Proteomic profiling of forskolin-induced differentiated BeWo cells: an in-vitro model of cytotrophoblast differentiation

Placental trophoblastic differentiation is characterized by the fusion of monolayer cytotrophoblasts into syncytiotrophoblasts. During this process of differentiation, several morphological and biochemical changes are known to occur, and this model has been employed to investigate the changes that occur at the gene and protein level during differentiation. Using the sensitive technique of proteomics [two-dimensional gel electrophoresis (2DGE)], changes in protein profile were evaluated in the control and forskolin-induced differentiated cells of trophoblastic choriocarcinoma BeWo cell line. Several proteins were differentially expressed in control and differentiated cells. Four major proteins were up-regulated as assessed by silver staining, and were further characterized as c-h-ras p 21 (phosphorylated), retinoblastoma susceptibility protein I and integrase interactor protein 1. These proteins are known to play an important role in growth arrest of cells, and thus may play a role in initiating the process of differentiation.

PriDyn: Enabling Differentiated I/O Services in Cloud Using Dynamic Priorities

Virtualization is one of the key enabling technologies for Cloud computing. Although it facilitates improved utilization of resources, virtualization can lead to performance degradation due to the sharing of physical resources like CPU, memory, network interfaces, disk controllers, etc. Multi-tenancy can cause highly unpredictable performance for concurrent I/O applications running inside virtual machines that share local disk storage in Cloud. Disk I/O requests in a typical Cloud setup may have varied requirements in terms of latency and throughput as they arise from a range of heterogeneous applications having diverse performance goals. This necessitates providing differential performance services to different I/O applications. In this paper, we present PriDyn, a novel scheduling framework which is designed to consider I/O performance metrics of applications such as acceptable latency and convert them to an appropriate priority value for disk access based on the current system state. This framework aims to provide differentiated I/O service to various applications and ensures predictable performance for critical applications in multi-tenant Cloud environment. We demonstrate through experimental validations on real world I/O traces that this framework achieves appreciable enhancements in I/O performance, indicating that this approach is a promising step towards enabling QoS guarantees on Cloud storage.

p53 and little brother p53/47: linking IRES activities with protein functions

The tumor suppressor p53 represents a paradigm for gene regulation. Its rapid induction in response to DNA damage conditions has been attributed to both increased half-life of p53 protein and also increased translation of p53 mRNA. Recent advances in our understanding of the post-transcriptional regulation of p53 include the discovery of internal ribosome entry sites (IRESs) within the p53 mRNA. These IRES elements regulate the translation of the full length as well as the N-terminally truncated isoform, p53/47. The p53/47 isoform is generated by alternative initiation at an internal AUG codon present within the p53 ORF. The aim of this review is to summarize the role of translational control mechanisms in regulating p53 functions. We discuss here in detail how diverse cellular stress pathways trigger alterations in the cap-dependent and cap-independent translation of p53 mRNA and how changes in the relative expression levels of p53 isoforms result in more differentiated p53 activity.

Who really ate the fruit? A novel approach to camera trapping for quantifying frugivory by ruminants

Tropical forest ruminants disperse several plants; yet, their effectiveness as seed dispersers is not systematically quantified. Information on frequency and extent of frugivory by ruminants is lacking. Techniques such as tree watches or fruit traps adapted from avian frugivore studies are not suitable to study terrestrial frugivores, and conventional camera traps provide little quantitative information. We used a novel time-delay camera-trap technique to assess the effectiveness of ruminants as seed dispersers for Phyllanthus emblica at Mudumalai, southern India. After being triggered by animal movement, cameras were programmed to take pictures every 2 min for the next 6 min, yielding a sequence of four pictures. Actual frugivores were differentiated from mere visitors, who did not consume fruit, by comparing the number of fruit remaining across the time-delay photograph sequence. During a 2-year study using this technique, we found that six terrestrial mammals consumed fallen P. emblica fruit. Additionally, seven mammals and one bird species visited fruiting trees but did not consume fallen fruit. Two ruminants, the Indian chevrotain Moschiola indica and chital Axis axis, were P. emblica's most frequent frugivores and they accounted for over 95% of fruit removal, while murid rodents accounted for less than 1%. Plants like P. emblica that are dispersed mainly by large mammalian frugivores are likely to have limited ability to migrate across fragmented landscapes in response to rapidly changing climates. We hope that more quantitative information on ruminant frugivory will become available with a wider application of our time-delay camera-trap technique.

An optimal weighted-average congestion based pricing scheme for enhanced QoS

Pricing is an effective tool to control congestion and achieve quality of service (QoS) provisioning for multiple differentiated levels of service. In this paper, we consider the problem of pricing for congestion control in the case of a network of nodes under a single service class and multiple queues, and present a multi-layered pricing scheme. We propose an algorithm for finding the optimal state dependent price levels for individual queues, at each node. The pricing policy used depends on a weighted average queue length at each node. This helps in reducing frequent price variations and is in the spirit of the random early detection (RED) mechanism used in TCP/IP networks. We observe in our numerical results a considerable improvement in performance using our scheme over that of a recently proposed related scheme in terms of both throughput and delay performance. In particular, our approach exhibits a throughput improvement in the range of 34 to 69 percent in all cases studied (over all routes) over the above scheme.

Link route pricing for enhanced QoS

Pricing is an effective tool to control congestion and achieve quality of service (QoS) provisioning for multiple differentiated levels of service. In this paper, we consider the problem of pricing for congestion control in the case of a network of nodes under multiple service classes. Our work draws upon [1] and [2] in various ways. We use the Tirupati pricing scheme in conjunction with the stochastic approximation based adaptive pricing methodology for queue control (proposed in [1]) for minimizing network congestion. However, unlike the methodology of [1] where pricing for entire routes is directly considered, we consider prices for individual link-service grade tuples. Further, we adapt the methodology proposed in [21 for a single-node scenario to the case of a network of nodes, for evaluating performance in terms of price, revenue rate and disutility. We obtain considerable performance improvements using our approach over that in [1]. In particular, our approach exhibits a throughput improvement in the range of 54 to 80 percent in all cases studied (over all routes) while exhibiting a lower packet delay in the range of 26 to 38 percent over the scheme in [1].

Regulation of Reproduction in the Primitively Eusocial Wasp Ropalidia marginata: on the Trail of the Queen Pheromone

Queens and workers are not morphologically differentiated in the primitively eusocial wasp, Ropalidia marginata. Upon removal of the queen, one of the workers becomes extremely aggressive, but immediately drops her aggression if the queen is returned. If the queen is not returned, this hyper-aggressive individual, the potential queen (PQ), will develop her ovaries, lose her hyper-aggression, and become the next colony queen. Because of the non-aggressive nature of the queen, and because the PQ loses her aggression by the time she starts laying eggs, we hypothesized that regulation of worker reproduction in R marginata is mediated by pheromones rather than by physical aggression. Based on the immediate loss of aggression by the PQ upon return of the queen, we developed a bioassay to test whether the queen's Dufour's gland is, at least, one of the sources of the queen pheromone. Macerates of the queen's Dufour's gland, but not that of the worker's Dufour's gland, mimic the queen in making the PQ decrease her aggression. We also correctly distinguished queens and workers of R. marginata nests by a discriminant function analysis based on the chemical composition of their respective Dufour's glands.

Heat-shock protein 70-2 (HSP70-2) expression in bladder urothelial carcinoma is associated with tumour progression and promotes migration and invasion

Purpose: Testis specific heat-shock protein 70-2 (HSP70-2), a member of HSP70 chaperone family, is essential for the growth of spermatocytes and cancer cells. We investigated the association of HSP70-2 expression with clinical behaviour and progression of urothelial carcinoma of bladder. Experimental design: We assessed the HSP70-2 expression by RT-PCR and HSP70-2 protein expression by immunofluorescence, flow cytometry, immunohistochemistry and Western blotting in urothelial carcinoma patient specimens and HTB-1, UMUC-3, HTB-9, HTB-2 and normal human urothelial cell lines. Further, to investigate the role of HSP70-2 in bladder tumour development, HSP70-2 was silenced in the high-grade invasive HTB-1 and UMUC-3 cells. The malignant properties of urothelial carcinoma cells were examined using colony formation, migration assay, invasion assay in vitro and tumour growth in vivo. Results: Our RT-PCR analysis and immunohistochemistry analysis revealed that HSP70-2 was expressed in both moderate to well-differentiated and high-grade invasive urothelial carcinoma cell lines studied and not in normal human urothelial cells. In consistence with these results, HSP70-2 expression was also observed in superficially invasive (70%) and muscle-invasive (90%) patient's tumours. Furthermore, HSP70-2 knockdown significantly suppressed cellular motility and invasion ability. An in vivo xenograft study showed that inhibition of HSP70-2 significantly suppressed tumour growth. Conclusions: In conclusion, our data suggest that the HSP70-2 expression is associated with early spread and progression of urothelial carcinoma of bladder cancer and that HSP70-2 can be the potential therapeutic target for bladder urothelial carcinoma. (C) 2009 Elsevier Ltd. All rights reserved.

QoS with selfish nodes in wireless networks

The IEEE 802.1le medium access control (MAC) standard provides distributed service differentiation or Quality-of- Service (QoS) by employing a priority system. In 802.1 le networks, network traffic is classified into different priorities or access categories (ACs). Nodes maintain separate queues for each AC and packets at the head-of-line (HOL) of each queue contend for channel access using AC-specific parameters. Such a mechanism allows the provision of differentiated QoS where high priority, performance sensitive traffic such as voice and video applications will enjoy less delay, greater throughput and smaller loss, compared to low priority traffic (e. g. file transfer). The standard implicitly assumes that nodes are honest and will truthfully classify incoming traffic into its appropriate AC. However, in the absence of any additional mechanism, selfish users can gain enhanced performance by selectively classifying low priority traffic as high priority, potentially destroying the QoS capability of the system.

Karyotype instability in the ponerine ant genus Diacamma

The queenless ponerine ant Diacamma ceylonense and a population of Diacamma from the Nilgiri hills which we refer to as `nilgiri', exhibit interesting similarities as well as dissimilarities. Molecular phylogenetic study of these morphologically almost similar taxa has shown that D ceylonense is closely related to `nilgiri' and indicates that `nilgiri' is a recent diversion in the Diacamma phylogenetic tree. However, there is a striking behavioural difference in the way reproductive monopoly is maintained by the respective gamergates (mated egg laying workers), and there is evidence that they are genetically differentiated, suggesting a lack of gene flow To develop a better understanding of the mechanism involved in speciation of Diacamma, we have analysed karyotypes of D. ceylonense and `nilgiri' In both, we found surprising inter-individual and intra-individual karyotypic mosaicism. The observed numerical variability, both at intra-individual and inter-individual levels, does not appear to have hampered the sustainability of the chromosomal diversity in each population under study Since the related D. indicum, displays no such intra-individual or inter-Individual variability whatsoever under identical experimental conditions, these results are unlikely to he artifacts. Although no known mechanisms can account for the observed karyotypic variability of this nature, we believe that the present findings on the ants under study would provide opportunities for exciting new discoveries concerning the origin, maintenance and significance of intra-individual and inter-individual karyotypic mosaicism.

Thermodynamics of Cobalt (II, III) Oxide (Co3O4): Evidence of Phase Transition

The Gibbs' energy change for the reaction, 3CoO (r.s.)+1/2O2(g)→Co3O4(sp), has been measured between 730 and 1250 K using a solid state galvanic cell: Pt, CuO+Cu2O|(CaO)ZrO2|CoO+Co3O4,Pt. The emf of this cell varies nonlinearly with temperature between 1075 and 1150 K, indicating a second or higher order phase transition in Co3O4around 1120 (±20) K, associated with an entropy change of ∼43 Jmol-1K-1. The phase transition is accompanied by an anomalous increase in lattice parameter and electrical conductivity. The cubic spinel structure is retained during the transition, which is caused by the change in CO+3 ions from low spin to high spin state. The octahedral site preference energy of CO+3 ion in the high spin state has been evaluated as -24.8 kJ mol-1. This is more positive than the value for CO+2 ion (-32.9 kJ mol-1). The cation distribution therefore changes from normal to inverse side during the phase transition. The transformation is unique, coupling spin unpairing in CO+3 ion with cation rearrangement on the spinel lattice, DTA in pure oxygen revealed a small peak corresponding to the transition, which could be differentiated from the large peak due to decomposition. TGA showed that the stoichiometry of oxide is not significantly altered during the transition. The Gibbs' energy of formation of Co3O4 from CoO and O2 below and above phase transition can be represented by the equations:ΔG0=-205,685+170.79T(±200) J mol-1(730-1080 K) and ΔG0=-157,235+127.53T(±200) J mol-1(1150-1250 K).

DNA Polymerase4 from the Silk Glands of Bombyx mori

The silk gland of Bombyx mori is a terminally differentiated tissue in which DNA replication continues without cell or nuclear division during larval development. DNA polymerase-delta activity increases in the posterior and middle silk glands during the development period, reaching maximal levels in the middle of the fifth instar larvae. The enzyme has been purified to homogeneity by a series of column chromatographic and affinity purification steps. It is a multimer comprising of three heterogeneous subunits, M(r) 170,000, 70,000, and 42,000. An auxiliary protein from B. mori silk glands, analogous to the proliferating cell nuclear antigen, enhances the processivity of the enzyme and stimulates catalytic activity by 3-fold. This auxiliary protein has also been purified to homogeneity. It is a dimer comprised of a single type M(r) 40,000 subunit. Polymerase-delta possesses an intrinsic 3' --> 5' exonuclease activity which participates in proofreading by mismatch match repair during DNA synthesis and is devoid of any primase activity. DNA polymerase-delta activity could be further distinguished from polymerase-alpha from the same tissue based on its sensitivity to various inhibitors and polyclonal antibodies to the individual enzymes. Like DNA polymerase-alpha, polymerase-delta is also tightly associated with the nuclear matrix. The polymerase alpha-primase complex could be readily separated from polymerase-delta (exonuclease) in the purification protocol adopted. DNA polymerase-delta from B. mori silk glands resembles the mammalian delta-polymerases. Considering that both DNA polymerase-delta and -alpha are present in nearly equal amounts in this highly replicative tissue and their close association with the nuclear matrix, the involvement of both the enzymes in the chromosomal endoreplication process in B. mori is strongly implicated.

Efficiency of nonhomologous DNA end joining varies among somatic tissues, despite similarity in mechanism

Failure to repair DNA double-strand breaks (DSBs) can lead to cell death or cancer. Although nonhomologous end joining (NHEJ) has been studied extensively in mammals, little is known about it in primary tissues. Using oligomeric DNA mimicking endogenous DSBs, NHEJ in cell-free extracts of rat tissues were studied. Results show that efficiency of NHEJ is highest in lungs compared to other somatic tissues. DSBs with compatible and blunt ends joined without modifications, while noncompatible ends joined with minimal alterations in lungs and testes. Thymus exhibited elevated joining, followed by brain and spleen, which could be correlated with NHEJ gene expression. However, NHEJ efficiency was poor in terminally differentiated organs like heart, kidney and liver. Strikingly, NHEJ junctions from these tissues also showed extensive deletions and insertions. Hence, for the first time, we show that despite mode of joining being generally comparable, efficiency of NHEJ varies among primary tissues of mammals.

DNA polymerase alpha-primase complex from the silk glands of the non-mulberry silkworm Philosamia ricini.

The DNA content in the silk glands of the non-mulberry silkworm Philosamia ricini increases continuously during the fourth and fifth instars of larval development indicating high levels of DNA replication in this terminally differentiated tissue. Concomitantly, the DNA polymerase alpha activity also increases in the middle and the posterior silk glands during development, reaching maximal levels in the middle of the fifth larval instar. A comparable level of DNA polymerase delta/epsilon was also observed in this highly replicative tissue. The DNA polymerase alpha-primase complex from the silk glands of P. ricini has been purified to homogeneity by conventional column chromatography as well as by immunoaffinity techniques. The molecular mass of the native enzyme is 560 kDa and the enzyme comprises six non-identical subunits. The identity of the enzyme as DNA polymerase alpha has been established by its sensitivity to inhibitors such as aphidicolin, N-ethylmaleimide, butylphenyl-dGTP, butylanilino-dATP and antibodies to polymerase alpha. The enzyme possesses primase activity capable of initiating DNA synthesis on single-stranded DNA templates. The tight association of polymerase and primase activities at a constant ratio of 6:1 is observed through all the purification steps. The 180 kDa subunit harbours the polymerase activity, while the primase activity is associated with the 45 kDa subunit.

Use of running fractal dimension for the analysis of changing patterns in electroencephalograms

Running fractal dimensions were measured on four channels of an electroencephalogram (EEG) recorded from a normal volunteer. The changes in the background activity due to eye closure were clearly differentiated by the fractal method. The compressed spectral array (CSA) and the running fractal dimensions of the EEG showed corresponding changes with respect to change in the background activity. The fractal method was also successful in detecting low amplitude spikes and the changes in the patterns in the EEG. The effects of different window lengths and shifts on the running fractal dimension have also been studied. The utility of fractal method for EEG data compression is highlighted.