AKT as locus of cancer angiogenic robustness and fragility

Angiogenesis get full robustness in metastatic cancer, relapsed leukemia or lymphoma when complex positive feedback loop signaling systems become integrative. A cancer hypoxic microenvironment generates positive loops inducing formation of the vascular functional shunts. AKT is an upstream angiogenic locus of integrative robustness and fragility activated by the positive loops. AKT controls two downstream nodes the mTOR and NOS in nodal organization of the signaling genes. AKT phosphorylation is regulated by a balance of an oxidant/antioxidant. Targeting AKT locus represents new principle to control integrative angiogenic robustness by the locus chemotherapy. J. Cell. Physiol. 228: 21–24, 2013. © 2012 Wiley Periodicals, Inc.     

Ataxia-telangiectasia: Linkage analysis in highly inbred Arab and Druze families and differentiation from an ataxia-microcephaly-cataract syndrome

Summary Ataxia-telangiectasia (A-T) is a progressive autosomal recessive disease featuring neurodegeneration, immunodeficiency, chromosomal instability, radiation sensitivity and a highly increased proneness to cancer. A-T is ethnically widespread and genetically heterogeneous, as indicated by the existence of four complementation groups in this disease. Several A-T-like genetic diseases share various clinical and cellular characteristics with A-T. By using linkage analysis to study North American and Turkish A-O families, the ATA (A-T, complementation group A) gene has been mapped to chromosome 11q23. A number of Israeli Arab A-T patients coming from large, highly inbred families were assigned to group A In one of these families, an additional autosomal recessive disease was identified, characterized by ataxia, hypotonia, microcephaly and bilateral congenital cataracts. In two patients with this syndrome, normal levels of serum immunoglobulins and alpha-fetoprotein, chromosomal stability in peripheral blood lymphocytes and skin fibroblasts, and normal cellular response to treatments with X-rays and the radiomimetic drug neocarzinostatin indicated that this disease does not share, with A-T, any additional features other than ataxia. These tests also showed that another patient in this family, who is also mentally retarded, is affected with both disorders. This conclusion was further supported by linkage analysis with 11q23 markers. Lod scores between A-O and these markers, cumulated over three large Arab families, were significant and confirmed the localization of the ATA gene to aq23. However, another Druze family unassigned to a specific complementation group, showed several recombinants between A-T and the same markers, leaving the localization of the A-T gene in this family open.     

Evaluation of scanning resolution,detector choice and detector orientation to be used for accurate and time-efficient commissioning of a 6MV clinical linear accelerator

The present study is aimed at exploring different scanning parameters, detectors and their orientations for time-efficient and accurate commissioning of a 6 MV clinical linear accelerator (LINAC). Beam profiles and percentage depth dose (PDD) curves were measured with a PTW dosimetry diode, a PTW Semiflex and a PinPoint ion chamber in different orientations. To acquire beam data, equidistant (step size of 0.5 mm, 1 mm, 2 mm and 3 mm) and fanline (step size of 2–0.5 mm, 2–1 mm, 3–0.5 mm and 3-1 mm) scanning modes were employed and data measurement time was recorded. Scan time per measurement point was also varied (0.2 s, 0.5 s and 1.0 s) to investigate its effect on the accuracy and acquisition time of beam data. Accuracy of the measured data was analyzed on the basis of the variation between measured data and data modeled by a treatment planning system. Beam profiles (particularly in penumbra region) were found to be sensitive to variation in scanning resolution and showed an improved accuracy with decrease in step size, while PDD curves were affected negligibly. The accuracy of beam data obtained with the PTW dosimetry diode and the PinPoint ion chamber was higher than those obtained with the PTW Semiflex ion chamber for small fields (2?×?2 cm² and 3?×?3 cm²). However, the response of the PTW diode and the PinPoint ion chamber was significantly indifferent in these fields. Furthermore, axial orientation of the PTW Semiflex ion chamber improved accuracy of profiles and PDDs as compared to radial orientation, while such a difference was not significant for the PinPoint ion chamber. It is concluded that a scan time of 0.2 s/point with a fanline scanning resolution of 2–1 mm for beam profiles and 3 mm for PDDs are most favorable in terms of accuracy and time efficiency. For small fields (2?×?2 cm² and 3?×?3 cm²), a PinPoint ion chamber in radial orientation or a dosimetry diode in axial orientation are recommended for both beam profiles and PDDs. If a PinPoint ion chamber and a PTW dosimetry diode are not available, a Semiflex ion chamber in axial orientation may be used for small fields.

     

Isolation, characterization and expression analysis of a leaf-specific phosphoenolpyruvate carboxylase gene in Oryza sativa.

Suppression subtractive hybridization was carried out to enrich gene fragments over-expressed in rice leaves by subtraction to rice roots, from which two identical cDNA fragments were identified to encode putative phosphoenolpyruvate carboxylase. Then the corresponding full-length cDNA (Osppc) is isolated by RT-PCR and sequenced, which indicates an open reading frame of 2895bp is contained. Its deduced protein is encoded in 10 exons and shows high similarity to many other plant PEPCs. Comparing with maize and bacterial PEPCs, it is revealed that OSPPC shares many conserved domains and active sites that responsible for the structure, activity and regulation of this enzyme. Phylogenetic analysis demonstrates that OSPPC is grouped with C3 form PEPCs of wheat, maize and sorghum, which is consistent with the classification of rice. And a putative promoter element is predicted with DOF binding box, CAAT box and TATA box in the 5'-flanking sequence of Osppc gene. Moreover, Quantitative RT-PCR analyses are performed in hybrid rice and its parents, which show that Osppc is specifically expressed in leaf including leaf vein and sheath.     

Continuous representations of time-series gene expression data.

We present algorithms for time-series gene expression analysis that permit the principled estimation of unobserved time points, clustering, and dataset alignment. Each expression profile is modeled as a cubic spline (piecewise polynomial) that is estimated from the observed data and every time point influences the overall smooth expression curve. We constrain the spline coefficients of genes in the same class to have similar expression patterns, while also allowing for gene specific parameters. We show that unobserved time points can be reconstructed using our method with 10-15% less error when compared to previous best methods. Our clustering algorithm operates directly on the continuous representations of gene expression profiles, and we demonstrate that this is particularly effective when applied to nonuniformly sampled data. Our continuous alignment algorithm also avoids difficulties encountered by discrete approaches. In particular, our method allows for control of the number of degrees of freedom of the warp through the specification of parameterized functions, which helps to avoid overfitting. We demonstrate that our algorithm produces stable low-error alignments on real expression data and further show a specific application to yeast knock-out data that produces biologically meaningful results.     

Lycopersicon esculentum: Trifoliate plants recovered from anther cultures of heterozygous tftf plants

The effects of the genotype and growth medium composition on callus induction and shoot regeneration from tomato (Lycopersicon esculentum Mill) anthers were studied. Five male sterile varieties, homozygous for the recessive gene ms 10³⁵, their isogenic fertile counterparts, and nineteen sterile mutants from an F₂ population segregating for ms 10³⁵, were tested. Callus induction and shoot formation were found to be affected by the genotype. The presence of the mutant gene ms 10³⁵ greatly increased callus induction. A significant interaction concerning callus induction was found between the ms 10³⁵ gene and the general genetic background. In most of the plants shoot regeneration from the anthers was associated with various degrees of callus production. However, there was no correlation between callus production and the ability to regenerate plants from that callus. Anthers isolated from plants which were heterozygous for the recessive leaf marker trifoliate, regenerated diploid plants with trifoliate leaves. The plants retained the trifoliate phenotype for over six months in culture under non-aseptic condition. Since the trifoliate phenotype appears only in the homozygous recessive state, the evidence that these trifoliate plants are doubled haploids of sporogenic origin is discussed.     

Bud proliferation and plant regeneration in liquid-cultured philodendron treated with ancymidol and paclobutrazol

Philodendron plants propagated in liquid shake or bioreactor cultures proliferated profusely in the presence of paclobutrazol (PAC) and to a lesser extent in the presence of ancymidol (ANC). The growth retardants inhibited leaf development and induced the formation of bud clusters. Short transient treatments with low concentrations (1.7–3.4 M) of the growth retardants limited leaf growth and proliferation to a lesser extent than higher concentrations (6.8–17 M). The growth retardants had a carryover dwarfing effect in the semi-solid hardening medium, which was more pronounced at the higher concentrations or prolonged exposure periods. Regenerated plants resumed normal growth 3–6 weeks after transplanting. Treatment with growth retardants may become a useful method in the prevention of abnormal leaf growth in large-scale liquid cultures, as well as in enhancing bud proliferation.     

Purification of peptidyl-tRNA on benzoylated DEAE-cellulose columns.

The o-nitrophenylsulfenyl group, and amino protecting group in the chemical synthesis of peptidyl-tRNA was used to attach newly synthesized peptidyl-tRNA to a benzoylated DEAE-cellulose column. This facilitated the isolation of a highly purified specific tRNA with a well defined peptide chain.