Characterization of LRRTM and NGR gene families: Expression and functions

Some leucine-rich repeat (LRR) -containing membrane proteins are known regulators of neuronal growth and synapse formation. In this work I characterize two gene families encoding neuronal LRR membrane proteins, namely the LRRTM (leucine-rich repeat, transmembrane neuronal) and NGR (Nogo-66 receptor) families. I studied LRRTM and NGR family member's mRNA tissue distribution by RT-PCR and by in situ hybridization. Subcellular localization of LRRTM1 protein was studied in neurons and in non-neuronal cells. I discovered that LRRTM and NGR family mRNAs are predominantly expressed in the nervous system, and that each gene possesses a specific expression pattern. I also established that LRRTM and NGR family mRNAs are expressed by neurons, and not by glial cells. Within neurons, LRRTM1 protein is not transported to the plasma membrane; rather it localizes to endoplasmic reticulum. Nogo-A (RTN4), MAG, and OMgp are myelin-associated proteins that bind to NgR1 to limit axonal regeneration after central nervous system injury. To better understand the functions of NgR2 and NgR3, and to explore the possible redundancy in the signaling of myelin inhibitors of neurite growth, I mapped the interactions between NgR family and the known and candidate NgR1 ligands. I identified high-affinity interactions between RTN2-66, RTN3-66 and NgR1. I also demonstrate that Rtn3 mRNA is expressed in the same glial cell population of mouse spinal cord white matter as Nogo-A mRNA, and thus it could have a role in myelin inhibition of axonal growth. To understand how NgR1 interacts with multiple structurally divergent ligands, I aimed first to map in more detail the nature of Nogo-A:NgR1 interactions, and then to systematically map the binding sites of multiple myelin ligands in NgR1 by using a library of NgR1 expression constructs encoding proteins with one or multiple surface residues mutated to alanine. My analysis of the Nogo-A:NgR1 -interactions revealed a novel interaction site between the proteins, suggesting a trivalent Nogo-A:NgR1-interaction. Our analysis also defined a central binding region on the concave side of NgR1's LRR domain that is required for the binding of all known ligands, and a surrounding region critical for binding MAG and OMgp. To better understand the biological role of LRRTMs, I generated Lrrtm1 and Lrrtm3 knock out mice. I show here that reporter genes expressed from the targeted loci can be used for maping the neuronal connections of Lrrtm1 and Lrrtm3 expressing neurons in finer detail. With regard to LRRTM1's role in humans, we found a strong association between a 70 kb-spanning haplotype in the proposed promoter region of LRRTM1 gene and two possibly related phenotypes: left-handedness and schizophrenia. Interestingly, the responsible haplotype was linked to phenotypic variability only when paternally inherited. In summary, I identified two families of neuronal receptor-like proteins, and mapped their expression and certain protein-protein interactions. The identification of a central binding region in NgR1 shared by multiple ligands may facilitate the design and development of small molecule therapeutics blocking binding of all NgR1 ligands. Additionally, the genetic association data suggests that allelic variation upstream of LRRTM1 may play a role in the development of left-right brain asymmetry in humans. Lrrtm1 and Lrrtm3 knock out mice developed as a part of this study will likely be useful for schizophrenia and Alzheimer s disease research.

Nano-confined synthesis of highly ordered mesoporous carbon and its performance as electrode material for electrochemical behavior of riboflavin (vitamin B2) and dopamine

Highly ordered mesoporous carbon (MC) has been synthesized from sucrose, a non-toxic and costeffective source of carbon. X-ray diffraction, N2 adsorption–desorption isotherm and transmission electron micrograph (TEM) were used to characterize the MC. The XRD patterns show the formation of highly ordered mesoporous structures of SBA15 and mesoporous carbon. The N2 adsorptiondesorption isotherms suggest that the MC exhibits a narrow pore-size distribution with high surface area of 1559 m2/g. The potential application of MC as a novel electrode material was investigated using cyclic voltammetry for riboflavin (vitamin B2) and dopamine. MC-modified glassy carbon electrode (MC/GC) shows increase in peak current compared to GC electrode in potassium ferricyanide which clearly suggest that MC/GC possesses larger electrode area (1.8 fold) compared with bare GC electrode. The electrocatalytic behavior of MC/GC was investigated towards the oxidation of riboflavin (vitamin B2) and dopamine using cyclic voltammetry which show larger oxidation current compared to unmodified electrode and thus MC/GC may have the potential to be used as a chemically modified electrode.

A Haplotype at the UCP1 Gene Locus Contributes to Genetic Risk for Type 2 Diabetes in Asian Indians (CURES-72)

Background: The gene encoding for uncoupling protein-1 (UCP1) is considered to be a candidate gene for type 2 diabetes because of its role in thermogenesis and energy expenditure. The objective of the study was to examine whether genetic variations in the UCP1 gene are associated with type 2 diabetes and its related traits in Asian Indians. Methods: The study subjects, 810 type 2 diabetic subjects and 990 normal glucose tolerant (NGT) subjects, were chosen from the Chennai Urban Rural Epidemiological Study (CURES), an ongoing population-based study in southern India. The polymorphisms were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Linkage disequilibrium (LD) was estimated from the estimates of haplotypic frequencies. Results: The three polymorphisms, namely -3826A -> G, an A -> C transition in the 5'-untranslated region (UTR) and Met229Leu, were not associated with type 2 diabetes. However, the frequency of the A-C-Met (-3826A -> G-5'UTR A -> C-Met229Leu) haplotype was significantly higher among the type 2 diabetic subjects (2.67%) compared with the NGT subjects (1.45%, P < 0.01). The odds ratio for type 2 diabetes for the individuals carrying the haplotype A-C-Met was 1.82 (95% confidence interval, 1.29-2.78, P = 0.009). Conclusions: The haplotype, A-C-Met, in the UCP1 gene is significantly associated with the increased genetic risk for developing type 2 diabetes in Asian Indians.

Linear time algorithms for Abelian group isomorphism and related problems

We consider the problem of determining if two finite groups are isomorphic. The groups are assumed to be represented by their multiplication tables. We present an O(n) algorithm that determines if two Abelian groups with n elements each are isomorphic. This improves upon the previous upper bound of O(n log n) [Narayan Vikas, An O(n) algorithm for Abelian p-group isomorphism and an O(n log n) algorithm for Abelian group isomorphism, J. Comput. System Sci. 53 (1996) 1-9] known for this problem. We solve a more general problem of computing the orders of all the elements of any group (not necessarily Abelian) of size n in O(n) time. Our algorithm for isomorphism testing of Abelian groups follows from this result. We use the property that our order finding algorithm works for any group to design a simple O(n) algorithm for testing whether a group of size n, described by its multiplication table, is nilpotent. We also give an O(n) algorithm for determining if a group of size n, described by its multiplication table, is Abelian. (C) 2007 Elsevier Inc. All rights reserved.

Approaches for improving the safety and efficacy of adenoviral gene therapy

Cancer is a devastating disease with poor prognosis and no curative treatment, when widely metastatic. Conventional therapies, such as chemotherapy and radiotherapy, have efficacy but are not curative and systemic toxicity can be considerable. Almost all cancers are caused due to changes in the genetic material of the transformed cells. Cancer gene therapy has emerged as a new treatment option, and past decades brought new insights in developing new therapeutic drugs for curing cancer. Oncolytic viruses constitute a novel therapeutic approach given their capacity to replicate in and kill specifically tumor cells as well as reaching tumor distant metastasis. Adenoviral gene therapy has been suggested to cause liver toxicity. This study shows that new developed adenoviruses, in particular Ad5/19p-HIT, can be redirected towards kidney while adenovirus uptake by liver is minimal. Moreover, low liver transduction resulted in a favorable tumor to liver ratio of virus load. Further, we established a new immunocompetent animal model Syrian hamsters. Wild type adenovirus 5 was found to replicate in Hap-T1 hamster tumors and normal tissues. There are no antiviral drugs available to inhibit adenovirus replication. In our study, chlorpromazine and cidofovir efficiently abrogated virus replication in vitro and showed significant reduction in vivo in tumors and liver. Once safety concerns were addressed together with the new given antiviral treatment options, we further improved oncolytic adenoviruses for better tumor penetration, local amplification and host system modulation. Further, we created Ad5/3-9HIF-Δ24-VEGFR-1-Ig, oncolytic adenovirus for improved infectivity and antiangiogenic effect for treatment of renal cancer. This virus exhibited increased anti-tumor effect and specific replication in kidney cancer cells. The key player for good efficacy of oncolytic virotherapy is the host immune response. Thus, we engineered a triple targeted adenovirus Ad5/3-hTERT-E1A-hCD40L, which would lead to tumor elimination due to tumor-specific oncolysis and apoptosis together with an anti-tumor immune response prompted by the immunomodulatory molecule. In conclusion, the results presented in this thesis constitute advances in our understanding of oncolytic virotherapy by successful tumor targeting, antiviral treatment options as a safety switch in case of replication associated side-effects, and modulation of the host immune system towards tumor elimination.  

Ion channel gene variants predisposing to severe human ventricular arrhythmias

Congenital long QT syndrome (LQTS) with an estimated prevalence of 1:2000-1:10 000 manifests with prolonged QT interval on electrocardiogram and risk for ventricular arrhythmias and sudden death. Several ion channel genes and hundreds of mutations in these genes have been identified to underlie the disorder. In Finland, four LQTS founder mutations of potassium channel genes account for up to 40-70% of genetic spectrum of LQTS. Acquired LQTS has similar clinical manifestations, but often arises from usage of QT-prolonging medication or electrolyte disturbances. A prolonged QT interval is associated with increased morbidity and mortality not only in clinical LQTS but also in patients with ischemic heart disease and in the general population. The principal aim of this study was to estimate the actual prevalence of LQTS founder mutations in Finland and to calculate their effect on QT interval in the Finnish background population. Using a large population-based sample of over 6000 Finnish individuals from the Health 2000 Survey, we identified LQTS founder mutations KCNQ1 G589D (n=8), KCNQ1 IVS7-2A>G (n=1), KCNH2 L552S (n=2), and KCNH2 R176W (n=16) in 27 study participants. This resulted in a weighted prevalence estimate of 0.4% for LQTS in Finland. Using a linear regression model, the founder mutations resulted in a 22- to 50-ms prolongation of the age-, sex-, and heart rate-adjusted QT interval. Collectively, these data suggest that one of 250 individuals in Finland may be genetically predisposed to ventricular arrhythmias arising from the four LQTS founder mutations. A KCNE1 D85N minor allele with a frequency of 1.4% was associated with a 10-ms prolongation in adjusted QT interval and could thus identify individuals at increased risk of ventricular arrhythmias at the population level. In addition, the previously reported associations of KCNH2 K897T, KCNH2 rs3807375, and NOS1AP rs2880058 with QT interval duration were confirmed in the present study. In a separate study, LQTS founder mutations were identified in a subgroup of acquired LQTS, providing further evidence that congenital LQTS gene mutations may underlie acquired LQTS. Catecholaminergic polymorphic ventricular tachycardia (CPVT) is characterized by exercise-induced ventricular arrhythmias in a structurally normal heart and results from defects in the cardiac Ca2+ signaling proteins, mainly ryanodine receptor type 2 (RyR2). In a patient population of typical CPVT, RyR2 mutations were identifiable in 25% (4/16) of patients, implying that noncoding variants or other genes are involved in CPVT pathogenesis. A 1.1 kb RyR2 exon 3 deletion was identified in two patients independently, suggesting that this region may provide a new target for RyR2-related molecular genetic studies. Two novel RyR2 mutations showing a gain-of-function defect in vitro were identified in three victims of sudden cardiac death. Extended pedigree analyses revealed some surviving mutation carriers with mild structural abnormalities of the heart and resting ventricular arrhythmias suggesting that not all RyR2 mutations lead to a typical CPVT phenotype, underscoring the relevance of tailored risk stratification of a RyR2 mutation carrier.

Data-aware task scheduling for all-to-all comparison problems in heterogeneous distributed systems

Solving large-scale all-to-all comparison problems using distributed computing is increasingly significant for various applications. Previous efforts to implement distributed all-to-all comparison frameworks have treated the two phases of data distribution and comparison task scheduling separately. This leads to high storage demands as well as poor data locality for the comparison tasks, thus creating a need to redistribute the data at runtime. Furthermore, most previous methods have been developed for homogeneous computing environments, so their overall performance is degraded even further when they are used in heterogeneous distributed systems. To tackle these challenges, this paper presents a data-aware task scheduling approach for solving all-to-all comparison problems in heterogeneous distributed systems. The approach formulates the requirements for data distribution and comparison task scheduling simultaneously as a constrained optimization problem. Then, metaheuristic data pre-scheduling and dynamic task scheduling strategies are developed along with an algorithmic implementation to solve the problem. The approach provides perfect data locality for all comparison tasks, avoiding rearrangement of data at runtime. It achieves load balancing among heterogeneous computing nodes, thus enhancing the overall computation time. It also reduces data storage requirements across the network. The effectiveness of the approach is demonstrated through experimental studies.

Gene expression profiling during Forskolin induced differentiation of BeWo cells by differential display RT-PCR

The differentiation of cytotrophoblasts into syncytiotrophoblasts in the placenta has been employed as a model to investigate stage specific expression as well as regulation of genes during this process. While the cytotrophoblasts are highly invasive and proliferative with relatively less capacity to synthesize pregnancy related proteins, the multinucleated syncytiotrophoblasts are non-proliferative and non-invasive. However, syncytiotrophoblasts are the site of synthesis of a variety of protein, peptide and steroid hormones as well as several growth factors. Both the freshly isolated cytotrophoblasts from human placenta as well as the BeWo cell, a choriocarcinoma cell line model which retain several characteristic of cytotrophoblasts has been employed by us to study regulation of differentiation. In the present study, we have employed the differential display RT-PCR analysis (DD-RT-PCR) to evaluate gene expression changes during Forskolin induced in vitro differentiation of BeWo cells. We have identified several genes which are differentially expressed during differentiation and the differential expression of 10 transcripts was confirmed by Northern blot analysis. Based on the identity of the transcripts an attempt has been made to relate the known function of the gene products, to changes observed during differentiation. Of the several transcripts, one of the transcripts, namely Secretory Leukocyte Protease Inhibitor (SLPI) which is known to have multiple functions was found to increase 15-fold in the syntiotrophoblast.

Gene Transfection Efficacies of Novel Cationic Gemini Lipids Possessing Aromatic Backbone and Oxyethylene Spacers

Six novel gemini cationic lipids based on aromatic backbone, bearing n-C14H29 or n-C16H33 hydrocarbon chains, differing in the length of oxyethylene type spacers −CH2-(CH2-O-CH2)m-CH2− between each ammonium headgroups have been synthesized, where m varies from 1 to 3. Each of these lipids formed stable suspensions in aqueous media. Cationic liposomes were prepared from each of these lipids individually and as mixtures of each cationic lipid and DOPE. These were used as nonviral gene delivery agents. Transfection studies showed that among lipids bearing n-C14H29 chains, the transfection efficacies decreased with the increase in the length of the spacer, whereas in case of lipids bearing n-C16H33 chains, the transfection efficacies increased with the increase in the length of the spacer. Lipid bearing n-C16H33 hydrocarbon chains with a [−(CH2-CH2-O-CH2-CH2-O-CH2-CH2-O-CH2-CH2)−] spacer was found to be a potent gene transfer agent and its transfection was highly serum compatible even in the presence of 50% serum conditions.

Characterization of the carbonic anhydrase gene family and other key osmoregulatory genes in Australian freshwater crayfish (genus Cherax)

Cherax quadricarinatus (Redclaw), C. destructor (Yabby) and C. cainii (Marron) are a group of economically important freshwater crayfish and have been developed for aquaculture production in many countries. As crayfish are farmed in a wide range of culture conditions, optimisation of water quality parameters, are crucial for their maximum growth performance. Previous reports have shown that fluctuations in water quality can negatively impact on growth of crayfish. Therefore, this project aims to identify and characterize the major genes that enable freshwater crayfish to persist in different water chemistries and evaluate their patterns of expression under different water parameters. Overall, this project found a number of candidate genes in all three species and determined that water chemistry had a strong influence on the expression of candidate genes. This information is important in the optimization of water quality parameters in freshwater crayfish aquaculture production.

Ordered spin-ice state in the geometrically frustrated metallic ferromagnet Sm2Mo2O7

The recent discovery of spin ice is a spectacular example of the noncoplanar spin arrangements that can arise in the pyrochlore A2B2O7 structure. We present magnetic and thermodynamic studies on the metallic ferromagnet pyrochlore Sm2Mo2O7. Our studies, carried out on oriented crystals, suggest that the Sm spins have an ordered spin-ice ground state below about T*=15 K. The temperature and field evolution of the ordered spin-ice state are governed by an antiferromagnetic coupling between the Sm and Mo spins. We propose that as a consequence of a robust feature of this coupling, the tetrahedra aligned with the external field adopt a one-in, three-out spin structure as opposed to the three-in, one-out structure in dipolar spin ices, as the field exceeds a critical value.

Neoadjuvant crizotinib in advanced inflammatory myofibroblastic tumour with ALK gene rearrangement

Background Inflammatory myofibroblastic tumours (IMTs) are rare sarcomas that were first described in the lung. They are composed of myofibroblastic mesenchymal spindle cells accompanied by an inflammatory infiltrate of plasma cells. Complete resection is the treatment of choice. There is currently no standard treatment for inoperable or recurrent disease. Expression of ALK protein triggered by ALK gene rearrangement at chromosome 2p23 has been found in 36%-60% of IMTs. Case report We report a rapid early response to crizotinib as neoadjuvant therapy, enabling surgical excision of a large ALK-translocated IMT, which resulted in complete disease clearance. To the best of our knowledge, this is the first case in the literature of a patient with IMT in whom crizotinib was used successfully in the neoadjuvant or curative setting.

Random existence of charge ordered stripes and its influence on the magnetotransport properties of La0.6Sr0.4MnO3 perovskite substituted with diamagnetic ions at Mn sublattice

Phase-singular solid solutions of La0.6Sr0.4Mn1-yMeyO3 (0 <= y <= 0.3) [Me=Li1+, Mg2+, Al3+, Ti4+, Nb5+, Mo6+ or W6+] [LSMey] perovskite of rhombohedral symmetry (space group: R (3) over barc) have been prepared wherein the valence of the diamagnetic substituent at Mn site ranged from 1 to 6. With increasing y-content in LSMey, the metal-insulator (TM-I) transition in resistivity-temperature rho(T) curves shifted to low temperatures. The magnetization studies M(H) as well as the M(T) indicated two groups for LSMey. (1) Group A with Me=Mg, Al, Ti, or Nb which are paramagnetic insulators (PIs) at room temperature with low values of M (< 0.5 mu(B)/Mn); the magnetic transition [ferromagnetic insulator (FMI)-PI] temperature (T-C) shifts to low temperatures and nearly coincides with that of TM-I and the maximum magnetoresistance (MR) of similar to 50% prevails near T-C (approximate to TM-I). (2) Group-B samples with Me=Li, Mo, or W which are FMIs with M-s=3.3-3.58 mu(B)/Mn and marginal reduction in T-C similar to 350 K as compared to the undoped LSMO (T-C similar to 378 K). The latter samples show large temperature differences Delta T=T-c-TM-I, reaching up to similar to 288 K. The maximum MR (similar to 60%) prevails at low temperatures corresponding to the M-I transition TM-I rather than around T-C. High resolution lattice images as well as microscopy analysis revealed the prevalence of inhomogeneous phase mixtures of randomly distributed charge ordered-insulating (COI) bistripes (similar to 3-5 nm width) within FMI charge-disordered regions, yet maintaining crystallographically single phase with no secondary precipitate formation. The averaged ionic radius < r(B)>, valency, or charge/radius ratio < CRR > cannot be correlated with that of large Delta T; hence cannot be used to parametrize the discrepancy between T-C and TM-I. The M-I transition is controlled by the charge conduction within the electronically heterogeneous mixtures (COI bistripes+FMI charge disordered); large MR at TM-I suggests that the spin-ordered FM-insulating regions assist the charge transport, whereas the T-C is associated with the bulk spin ordered regions corresponding to the FMI phase of higher volume fraction of which anchors the T-C to higher temperatures. The present analysis showed that the double-exchange model alone cannot account for the wide bifurcation of the magnetic and electric transitions, contributions from the charge as well as lattice degrees of freedom to be separated from spin/orbital ordering. The heterogeneous phase mixtures (COI+FMI) cannot be treated as of granular composite behavior. (c) 2008 American Institute of Physics.

First-Line afatinib versus chemotherapy in patients with non–small cell lung cancer and common epidermal growth factor receptor gene mutations and brain metastases

Introduction Metastatic spread to the brain is common in patients with non–small cell lung cancer (NSCLC), but these patients are generally excluded from prospective clinical trials. The studies, phase III study of afatinib or cisplatin plus pemetrexed in patients with metastatic lung adenocarcinoma with EGFR mutations (LUX-Lung 3) and a randomized, open-label, phase III study of BIBW 2992 versus chemotherapy as first-line treatment for patients with stage IIIB or IV adenocarcinoma of the lung harbouring an EGFR activating mutation (LUX-Lung 6) investigated first-line afatinib versus platinum-based chemotherapy in epidermal growth factor receptor gene (EGFR) mutation-positive patients with NSCLC and included patients with brain metastases; prespecified subgroup analyses are assessed in this article. Methods For both LUX-Lung 3 and LUX-Lung 6, prespecified subgroup analyses of progression-free survival (PFS), overall survival, and objective response rate were undertaken in patients with asymptomatic brain metastases at baseline (n = 35 and n = 46, respectively). Post hoc analyses of clinical outcomes was undertaken in the combined data set (n = 81). Results In both studies, there was a trend toward improved PFS with afatinib versus chemotherapy in patients with brain metastases (LUX-Lung 3: 11.1 versus 5.4 months, hazard ratio [HR] = 0.54, p = 0.1378; LUX-Lung 6: 8.2 versus 4.7 months, HR = 0.47, p = 0.1060). The magnitude of PFS improvement with afatinib was similar to that observed in patients without brain metastases. In combined analysis, PFS was significantly improved with afatinib versus with chemotherapy in patients with brain metastases (8.2 versus 5.4 months; HR, 0.50; p = 0.0297). Afatinib significantly improved the objective response rate versus chemotherapy in patients with brain metastases. Safety findings were consistent with previous reports. Conclusions These findings lend support to the clinical activity of afatinib in EGFR mutation–positive patients with NSCLC and asymptomatic brain metastases.