Application of two machine learning algorithms to genetic association studies in the presence of covariates

Background

achaete-scute complexe (AS-C) has been widely studied at genetic, developmental and evolutional levels. Genes of this family encode proteins containing a highly conserved bHLH domain, which take part in the regulation of the development of central nervous system and peripheral nervous system. Many AS-C homologs have been isolated from various vertebrates and invertebrates. Also, AS-C genes are duplicated during the evolution of Diptera. Functions besides neural development controlling have also been found in Drosophila AS-C genes.

Results

We cloned four achaete-scute homologs (ASH) from the lepidopteran model organism Bombyx mori, including three proneural genes and one neural precursor gene. Proteins encoded by them contained the characteristic bHLH domain and the three proneural ones were also found to have the C-terminal conserved motif. These genes regulated promoter activity through the Class A E-boxes in vitro. Though both Bm-ASH and Drosophila AS-C have four members, they are not in one by one corresponding relationships. Results of RT-PCR and real-time PCR showed that Bm-ASH genes were expressed in different larval tissues, and had well-regulated expressional profiles during the development of embryo and wing/wing disc.

Conclusion

There are four achaete-scute homologs in Bombyx mori, the second insect having four AS-C genes so far, and these genes have multiple functions in silkworm life cycle. AS-C gene duplication in insects occurs after or parallel to, but not before the taxonomic order formation during evolution.     

Novel tumorigenic rearrangement,Delta rfp/ret,in a papillary thyroid carcinoma from externally irradiated patient

Molecular analysis of cDNA derived from a papillary thyroid carcinoma (PTC) (follicular variant of papillary thyroid carcinoma on histology) which developed in an externally irradiated patient 4 years after exposure identified a portion of the 5' region, exons 1-3, of the rfp gene juxtaposed upstream of the fragment encoding the tyrosine kinase (TK) domain of the ret gene. The fusion gene, termed Delta rfp/ret, was the result of a balanced chromosomal translocation t(6;10) (p21.3;q11.2) confirmed by interphase FISH painting, with breakpoints occurring in introns 3 and 11 of the rfp and ret genes, respectively. Both Delta rfp/ret and reciprocal ret/rfp chimeric introns had small deletions around breakpoints consistent with presumed misrepair of a radiation-induced double-strand DNA break underlying the rearrangement. No extensive sequence homology was found between the fragments flanking the breakpoints. The fusion protein retained the propensity to form oligomers likely to be mediated by a coiled-coil of the RFP polypeptide as assessed by a yeast two-hybrid system. NIH 3T3 fibroblasts stably transfected with a mammalian expression vector encoding full-length Delta RFP/RET readily gave rise to the tumors in athymic mice suggestive of high transforming potential of the fusion protein. Thus, the Delta rfp/ret rearrangement may be involved in a causative manner in cancerogenesis and provides additional evidence of the role of activated ret oncogene in the development of a subset of papillary thyroid carcinoma.     

The apoE isoform binding properties of the VLDL receptor reveal marked differences from LRP and the LDL receptor

Apolipoprotein E (apoE) associates with lipoproteins and mediates their interaction with members of the LDL receptor family. ApoE exists as three common isoforms that have important distinct functional and biological properties. Two apoE isoforms, apoE3 and apoE4, are recognized by the LDL receptor, whereas apoE2 binds poorly to this receptor and is associated with type III hyperlipidemia. In addition, the apoE4 isoform is associated with the common late-onset familial and sporadic forms of Alzheimer's disease. Although the interaction of apoE with the LDL receptor is well characterized, the specificity of other members of this receptor family for apoE is poorly understood. In the current investigation, we have characterized the binding of apoE to the VLDL receptor and the LDL receptor-related protein (LRP). Our results indicate that like the LDL receptor, LRP prefers lipid-bound forms of apoE, but in contrast to the LDL receptor, both LRP and the VLDL receptor recognize all apoE isoforms. Interestingly, the VLDL receptor does not require the association of apoE with lipid for optimal recognition and avidly binds lipid-free apoE. It is likely that this receptor-dependent specificity for various apoE isoforms and for lipid-free versus lipid-bound forms of apoE is physiologically significant and is connected to distinct functions for these receptors.     

Drought effects on the dynamics of leaf production and senescence in field-grown Medicago arborea and Medicago citrina

Forage shrub production in the Mediterranean region is frequently limited by soil water availability. To study plant responses to water deficit under such conditions is important for improving crop management and for selecting better yielding forage shrub species. Pre-dawn leaf water potential (Ψ_pd), plant leaf area (PLA), leaf area per stem (LA_s), leaf appearance rate (LAR₁;), leaf senescence rate (LSR), individual leaf area (LA) and maximal leaf elongation rate (LER) were studied throughout the year for Medicago arborea (MA) and Medicago citrina (MC) under irrigated (control) and low rainfall field conditions, at the experimental field site of the University of the Balearic Islands in Spain. With irrigation, the highest LA and LER were observed in autumn and spring and the lowest in winter and summer. LAR; was similar for both species in autumn and winter. Throughout the spring, LAR₁ was higher for MC compared to MA. PLA was similar for both species during the autumn, winter and spring seasons; however, during the summer PLA of MA was significantly reduced by 53%. This decline was attributed to higher leaf senescence during seed maturity. As a consequence, MC maintained higher leaf area (∼ 5 m² plant⁻¹) than MA (3 m² plant⁻¹). Under natural field conditions, soil water deficit increased from February to late August. The main effect of water stress was a marked reduction in LAR₁, LA and LER reflected in lower LA_s and PLA. Leaf area was severely reduced for both species during the summer, but much more intensively in MA, which developed full leaf senescence. Thus, MC maintained higher PLA than MA (0.5 m² compared to 0.0 m²). Throughout the year, but especially in the driest months, MC was superior to MA in leaf growth parameters and PLA.     

Role of the low density lipoprotein-related protein receptor in mediation of factor VIII catabolism

In the present study, we found that catabolism of coagulation factor VIII (fVIII) is mediated by the low density lipoprotein receptor-related protein (LPR), a liver multiligand endocytic receptor. In a solid phase assay, fVIII was shown to bind to LRP (K(d) 116 nM). The specificity was confirmed by a complete inhibition of fVIII/LRP binding by 39-kDa receptor-associated protein (RAP), an antagonist of all LRP ligands. The region of fVIII involved in its binding to LRP was localized within the A2 domain residues 484-509, based on the ability of the isolated A2 domain and the synthetic A2 domain peptide 484-509 to prevent fVIII interaction with LRP. Since vWf did not inhibit fVIII binding to LRP, we proposed that LRP receptor may internalize fVIII from its complex with vWf. Consistent with this hypothesis, mouse embryonic fibroblasts that express LRP, but not fibroblasts genetically deficient in LRP, were able to catabolize (125)I-fVIII complexed with vWf, which was not internalized by the cells. These processes could be inhibited by RAP and A2 subunit of fVIII, indicating that cellular internalization and degradation were mediated by interaction of the A2 domain of fVIII with LRP. In vivo studies of (125)I-fVIII.vWf complex clearance in mice demonstrated that RAP completely inhibited the fast phase of the biphasic (125)I-fVIII clearance that is responsible for removal of 60% of fVIII from circulation. Inhibition of the RAP-sensitive phase prolonged the half-life of (125)I-fVIII in circulation by 3.3-fold, indicating that LRP receptor plays an important role in fVIII clearance.     

Effect of different soil and clove treatments in the control of white rot of garlic

Soil solarisation was consistently efficacious in reducing inoculum density to undetectable levels in a field naturally‐infested with Sclerotium cepivorum. This treatment delayed epidemic onset of white rot of garlic 2–3 months as compared with the untreated control or the inoculation of planting furrows with Glomus intraradices. Furthermore, significant reductions of disease incidence and of the standardised AUDPC were also observed in solarised plots, resulting in quantitative and qualitative yield improvement. Similar effects were observed in plots planted with tebuconazole‐treated cloves, confirming previous results, whereas Trichoderma harzianum was ineffective as a biocontrol agent, when applied to planting furrows. The inoculation of plots with G. intraradices before planting, in three consecutive years, was neither effective for disease control nor on the development of garlic, although the root systems of garlic plants from all the experimental treatments were heavily mycorrhizal at harvest, indicating the presence of native arbuscular mycorrhizal propagules in the soil and their survival after soil solarisation.     

DNA replication in mammalian cells after the action of factors of a physical, chemical or biological nature. V. The structural reorganization of replicating DNA in HeLa cells after incubation with 5-fluorodeoxyuridine

A study was made of sedimentation properties of the nucleoid (chromatin) of HeLa cells with radio- and thermostable mode of DNA synthesis induced by 5-fluorodeoxyuridine (FUdR). After the incubation of HeLa cells with FUdR (10(-6) M, 6 h or 24 h) the rate of nucleoid sedimentation was shown to rise by 40 and 25%, respectively. Maximum relaxation of the nucleoid was observed under 5 mg/ml ethidium bromide concentration in sucrose gradients. After the incubation with FUdR the nucleoid relaxes to a lesser extent, and after irradiation its response to ethidium bromide in various concentrations was similar to that of intact nucleoid, and by this property the "FUdR nucleoid" differs essentially from the irradiated "normal nucleoid". A model of chromatin structure of cells exposed to FUdR is proposed, based on the transformation of large domains in small ones, for the explanation of radioresistant DNA synthesis.     

Laser stimulation of the acupoint ‘Zusanli’ (ST.36) on the radiopharmaceutical biodistribution in <Emphasis Type="BoldItalic">Wistar</Emphasis> rats

Laser used to stimulate acupoints is called laser acupuncture (LA). It is generally believed that similar clinical responses to manual acupuncture can be achieved. Here we analysed the effects of the laser (904 nm) at the ‘Zusanli’ acupoint (ST.36) of the stomach meridian on the biodistribution of the radiopharmaceutical Na^99mTcO₄. Wistar rats were divided into control (CG) and experimental groups (EG). The EG were exposed daily to the laser (904 nm) at ST.36 with 1 joule/min (40 mW/cm²) for 1 min. The animals of the CG were not exposed to laser at all. On the 8th day after LA, the animals were sedated and Na^99mTcO₄ was administered. After 10 min, the animals were all sacrificed and the organs removed. The radioactivity was counted in each organ to calculate the percentage of radioactivity of the injected dose per gram (%ATI/g). Comparison of the %ATI/g in EG and CG was performed by Mann-Whitney test. The %ATI/g was significantly increased in the thyroid due to the stimulation of the ST.36 by laser. It is possible to conclude that the stimulation of ST.36 does lead to biological phenomena that interfere with the metabolism of the thyroid.