In silico gene selection strategy for custom microarray design

Microarray technology has become an important tool for studying large-scale gene expression for a diversity of biological applications. However, there are a number of experimental settings for which commercial arrays are either unsuitable or unavailable despite the existence of sequence information. With the increasing availability of custom array manufacturing services, it is now feasible to design high-density arrays for any organism having sequence data. However, there have been relatively few reports discussing gene selection, an important first step in array design. Here we propose an in silico strategy for custom microarray gene selection that is applicable to a wide range of organisms, based on utilizing public domain microarray information to interrogate existing sequence data and to identify a set of homologous genes in any organism of interest. We demonstrate the utility of this approach by applying it to the selection of candidate genes for a custom Xenopus laevis microarray. A significant finding of this study is that 3%-4% of Xenopus expressed sequence tags (ESTs) are in an orientation contrary to that indicated in the public database entry (http://mssaha.people.wm.edu/suppMSS.html).     

Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes

Background  

Inteins are self-splicing protein elements. They are translated as inserts within host proteins that excise themselves and ligate the flanking portions of the host protein (exteins) with a peptide bond. They are encoded as in-frame insertions within the genes for the host proteins. Inteins are found in all three domains of life and in viruses, but have a very sporadic distribution. Only a small number of intein coding sequences have been identified in eukaryotic nuclear genes, and all of these are from ascomycete or basidiomycete fungi.     

The lateral hypothalamic area

Summary An ultrastructural analysis of the rat lateral hypothalamic area (LHA) was undertaken in order to provide an initial step in the characterization of this complex area which appears to participate in a number of important neural functions. The organization of the normal tuberal LHA was compared to the area following acute and chronic denervating lesions. In the normal animal, the principal features of the LHA are the presence of lateral hypothalamic neurons, a major sagittal pathway (the medial forebrain bundle, MFB) and the interposed neuropil richly populated by a variety of synaptic terminal types. Alterations in the synaptic organization of the LHA following rostral and caudal MFB lesions were most pronounced in animals with acute and chronic caudal lesions. A 10% reduction of synaptic terminals containing 800–1000 Å diameter dense core vesicles and a 10% increase in terminals containing lucent core vesicles was observed in animals with caudal lesions while no significant redistribution of synaptic terminal types occurred with rostral lesions. The preliminary degeneration experiments indicate that identification of the numerous and diverse afferents to the LHA neuropil may be aided by this method but that a detailed and systematic ultrastructural analysis will be required to identify sources of input with certainty.Presented in part at the 27th Annual Meeting of the American Academy of Neurology, Bal Harbour, FLA, 1975Recipient of Research Associate Award, Veterans AdministrationSupported by the Veterans Administration and by NIH Grants NS 12080. Skilled technical assistance was provided by Robin Isaacs, Marilyn Woodward and Sharon Keigher     

Echinococcus multilocularis: relationship between persistent inflammation, serum amyloid A protein response and amyloidosis in four mouse strains

LPS-hyporesponsive (C3H/HeJ) and LPS-sensitive (C57BL/6, CBA/J, C3H/HeSn) strains of mice were infected intraperitoneally with 50 alveolar hydatid cysts (AHC) to assess the effect of protracted severe inflammation on serum amyloid A protein (SAA) concentrations, splenic amyloid deposition, and pre- and postamyloidotic alterations in the splenic architecture. In general, the SAA concentrations in all the four mouse strains showed a moderate but steady increase throughout the course of infection. Splenic amyloid deposition commenced between 6 to 8 weeks postinfection (p.i.) when the SAA concentrations were relatively low and increased progressively until 12 weeks p.i. when 52 to 78% of the splenic parenchyma was obliterated. CBA mice which harbored the largest AHC throughout the 12-week course of infection showed the poorest SAA and amyloid responses; the situation was reversed in the C3H/HeSn strain. Histologically, most of the splenic follicles, during the stage of maximum amyloid deposition, appeared hypocellular. Their T-cell-dependent periarterial sinuses were either totally depleted of cells or contained plasma cells or myeloid cells. These results show that (a) there is no direct correlation between the intensity of inflammation, SAA concentrations, or amounts of amyloid deposition in either of the four mouse strains and (b) amyloidosis secondary to AHC infection differs from other experimental mouse models of amyloidosis in the magnitude of SAA elevation during the preamyloid phase.