial) (6.21) > Cnidoscolus aconitifolius (5.6). The TP contents of Spartina alterniflora species were below the detection limit.

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.

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.

Nonalcoholic steatohepatitis (NASH) with diabetes: predictors of liver fibrosis

INTRODUCTION

Nonalcoholic steatohepatitis (NASH) is common cause of chronic liver disease strongly associated with insulin resistance leading to fibrosis. No factors that determine increasing fibrosis have been well recognized. Liver biopsy is considered as gold standard for diagnosis and prognosis of this disease.

AIM

To identify independent predictive factors of liver fibrosis in patients of NASH with diabetes.

MATERIAL AND METHODS

During the year 2001 and 2002 total 36 patients of NASH associated with diabetes were included in the study. The diagnosis of NASH was based on 1) presence of steatosis, inflammation and ballooning on liver biopsy 2) Intake of alcohol < 20 gm of ethanol per week 3) Exclusion of other liver diseases. Patients were labeled as diabetic if random glucose was > 200 mg/dL or fasting glucose more than 140 mg/dL on 2 occasion or having documented use of oral hypoglycemic medications or insulin. Clinical and biochemical variables such as age, sex, obesity, hypercholesterolemia, AST, ALT and AST: ALT were examined for predictors of fibrosis using univariate and multiple regression statistical analysis. Obesity was defined as BMI > 30 for both males and females. Hypercholesterolemia was considered when fasting cholesterol level was above 95th percentile of normal on at least 2 occasions. Fibrosis was noted as present or absent on histology.

RESULTS

Of 36 patients 17 were females and 19 males with age range of 25 to 75 years, mean age 50.8 years. Fibrosis was present in 11 (30.5%) and absent in 25 (69.4%) patients. Univariate and multiple correlations co-efficient failed to detect significant association of fibrosis with above mentioned variables. However multiple regression and logistic regression analysis (MLR) detected statistical significance for AST, ALT levels and AST: ALT ratio between fibrosis and no fibrosis in 80.6% patients.

CONCLUSION

There is no definite noninvasive test that helps to predict liver fibrosis however AST, ALT levels and AST: ALT ratio may help to determine the fibrosis in patients of NASH with diabetes in majority of cases.

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.

Postage stamps as a health promotion tool in the Nepalese community

Over the last 15 years the government of Nepal has issued postage stamps as a way of raising awareness of health issues in the general population and especially in remote communities. The topics covered by 8 different stamps are good child health care practices, combating drug abuse, hazards of smoking, prevention of AIDS, prevention of blindness due to cataract, fighting cancer and rehabilitation of disabled people

Postage stamps as a health promotion tool in the Nepalese community

Over the last 15 years the government of Nepal has issued postage stamps as a way of raising awareness of health issues in the general population and especially in remote communities. The topics covered by 8 different stamps are good child health care practices, combating drug abuse, hazards of smoking, prevention of AIDS, prevention of blindness due to cataract, fighting cancer and rehabilitation of disabled people.

Physical fitness status among the students of a medical college in Kathmandu, Nepal

The physical fitness of Nepalese students at a medical college in Kathmandu was measured. The proportions of students with poor fitness, average fitness, good fitness, very good fitness and excellent fitness were 10.4%, 23.6%, 39.6%, 17.9% and 8.5% respectively. No significant difference between the male and female students in physical fitness index score was noticed in any of the fitness level groups.

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.

Physical fitness status among the students of a medical college in Kathmandu, Nepal

The physical fitness of Nepalese students at a medical college in Kathmandu was measured. The proportions of students with poor fitness, average fitness, good fitness, very good fitness and excellent fitness were 10.4%, 23.6%, 39.6%, 17.9% and 8.5% respectively. No significant difference between the male and female students in physical fitness index score was noticed in any of the fitness level groups.

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.

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%

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.

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%.

Negligible male gene flow across ethnic boundaries in India, revealed by analysis of Y-chromosomal DNA polymorphisms

From the historically prevalent social structure of Indian populations it may be predicted that there has been very little male gene flow across ethnic boundaries. To test this finding, we have analyzed DNA samples of individuals belonging to 10 ethnic groups, speaking Indo-European or Austroasiatic languages and inhabiting the eastern and northern regions of India. Eight Y-chromosomal markers, two biallelic and six microsatellite, were studied. All populations were monomorphic for the deletion allele at the YAP (DYS287) locus and for the 119-bp allele at the DYS288 locus. Y-chromosomal haplotypes were constructed on the basis of one RFLP locus and five microsatellite loci. The haplotype distribution among the groups showed that different ethnic groups harbor nearly disjoint sets of haplotypes. This indicates that there has been virtually no male gene flow among ethnic groups. Analysis of molecular variance revealed that there was significant haplotypic variation between castes and tribes, but nonsignificant variation among ranked caste clusters. Haplotypic variation attributable to differences in geographical regions of habitat was also nonsignificant.

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

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.

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.

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.

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.

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 new data model for biological classification

In the domain of biological classification, classifications are performed hierarchically. There are no standard classifications which are unanimously accepted by the community of each domain; many different interacting views of classification exist about the same data, and the discovery of new data results in changes to the existing classification. Even a single individual may change his or her own classification of a particular group. Since multiple classification views interact, they are semantically related. It is difficult to model this kind of dynamically evolving and semantically interacting classification system using traditional data models, which lack the structural flexibility necessary to support dynamic views of hierarchic classifications, and cannot properly capture the history of these complex interactions. We have developed a new data model which is suitable for supporting semantically interacting dynamic views of hierarchic biological classifications. On the basis of our new data model we have developed a prototype database system called HICLAS (HIerarchical CLAssification System); its domain is plant taxonomy. HICLAS is available through the Internet and an X-window interface has been implemented to support queries to classification data.

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.