Increase in primary cilia number and length upon VDAC1 depletion contributes to attenuated proliferation of cancer cells

Primary cilia (PCs) that are present in most human cells and perform sensory function or signal transduction are lost in many solid tumors. Previously, we identified VDAC1, best known to regulate mitochondrial bioenergetics, to negatively regulate ciliogenesis. Here, we show that downregulation of VDAC1 in pancreatic cancer-derived Panc1 and glioblastoma-derived U-87MG cells significantly increased ciliation. Those PCs were significantly longer than the control cells. Such increased ciliation possibly inhibited cell cycle, which contributed to reduced proliferation of these cells. VDAC1-depletion also led to longer PCs in quiescent RPE1 cells. Therefore, serum-induced PC disassembly was slower in VDAC1-depleted RPE1 cells. Overall, this study reiterates the importance of VDAC1 in modulating tumorigenesis, due to its novel role in regulating PC disassembly and cilia length.

Molecular regulation of hypoxia through the lenses of noncoding RNAs and epitranscriptome

Cells maintain homeostasis in response to environmental stress through specific cell stress responses. Hypoxic stress, well known to be associated with diverse solid tumors, is one of the main reasons for cancer-related mortality. Although cells can balance themselves well during hypoxic stress, the underlying molecular mechanisms are not well understood. The enhanced appreciation of diverse roles played by noncoding transcriptome and epigenome in recent years has brought to light the involvement of noncoding RNAs and epigenetic modifiers in hypoxic regulation. The emergence of techniques like deep sequencing has facilitated the identification of large numbers of long noncoding RNAs (lncRNAs) that are differentially regulated in various cancers. Similarly, proteomic studies have identified diverse epigenetic modifiers such as HATs, HDACs, DNMTs, polycomb groups of proteins, and their possible roles in the regulation of hypoxia. The crosstalk between lncRNAs and epigenetic modifiers play a pivotal role in hypoxia-induced cancer initiation and progression. Besides the lncRNAs, several other noncoding RNAs like circular RNAs, miRNAs, and so forth are also expressed during hypoxic conditions. Hypoxia has a profound effect on the expression of noncoding RNAs and epigenetic modifiers. Conversely, noncoding RNAs/epigenetic modifies can regulate the hypoxia signaling axis by modulating the stability of the hypoxia-inducible factors (HIFs). The focus of this review is to illustrate the molecular orchestration underlying hypoxia biology, especially in cancers, which can help in identifying promising therapeutic targets in hypoxia-induced cancers. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.

Long noncoding RNAs are substrates for cytoplasmic capping enzyme

Cytoplasmic capping returns a cap to specific mRNAs, thus protecting uncapped RNAs from decay. Prior to the identification of cytoplasmic capping, uncapped mRNAs were thought to be degraded. Here, we test whether long noncoding RNAs (lncRNAs) are substrates of the cytoplasmic capping enzyme (cCE). The subcellular localisation of 14 lncRNAs associated with sarcomas were examined in U2OS osteosarcoma cells. We used 5' rapid amplification of cDNA ends (RACE) to assay uncapped forms of these lncRNAs. Inhibiting cytoplasmic capping elevated uncapped forms of selected lncRNAs indicating a plausible role of cCE in targeting them. Analysis of published cap analysis of gene expression (CAGE) data shows increased prevalence of certain 5'-RACE cloned sequences, suggesting that these uncapped lncRNAs are targets of cytoplasmic capping.

Boron carbide thin film surface characterization after graphitic carbon removal using low-pressure oxygen gas RF plasma

B ₄ C-coated thin film mirrors are used in high brilliance synchrotron and x-ray free electron laser beamlines due to their low absorption coefficient and high thermal stability. As in the case of gold, platinum, and other thin film mirrors, B ₄ C-coated mirrors also are affected due to synchrotron radiation-induced carbon contaminations in beamlines. In the present study, a graphitic carbon (C) layer deposited on top of boron carbide (B _x C) thin film surface is removed by five successive oxygen radio frequency (RF) plasma exposures (RF power, 10 W; O ₂ flow, 30 sccm; exposure time, 10 min each). Before and after the carbon layer removal, structural and compositional properties of the B _x C/C bilayer are characterized by soft x-ray reflectivity, x-ray photoelectron spectroscopy, grazing angle x-ray diffraction, and Raman spectroscopy techniques. Characterization results reveal that in the first four exposures the carbon layer thickness decreases continuously without affecting the B _x C layer properties; however, in the fifth exposure, the carbon layer is completely removed along with a partial etching of the B _x C layer too.

Active microrheology using pulsed optical tweezers to probe viscoelasticity of lamin A

Lamins are nucleoskeletal proteins of mammalian cells that stabilize the structure and maintain the rigidity of the nucleus. These type V intermediate filament proteins which are predominantly of A and B types provide necessary tensile strength to the nucleus. Single amino acid missense mutations occurring all over the lamin A protein form a cluster of human diseases termed as laminopathies, most of which principally affect the muscle and cardiac tissues responsible for load bearing functionalities of the body. One such mutation is A350P which causes dilated cardiomyopathy in patients. It is postulated that a change from alanine to proline in the α-helical coiled-coil forming 2B rod domain of the protein might severely disrupt the propensity of the filaments to polymerise into functional higher order structures required to form a fully functional lamina with its characteristic elasticity. In this study, we have elucidated for the very first time, the application of active microrheology employing oscillating optical tweezers to investigate any alterations in the viscoelastic parameters of the mutant protein meshwork in vitro, which might translate into possible changes in nuclear plasticity. We confirmed our findings from this robust yet fast method by imaging both the wild type and mutant lamin A networks using a super resolution microscope, and observed changes in the mesh size which corroborate our measured changes in the viscoelastic parameters of the lamins. This method could thus be extended to conduct microrheological measurements on any intermediate filament protein thus bearing significant implications in laminopathies and other diseases associated with intermediate filaments.

Germ cell ribonucleoprotein granules in different clades of life: From insects to mammals

Ribonucleoprotein (RNP) granules are no newcomers in biology. Found in all life forms, ranging across taxa, these membrane-less "organelles" have been classified into different categories based on their composition, structure, behavior, function, and localization. Broadly, they can be listed as stress granules (SGs), processing bodies (PBs), neuronal granules (NGs), and germ cell granules (GCGs). Keeping in line with the topic of this review, RNP granules present in the germ cells have been implicated in a wide range of cellular functions including cellular specification, differentiation, proliferation, and so forth. The mechanisms used by them can be diverse and many of them remain partly obscure and active areas of research. GCGs can be of different types in different organisms and at different stages of development, with multiple types coexisting in the same cell. In this review, the different known subcategories of GCGs have been studied with respect to five distinct model organisms, namely, Drosophila, Caenorhabditis elegans, Xenopus, Zebrafish, and mammals. Of them, the cytoplasmic polar granules in Drosophila, P granules in C. elegans, balbiani body in Xenopus and Zebrafish, and chromatoid bodies in mammals have been specifically emphasized upon. A descriptive account of the same has been provided along with insights into our current understanding of their functional significance with respect to cellular events relating to different developmental and reproductive processes. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Export and Localization > RNA Localization RNA in Disease and Development > RNA in Disease.

Structural, optical and electronic properties of Ni1-x Co x O in the complete composition range

Crystallographic and electronic structures of phase pure ternary solid solutions of Ni_1−xCo_xO (x = 0 to 1) have been studied using XRD, EXAFS and XAS measurements. The lattice parameter of the cubic rock-salt (RS) Ni_1−xCo_xO solid solutions increases linearly with increasing Co content and follows Vegard's law, in the complete composition range. A linear increase in the bond lengths (Ni/Co–O, Ni–Ni and Ni–Co) with “x”, closely following the bond lengths determined from virtual crystal approximation (VCA), is observed, which implies that there is only a minimal local distortion of the lattice in the mixed crystal. The optical gap of the ternary solid solution determined from diffuse reflectivity measurements shows neither a linear variation with Co composition nor bowing, as observed in many ternary semiconductors. This trend in the variation of optical gaps is explained by probing the conduction band using XAS at the O K-edge. We have observed that the variation in the onset energy of the conduction band edge with “x” is very similar to the variation in the optical gap with “x”, thus clearly indicating the dominant role played by the conduction band position in determining the optical gap. The variation in the intensities of the pre-edge peak in the XANES spectra measured at Ni and Co K-edges, and the L_1/2 peak in XAS spectra measured at Ni and Co L-edges, is found to depend on the unoccupied O 2p-metal-(Ni/Co) 3d hybridized states and the bond lengths.

The optical gap of Ni_1−xCo_xO solid solutions neither varies linearly with Co composition nor shows any bowing in the complete composition range. The nature of this variation of the gap is governed by the position of conduction band edge.

Investigation of Dual-Ion Beam Sputter-Instigated Plasmon Generation in TCOs: A Case Study of GZO

The use of the high free-electron concentration in heavily doped semiconductor enables the realization of plasmons. We report a novel approach to generate plasmons in Ga:ZnO (GZO) thin films in the wide spectral range of ∼1.87-10.04 eV. In the grown GZO thin films, dual-ion beam sputtering (DIBS) instigated plasmon is observed because of the formation of different metallic nanoclusters are reported. Moreover, formation of the nanoclusters and generation of plasmons are verified by field emission scanning electron microscope, electron energy loss spectra obtained by ultraviolet photoelectron spectroscopy, and spectroscopic ellipsometry analysis. Moreover, the calculation of valence bulk, valence surface, and particle plasmon resonance energies are performed, and indexing of each plasmon peaks with corresponding plasmon energy peak of the different nanoclusters is carried out. Further, the use of DIBS-instigated plasmon-enhanced GZO can be a novel mean to improve the performance of photovoltaic, photodetector, and sensing devices.

RNA guanine-7 methyltransferase catalyzes the methylation of cytoplasmically recapped RNAs

Cap homeostasis is a cyclical process of decapping and recapping that impacts a portion of the mRNA transcriptome. The metastable uncapped forms of recapping targets redistribute from polysomes to non-translating mRNPs, and recapping is all that is needed for their return to the translating pool. Previous work identified a cytoplasmic capping metabolon consisting of capping enzyme (CE) and a 5′-monophosphate kinase bound to adjacent domains of Nck1. The current study identifies the canonical cap methyltransferase (RNMT) as the enzyme responsible for guanine-N7 methylation of recapped mRNAs. RNMT binds directly to CE, and its presence in the cytoplasmic capping complex was demonstrated by pulldown assays, gel filtration and proximity-dependent biotinylation. The latter also identified the RNMT cofactor RAM, whose presence is required for cytoplasmic cap methyltransferase activity. These findings guided development of an inhibitor of cytoplasmic cap methylation whose action resulted in a selective decrease in levels of recapped mRNAs.

Clinical pharmacogenomics: patient perspectives of pharmacogenomic testing and the incidence of actionable test results in a chronic disease cohort

Aim

This study aimed to examine pharmacogenomic test results and patient perspectives at an academic cardiovascular medicine clinic.

Patients & methods

Test results for three common cardiovascular drug-gene tests (warfarin-CYP2C9-VKORC1, clopidogrel-CYP2C19 and simvastatin-SLCO1B1) of 208 patients in the Ohio State University-Coriell Personalized Medicine Collaborative were examined to determine the incidence of potentially actionable test results. A post-hoc, anonymous, patient survey was also conducted.

Results

Potentially actionable test results for at least one of the three drug-gene tests were determined in 170 (82%) patients. Survey responses (n = 134) suggested that patients generally considered their test results to be important (median of 7.5 on a 10-point scale of importance) and were interested (median of 7.3 on a 10-point scale of interest) in a Clinical Pharmacogenomic Service.

Conclusion

Attitudes toward pharmacogenomic testing were generally favorable, and potentially actionable test results were not uncommon in this cardiovascular medicine cohort.

Effect of oxygen partial pressure in deposition ambient on the properties of RF magnetron sputter deposited Gd2O3 thin films

Gadolinium oxide is an excellent optical material that offers high transmission in a wide wavelength range of 200-1600 nm and exhibits a high bulk refractive index of ∼1.80 at 550 nm. In the present study, a set of Gd₂O₃ thin films has been deposited on fused silica substrates by RF sputtering of a Gd₂O₃ target under various O₂ to Ar flow ratios. The samples have been characterized by grazing incidence x-ray diffraction (GIXRD) to study the long range structural behavior, by GIXR to study density and surface roughness of the films, by atomic force microscopy measurements to study morphological properties, by Rutherford backscattering measurements for compositional studies, and by transmission spectrophotometry and spectroscopic ellipsometry techniques to study their optical properties. It has been observed that the films deposited with 10% oxygen partial pressure have low density, high surface roughness, and high void content, which results in a low value of refractive index of this film, and film quality improves as oxygen partial pressure is further increased. Extended x-ray absorption fine structure measurement with synchrotron radiation has also been employed to extract local structural information around Gd sites, which has in turn been used to explain some of the observed macroscopic properties of the films.

A novel mannoside-glycocluster adjuvant: Compared in vitro to CpG ODN and MPL and tested in vivo in mouse asthma model

BACKGROUND

Allergen-specific immunotherapy balances the Th2-biased immunity towards Th1 and Treg responses. Adjuvants are used in allergen preparations to intensify the immune responses. The increased prevalence of allergies in developed societies has been associated with decreased microbial load during childhood. This has initiated a search for microbial structures to be used as adjuvants. Our study has shown that a synthetic triacedimannose (TADM) may suppress the Th2-type allergic inflammatory response. The aim of this study was to compare the properties of TADM with capacities of other adjuvants, CpG ODN and MPL, to modulate cytokine production in PBMC and regulate sensitisation in an OVA-sensitised mouse asthma model.

METHODS

The effects of TADM were studied in vitro on birch stimulated PBMC cultures of birch allergic rhinitis patients with other known adjuvants. Cytokines in supernatants were measured by Luminex. Effects of TADM were analysed in vivo in a mouse model of OVA-induced allergic asthma by analysing BAL, cytokine mRNA and serum antibodies.

RESULTS

TADM was the only adjuvant that significantly suppressed the production of all birch induced Th2-type cytokines. In a murine model, TADM significantly suppressed the specific IgE production and enhanced IFN-γ production.

CONCLUSIONS

TADM suppresses the birch allergen induced Th2-type cytokine responses in allergic subjects more efficiently than the two other adjuvants, MPL and CpG ODN. TADM is immunomodulatory also in vivo and decreases the IgE levels and increases the IFN-γ responses in a murine model. These results suggest that TADM may be a promising candidate for novel adjuvants in immunotherapy.

Study of the microstructure information of GaAs epilayers grown on silicon substrate using synchrotron radiation

Williamson-Hall (WH) analysis is a well established method for studying the microstructural properties of epilayers grown on foreign substrates. However, the method becomes inapplicable in specific cases where the structure factor considerations and the presence of anti-phase domains forbid the data acquisition for certain reflections in conventional high-resolution X-ray diffraction (HRXRD) measurements. Here, this limitation is overcome by exploiting the large intensity (25 µW mm(-2)) and high photon energy (15.5 keV) of the X-ray beam obtained from a synchrotron radiation source. The lateral coherence length, vertical coherence length, tilt and micro-strain of GaAs epilayers grown on Si substrate have been successfully measured using the conventional WH analysis. The microstructure information obtained from the conventional WH analysis based on the data acquired at the synchrotron radiation source is in reasonable agreement with the results obtained from atomic force microscope and surface profiler measurements. Such information cannot be obtained on a laboratory-based HRXRD system where modification of the WH method by involving a set of parallel asymmetric crystallographic planes is found to be essential. However, the information obtained from the modified WH method is along a different crystallographic orientation.

Localized surface plasmon resonance on Au nanoparticles: tuning and exploitation for performance enhancement in ultrathin photovoltaics

We report a detailed correlation analysis of the size, shape, and distribution of Au nanoparticles (NPs) on fine-tuning of localized surface plasmon resonance and optical absorption cross-section.

Cap homeostasis is independent of poly(A) tail length

Cap homeostasis is a cyclical process of decapping and recapping that maintains the cap on a subset of the cytoplasmic transcriptome. Interfering with cytoplasmic capping results in the redistribution of target transcripts from polysomes to non-translating mRNPs, where they accumulate in an uncapped but nonetheless stable form. It is generally thought that decapping is preceded by shortening of the poly(A) tail to a length that can no longer support translation. Therefore recapped target transcripts would either have to undergo cytoplasmic polyadenylation or retain a reasonably long poly(A) tail if they are to return to the translating pool. In cells that are inhibited for cytoplasmic capping there is no change in the overall distribution of poly(A) lengths or in the elution profile of oligo(dT)-bound targets. Poly(A) tail lengths were similar for target mRNAs on polysomes or in non-translating mRNPs, and the presence of polyadenylated uncapped mRNA in mRNPs was confirmed by separation into capped and uncapped pools prior to assay. Finally, in silico analysis of cytoplasmic capping targets revealed significant correlations with genes encoding transcripts with uridylated or multiply modified 3′ ends, and genes possessing multiple 3′-untranslated regions (UTRs) generated by alternative cleavage and polyadenylation.

The cytoplasmic capping complex assembles on adapter protein nck1 bound to the proline-rich C-terminus of Mammalian capping enzyme

mRNA capping and decapping requires a cytoplasmic complex to maintain and/or restore the 5′ cap on a subset of the mammalian transcriptome; Nck1, an SH2/SH3 adapter, creates a scaffold upon which the cytoplasmic capping complex forms.

Cytoplasmic capping is catalyzed by a complex that contains capping enzyme (CE) and a kinase that converts RNA with a 5′-monophosphate end to a 5′ diphosphate for subsequent addition of guanylic acid (GMP). We identify the proline-rich C-terminus as a new domain of CE that is required for its participation in cytoplasmic capping, and show the cytoplasmic capping complex assembles on Nck1, an adapter protein with functions in translation and tyrosine kinase signaling. Binding is specific to Nck1 and is independent of RNA. We show by sedimentation and gel filtration that Nck1 and CE are together in a larger complex, that the complex can assemble in vitro on recombinant Nck1, and Nck1 knockdown disrupts the integrity of the complex. CE and the 5′ kinase are juxtaposed by binding to the adjacent domains of Nck1, and cap homeostasis is inhibited by Nck1 with inactivating mutations in each of these domains. These results identify a new domain of CE that is specific to its function in cytoplasmic capping, and a new role for Nck1 in regulating gene expression through its role as the scaffold for assembly of the cytoplasmic capping complex.

We previously described a cyclical process of mRNA decapping and recapping termed “cap homeostasis.” Recapping is catalyzed by a complex of cytoplasmic proteins that includes the enzyme known to catalyze nuclear capping, and a kinase that converts RNA with a 5′-monophosphate end to a 5′-diphosphate capping substrate. The current study shows these two enzymatic activities are brought together in the cytoplasmic capping complex as both bind to adjacent domains of the adapter protein Nck1. Nck1 is a cytoplasmic protein best known for transducing receptor tyrosine kinase signaling. We identify a proline-rich sequence at the C-terminus of a human capping enzyme that is required for binding to Nck1, and we show that this interaction is required for integrity of the cytoplasmic capping complex. Depletion of Nck1 causes the cytoplasmic capping complex to dissociate. The inhibition of cytoplasmic capping by Nck1 with mutations in either the 5′-kinase or capping enzyme binding sites identified a functional role for Nck1 in cap homeostasis and a previously unknown function for Nck1 in cell biology.

Interface properties of atomic layer deposited TiO2/Al2O3 films on In(0.53)Ga(0.47)As/InP substrates

Electrical and interfacial properties of metal-oxide-semiconductor (MOS) capacitors fabricated using atomic layer deposited bilayer TiO2/Al2O3 films on In0.53Ga0.47As/InP substrates are reported. Vacuum annealing at 350 °C is shown to improve the interface quality. Capacitance-voltage (C-V) characteristics with higher accumulation capacitance, negligible frequency dispersion, small hysteresis and low interface state density (∼1.5 × 10(11) cm(-2) eV(-1)) have been observed for MOS capacitors. Low frequency (1/f) noise characterization and inelastic electron tunneling spectroscopy (IETS) studies have been performed to determine defects and interface traps and explain the lattice dynamics and trap state generation mechanisms. Both the IETS and 1/f noise studies reveal the spatial locations of the traps near the interface and also the nature of the traps. The IETS study further revealed the dynamic evolution of trap states related to low frequency noise sources in the deposited TiO2/Al2O3 stacks. It is shown that deposition of an ultrathin layer of TiO2 on Al2O3 can effectively control the diffusion of As in the dielectric and the oxidation states of In and Ga at the In0.53Ga0.47As surface.

Nasal polyps - histopathologic spectrum

Analysis of 345 polypoidal masses in nose and nasal sinuses with clinical diagnosis of nasal polyp, observed in 10 years, revealed 175 (50.7%) non- neoplastic lesions and 170 (49.3%) neoplasms. Among the non- neoplastic lesions, there were 110 cases (62.8%) of true nasal polyps including 74 cases (67.3%) of allergic polyps and 36 (32.7%) inflammatory ones. The next common non- neoplastic polyp was due to rhinosporidiosis (31.4%). Benign neoplastic lesions consisted mainly of haemangioma (45.7%), angiofibroma (23.2%), fibroma (6.2%), transitional cell papilloma, inverted papilloma, adenoma-3.9% each. Squamous cell carcinoma was the commonest malignant lesion encountered (36.6%) followed by 19.5% of adenoid cystic carcinoma,17.1% of anaplastic carcinoma and 12.2% of transitional cell carcinoma. Adeno carcinoma (4.9%), Mucoepidermoid carcinoma (2.4%), non- Hodgkin lymphoma (4.9%) and embryonal rhabdomyosarcoma (2.4%) were the other malignant lesions.

Identification of cytoplasmic capping targets reveals a role for cap homeostasis in translation and mRNA stability

The notion that decapping leads irreversibly to messenger RNA (mRNA) decay was contradicted by the identification of capped transcripts missing portions of their 5' ends and a cytoplasmic complex that can restore the cap on uncapped mRNAs. In this study, we used accumulation of uncapped transcripts in cells inhibited for cytoplasmic capping to identify the targets of this pathway. Inhibition of cytoplasmic capping results in the destabilization of some transcripts and the redistribution of others from polysomes to nontranslating messenger ribonucleoproteins, where they accumulate in an uncapped state. Only a portion of the mRNA transcriptome is affected by cytoplasmic capping, and its targets encode proteins involved in nucleotide binding, RNA and protein localization, and the mitotic cell cycle. The 3' untranslated regions of recapping targets are enriched for AU-rich elements and microRNA binding sites, both of which function in cap-dependent mRNA silencing. These findings identify a cyclical process of decapping and recapping that we term cap homeostasis.

Prediction of the annuloplasty ring size in patients undergoing mitral valve repair using real-time three-dimensional transoesophageal echocardiography

Aims

We sought to investigate the additional value of real-time three-dimensional transoesophageal echocardiography (RT 3D TOE)-guided sizing for predicting annuloplasty ring size during mitral valve repair.

Methods and results

In 53 patients undergoing elective mitral valve repair, an RT 3D TOE was performed pre- and post-operatively. The digitally stored loops were imported into a software for mitral valve assessment. The annuloplasty ring size was predicted by superimposing computer-aided design (CAD) models of annuloplasty rings onto Live 3D zoom loops, measurement of the intercommissural distance, or the height of the anterior mitral leaflet. The surgeon implanted the annuloplasty ring according to the usual surgical technique and was blinded to the echocardiographic measurement results. Pre-operative correlation between the selected ring size with mitral valve assessment and the actual implanted annuloplasty ring size was 0.91. The correlation for measurement of the intercommissural distance was 0.55 and for measurement of the height of the anterior mitral leaflet 0.75. The post-operative correlation with the actual implanted ring size was 0.96 for mitral valve assessment, 0.92 for intercommissural distance, and 0.79 for the anterior mitral leaflet height.

Conclusion

Superimposition of annuloplasty ring CAD models on the Live 3D zoom loops of the mitral valve using mitral valve assessment is superior to two-dimensional measurements of the intercommissural distance or the height of the anterior mitral leaflet in predicting correct annuloplasty ring size.

Inter-cellular variation in DNA content of Entamoeba histolytica originates from temporal and spatial uncoupling of cytokinesis from the nuclear cycle

Accumulation of multiple copies of the genome in a single nucleus and several nuclei in a single cell has previously been noted in Entamoeba histolytica, contributing to the genetic heterogeneity of this unicellular eukaryote. In this study, we demonstrate that this genetic heterogeneity is an inherent feature of the cell cycle of this organism. Chromosome segregation occurs on a variety of novel microtubular assemblies including multi-polar spindles. Cytokinesis in E. histolytica is completed by the mechanical severing of a thin cytoplasmic bridge, either independently or with the help of neighboring cells. Importantly, cytokinesis is uncoupled from the nuclear division cycle, both temporally and spatially, leading to the formation of unequal daughter cells. Sorting of euploid and polyploid cells showed that each of these sub-populations acquired heterogeneous DNA content upon further growth. Our study conclusively demonstrates that genetic heterogeneity originates from the unique mode of cell division events in this protist.

Proliferating eukaryotic cells regulate their DNA synthesis, chromosome segregation, and cell division with great precision so that daughter cells are genetically identical. Our study demonstrates that in proliferating cells of the protist pathogen Entamoeba histolytica re-duplication of DNA followed by segregation on atypical and diverse microtubular structures is frequently observed. In this parasite, cell division is erratic, so that each daughter cell may contain one or more nuclei and sometimes no nuclei. This uncoupling of cell cycle events and survival of daughter cells with unequal DNA contents leads to genetic heterogeneity in E. histolytica. Our study highlights the inherent plasticity of the Entamoeba genome and the ability of this protist to survive in the absence of strict regulatory mechanisms that are a hallmark of the eukaryotic cell cycle.

Entamoeba shows reversible variation in ploidy under different growth conditions and between life cycle phases

Under axenic growth conditions, trophozoites of Entamoeba histolytica contain heterogenous amounts of DNA due to the presence of both multiple nuclei and different amounts of DNA in individual nuclei. In order to establish if the DNA content and the observed heterogeneity is maintained during different growth conditions, we have compared E. histolytica cells growing in xenic and axenic cultures. Our results show that the nuclear DNA content of E. histolytica trophozoites growing in axenic cultures is at least 10 fold higher than in xenic cultures. Re-association of axenic cultures with their bacterial flora led to a reduction of DNA content to the original xenic values. Thus switching between xenic and axenic growth conditions was accompanied by significant changes in the nuclear DNA content of this parasite. Changes in DNA content during encystation-excystation were studied in the related reptilian parasite E. invadens. During excystation of E. invadens cysts, it was observed that the nuclear DNA content increased approximately 40 fold following emergence of trophozoites in axenic cultures. Based on the observed large changes in nuclear size and DNA content, and the minor differences in relative abundance of representative protein coding sequences, rDNA and tRNA sequences, it appears that gain or loss of whole genome copies may be occurring during changes in the growth conditions. Our studies demonstrate the inherent plasticity and dynamic nature of the Entamoeba genome in at least two species.

In contrast to the perception that DNA content of an organism is stable and maintained during different conditions and life cycle stages, new evidence shows that many organisms display changes in their DNA content at different stages of their life cycle. We have earlier identified intra-cellular and inter-cellular differences in DNA content of the protist pathogen Entamoeba histolytica and established that this organism can tolerate large variations in DNA content during axenic culture. In this study we have made an important advancement in the understanding of amoeba biology where we have shown that changes in growth conditions and life cycle stages are accompanied by large differences in DNA content involving gain or loss of whole genome copies. This property may well regulate the outcome of infection and subsequently the disease.

Growth of textured nanocrystalline cobalt ferrite thin films by pulsed laser deposition

Cobalt ferrite thin films have been deposited on fused quartz substrates by pulsed laser deposition at various substrate temperatures, T(s) (25 degrees C, 300 degrees C, 550 degrees C and 750 degrees C). Single phase, nanocrystalline, spinel cobalt ferrite formation is confirmed by X-ray diffraction (XRD) for T(s) > or = 300 degrees C. Conventional XRD studies reveal strong (111) texturing in the as deposited films with T(s) > or = 550 degrees C. Bulk texture measurements using X-ray orientation distribution function confirmed (111) preferred orientation in the films with T(s) > or = 550 degrees C. Grain size (13-16 nm for T(s) > or = 300 degrees C) estimation using grazing incidence X-ray line broadening analysis shows insignificant grain growth with increasing T(s), which is in good agreement with grain size data obtained from transmission electron microscopy.

Genome re-duplication and irregular segregation occur during the cell cycle of Entamoeba histolytica

Heterogeneity of genome content is commonly observed in axenic cultures of Entamoeba histolytica. Cells with multiple nuclei and nuclei with heterogenous genome contents suggest that regulatory mechanisms that ensure alternation of DNA synthesis and mitosis are absent in this organism. Therefore, several endo-reduplicative cycles may occur without mitosis. The data also shows that unlike other endo-reduplicating organisms, E.histolytica does not undergo a precise number of endo-reduplicative cycles. We propose that irregular endo-reduplication and genome partitioning lead to heterogeneity in the genome content of E.histolytica trophozoites in their proliferative phase. The goal of future studies should be aimed at understanding the mechanisms that are involved in (a) accumulation of multiple genome contents in a single nucleus; (b) genome segregation in nuclei that contain multiple genome contents and (c) maintenance of genome fidelity in E. histolytica.

Prevalence of major neurological disorders among geriatric population in the metropolitan city of Kolkata

Well-conducted neuroepidemiological studies for the geriatric population are rare in India. In view of the growing aging population, we planned to determine the prevalence of common neurological disorders among the elderly population in the city of Kolkata. This was a cross-sectional study of a stratified random sample of the city population and carried in two stages through house to house survey. Initially, trained non-medical workers screened the cases with a validated family questionnaire and then a neurologist examined all the screened positive cases. A validated neuropsychological screening test was also applied among the elderly population with cognitive complaints. Results showed prevalence rates (per 1000 elderly population--> or = 60 years) of following disorders in decreasing order: stroke--33.93, essential tremor--13.76, dementia--7.89, Parkinsonism--3.30 and epilepsy--2.57. Sex-specific prevalence showed that stroke was commoner among men and that of other disorders among women. Age-specific prevalence recorded progressive increase in the rates of all disorders among both genders, though not uniformly among women. Overall the crude prevalence of neurological disorders was 60.9 per 1000. The present study shows higher rate of stroke as compared to other neurological disorders among elderly population in India, which needs urgent attention.

Structure and content of the Entamoeba histolytica genome

The intestinal parasite Entamoeba histolytica is one of the first protists for which a draft genome sequence has been published. Although the genome is still incomplete, it is unlikely that many genes are missing from the list of those already identified. In this chapter we summarise the features of the genome as they are currently understood and provide previously unpublished analyses of many of the genes.

Pulsed laser deposition of metal films and nanoparticles in vacuum using subnanosecond laser pulses

A study of silver, chromium, stainless-steel, and indium thin films prepared by subnanosecond laser deposition in vacuum is reported. We compare the laser ablation in vacuum at the weak- and tight-focusing conditions of a Ti:sapphire laser beam and analyze the nanoparticles synthesized in the latter case using absorption spectroscopy, x-ray fluorescence, atomic force microscopy, and scanning electron microscopy. Our results show that the nanoparticle formation can be accomplished using long laser pulses under tight-focusing conditions.

The genome of the protist parasite Entamoeba histolytica

Entamoeba histolytica is an intestinal parasite and the causative agent of amoebiasis, which is a significant source of morbidity and mortality in developing countries. Here we present the genome of E. histolytica, which reveals a variety of metabolic adaptations shared with two other amitochondrial protist pathogens: Giardia lamblia and Trichomonas vaginalis. These adaptations include reduction or elimination of most mitochondrial metabolic pathways and the use of oxidative stress enzymes generally associated with anaerobic prokaryotes. Phylogenomic analysis identifies evidence for lateral gene transfer of bacterial genes into the E. histolytica genome, the effects of which centre on expanding aspects of E. histolytica's metabolic repertoire. The presence of these genes and the potential for novel metabolic pathways in E. histolytica may allow for the development of new chemotherapeutic agents. The genome encodes a large number of novel receptor kinases and contains expansions of a variety of gene families, including those associated with virulence. Additional genome features include an abundance of tandemly repeated transfer-RNA-containing arrays, which may have a structural function in the genome. Analysis of the genome provides new insights into the workings and genome evolution of a major human pathogen.

Constitutive association of Mcm2-3-5 proteins with chromatin in Entamoeba histolytica

Eukaryotic cells duplicate their genome once and only once per cell cycle. Our earlier studies with the protozoan parasite, Entamoeba histolytica, have shown that genome reduplication may occur several times without nuclear or cellular division. The Mcm2-7 protein complex is required for licensing of DNA replication. In an effort to understand whether genome reduplication occurs due to absence or failure of the DNA replication licensing system, we analysed the function of Mcm2-3-5 proteins in E. histolytica. In this study, we have cloned E. histolytica (Eh) MCM2 and Eh MCM5 genes, while Eh MCM3 was cloned earlier. The sequence of Eh MCM2-3-5 genes is well conserved with other eukaryotic homologues. We have shown that Eh Mcm2,3 proteins are functional in Saccharomyces cerevisiae. Our studies in E. histolytica showed that Eh Mcm2-3-5 proteins are associated with chromatin constitutively in cycling cells and during arrest of DNA synthesis induced by serum starvation. Alternation of genome duplication with mitosis is regulated by association-dissociation of Mcm2-7 proteins with chromatin in other eukaryotes. Our results suggest that constitutive association of Mcm proteins with chromatin could be one of the reasons why genome reduplication occurs in E. histolytica.

Homology modelling of the ligand-binding domain of glucocorticoid receptor: binding site interactions with cortisol and corticosterone

Glucocorticoids are involved in the growth, development and homeostasis of a number of tissues. The physiological effects of this class of lipophilic steroids are mediated by ligand-inducible nuclear transcription factor, the glucocorticoid receptor/mineralocorticoid receptor, a member of the steroid/nuclear receptor superfamily. The glucocorticoid receptor interacts specifically with glucocorticoids, whereas the mineralocorticoid receptor interacts with both glucocorticoids and mineralocorticoids. The molecular structure of progesterone complexed to its receptor obtained from X-ray crystal structure analysis is used to build up a homology model of mouse glucocorticoid receptor ligand-binding domain (mGR LBD). The secondary structure of mGR LBD contains 11 helices, nine turns and four sheets. The mGR LBD contains a long helix, H9, with 30 residues, and exhibits slight deformation when the receptor protein binds with its cognate ligands. The mGR LBD has a 12-residue C-terminal extension (residues 772-783) that is essential for hormone binding. This extension is tightly fixed in position by an antiparallel beta-sheet interaction between amino acids 680-682 (S3) and 775-777 (S4). The three-dimensional model reveals two polar sites located at the extremities of the elongated hydrophobic ligand-binding pocket. Cortisol and corticosterone are docked to this ligand-binding pocket. The difference accessible surface area study revealed the steroid-binding region of mGR LBD.

Torture from legal viewpoint in the eyes of Human Rights Commission

The author describes the legal view points against torture in national and international level and gives a detailed idea of how Human Rights Commission views torture.

Argyrophilic nucleolar organiser regions (AgNORs) in breast lesions

Nucleolar organiser regions (NORs) demonstrated by argyrophilia of NOR-proteins are indicator of cellular proliferative activity. The NORs can be identified in the nuclei as brown or black dots with silver colloidal staining technique in formalin fixed paraffin sections and in cytology smears. Seventy-five cases including 45 tissue sections and 30 fine needle aspiration cytology (FNAC) smears of benign and malignant lesions of breast have been studied to evaluate the significance and practical application of AgNOR count per nucleus. Out of 45 tissue sections 15 belonged to fibrocystic disease, 10 fibro-adenomas and 20 carcinomas and of the 30 FNAC smears, 10 were fibrocystic disease, 8 fibro-adenomas and 12 carcinomas. In fibrocystic disease the mean AgNOR count was 1.60 (FNAC group-0.75, tissue section-1.61). In fibro-adenomas it was 1.61 (FNAC-1.63, tissue section-1.59). The mean count in carcinoma was 12.10 (FNAC-12.08, tissue section-12.10). The difference in AgNOR count in fibrocystic disease and fibro-adenoma was not significant, but that between benign breast lesion and carcinoma was significant. No difference was observed between FNAC and tissue section groups in benign or malignant lesions. The simple staining technique can be used as an additional criterion to differentiate the benign and malignant lesions of breast.

Clinicopathological study of clinically undiagnosed cases of kala-azar with special reference to grading of parasites

Clinicopathological study of 34 clinically undiagnosed cases of kala-azar has been undertaken with a view to establish the diagnosis and correlate the quantitative grading of Leishmania donovani in bone marrow/splenic aspirates with clinical features and duration of disease. The ages of the patients were between 5 and 45 years. The duration of illnesses ranged from 2-24 months with 47% having 2 months' duration. Splenomegaly was less than 7 cm in 70.5% cases. Anaemia, leucopenia and mild thrombocytopenia were present in all the cases. Aldehyde test was positive in 47% cases. Bone marrow aspiration revealed the parasites in 82.3% cases. L donovani was also observed in 66.6% cases of splenic aspiration including 6 cases where bone marrow failed to reveal the parasite. Grading of the parasites in bone marrow and splenic aspirates revealed majority of the cases (73.5%) were in 3+ and 4+ grades. No correlation between splenic size and duration of illness or parasite grading was detected. Neither any positive correlation between parasite grading and duration of illness was observed.

Dynamics of family size and composition: a computer simulation study with reference to rural India

"This study attempts to understand the dynamics that produce the persistent observation of a strong positive correlation between family size and extent of landholdings in predominantly agrarian economies [in India]. Such a correlation can arise from different types of demographic configurations including the rules of family formation. For example, big landholdings may be associated with large families, despite the lack of differentials across holdings of different size in fertility and mortality, simply because these families may remain undivided for long periods. In the absence of conclusive data to analyse this relationship in the Indian case, this study sets up a computer simulation model for studying the results of alternative demographic configurations."

Fine needle aspiration cytology of cervical lymphadenopathy with special reference to tuberculosis

One hundred eighty cases of cervical lymphadenopathy have been studied by fine needle aspiration cytological examination followed by histopathologic examination of the excised lymph nodes. The diagnostic accuracy was 84.4% for tuberculous lymphadenitis by fine needle aspiration cytological examination. Observation of caseous necrosis (84.2%) and epithelioid cells (73.6%) were the most characteristic diagnostic features in the aspirated smears. Acid-fast bacilli were observed in 45.6% cases. Metastatic carcinoma also yielded a high diagnostic accuracy ie, 89%. Fine needle aspiration cytology has been found to be safe, quick, inexpensive with high diagnostic accuracy in cervical lymphadenopathy.