Programs,databases, and expert systems for human geneticists — a survey

We present an overview of the variety of databases and programs that offer substantial aid to medical and molecular geneticists. Databases and expert systems for genetic diseases and birth defects, programs for segregation and linkage analysis, certain DNA and protein sequence databases, and information resources in general for molecular biology are addressed. These systems cannot be used effectively without the newly developed techniques of information exchange based on international computer networks. A short introduction is given to the Internet and to European institutions and organizations that offer help with the aquisition and use of bioinformatic resources.     

Inheritance of the S113L mutation within an inbred family with carnitine palmitoyltransferase enzyme deficiency

Deficiency of carnitine palmitoyltransferase type II (CPT II) is a clinically heterogeneous autosomal recessive disorder of lipid metabolism. The most common mutation in the CPT 11 gene is the S113L mutation, which substitutes leucine for serine at amino acid position 113. We studied an inbred family with three affected cousins with CPT II deficiency and found the S113L mutation to be present in a homozygous state in all three patients. Pedigree analysis traced the S 113L mutation back to one common ancestor. Although the patients in this family have an identical genotype at the CPT II locus, their clinical picture ranges from asymptomatic to lethal.     

A ZYGOTE-SPECIFIC PROTEIN WITH HYDROXYPROLINE-RICH GLYCOPROTEIN DOMAINS AND LECTIN-LIKE DOMAINS INVOLVED IN THE ASSEMBLY OF THE CELL WALL OF CHLAMYDOMONAS REINHARDTII (CHLOROPHYTA)

The cell wall of Chlamydomonas reinhardtii zygotes, which forms rapidly after the fusion of wall-free gametes, provides a tractable system for studying the properties and assembly of hydroxyproline-rich glycoproteins, the major proteinaceous components of green algal and plant cell walls. We report the cloning of the zsp2 gene and the analysis of its ZSP-2 product, a 58.9 kDa polypeptide that is synthesized exclusively by zygotes. The protein contains two (SP)_x repeats, establishing it as a member of the cell wall hydroxyproline-rich glycoproteins family. It also contains a 4-fold iteration of an amino acid sequence centered around cysteine residues, a configuration found in both plant and animal lectins. Furthermore, we report four observations on pellicle composition and production. First, cell-free preparations of the pellicle matrix are rich in hydroxyproline, arabinose, and galactose and contain bundles of very long fibrils. Second, glutathione blocks pellicle formation and results in the accumulation of long fibrils in the growth medium. Third, antibody to ZSP-2 also blocks pellicle formation. Fourth, ZSP-2 immunolocalizes to the boundary between the outer layers of the wall proper and the pellicle matrix. These observations are consistent with the possibility that the Cys-rich (glutathione-sensitive) lectin-like domains of ZSP-2 may bind to sugar residues on the long fibrils and anchor them to the cell wall, thereby initiating and maintaining pellicle formation.     

Profiling gene expression in whole blood samples following an in-vitro challenge.

Genomics tools (gene- and protein-expression studies) can be used to find possible target genes involved in a quantifiable trait or disease state. However in many instances, cells and tissues directly involved in the trait's expression, for example, brain tissue, are not amenable for gene expression analysis. Whole blood cells share a molecular make-up for cellular communication and gene regulation systems with many other cell types, for example, neuronal cells, and have the advantage of being very accessible for gene profiling. We investigated the feasibility of nationwide blood sample collection for lymphocyte RNA isolation and real-time PCR analysis to quantify genomic responses. We tested several designs for blood collection and storage: blood sampling in PAXgene blood collection tubes and storage at -20 degrees C, blood sampling in heparin tubes and decanting the samples (with or without in-vitro stimulus) into either PAXgene blood collection tubes and storage at -20 degrees C, or polypropylene tubes followed by snap-freezing and storage at -80 degrees C. The latter procedure is the best cost-wise when only small amounts of total RNA are needed for downstream applications. Lymphocyte gene expression studies are most likely hampered by the quality of isolated RNA rather than the sampling method. We show that large-scale nationwide sample collections did not alter RNA quality or gene expression levels when compared to sampling and processing in a more controlled way. To this end, we present an optimized protocol for easy and standardized isolation of high quality RNA using the PAXgene isolation kit. Based on these results, we suggest that whole blood genomic data can be used as a genomic probe in experimental and clinical research.     

Vegetative morphology and anatomy of Maundia (Maundiaceae: Alismatales) and patterns of peripheral bundle orientation in angiosperm leaves with three‐dimensional venation

Collateral bundles with external position of the phloem characterize the stem vasculature of most seed plants. An earlier study highlighted the occurrence of inverted peripheral bundles in the leafless inflorescence peduncle of the rare Australian aquatic Maundia triglochinoides. This unusual feature and other morphological and molecular data supported the recognition of the monogeneric Maundiaceae, but the anatomy of the leaves, rhizomes and roots of Maundia remained unknown and is studied here. Maundia has an iterative sympodial growth with all shoots bearing five tubular cataphylls splitting longitudinally and simulating open sheaths at maturity and two (or three) linear foliage leaves without a conspicuous basal sheath. This morphology distinguishes Maundiaceae from all other Alismatales. The rhizome has an atactostele with collateral bundles of normal orientation; peripheral bundles are absent. Cataphylls have a series of normally oriented bundles. Foliage leaves are thick, bifacial, semi‐elliptical in cross‐section, with a thin subepidermal layer of chlorenchyma on both sides, accompanied by peripheral bundles with xylem facing outwards (thus abaxial peripheral bundles are inverted) and central large bundles of normal orientation. Strong anatomical similarity between leaves and peduncles is related to their shared function as assimilatory organs. As in angiosperm succulents, the three‐dimensional leaf venation in thick aquatic and helophyte leaves of Alismatales serves to reduce transport distances between veins and photosynthetic cells. In both cases, the patterns of orientation of peripheral bundles (with inverted adaxial or abaxial bundles) are unstable in large clades. These slender bundles cannot be used for the identification of unifacial leaves. Some anatomical characters express homoplastic similarities between Maundiaceae and Aponogetonaceae.     

XPO1 Inhibition Preferentially Disrupts the 3D Nuclear Organization of Telomeres in Tumor Cells

Previous work has shown that the three‐dimensional (3D) nuclear organization of telomeres is altered in cancer cells and the degree of alterations coincides with aggressiveness of disease. Nuclear pores are essential for spatial genome organization and gene regulation and XPO1 (exportin 1/CRM1) is the key nuclear export protein. The Selective Inhibitor of Nuclear Export (SINE) compounds developed by Karyopharm Therapeutics (KPT‐185, KPT‐330/selinexor, and KPT‐8602) inhibit XPO1 nuclear export function. In this study, we investigated whether XPO1 inhibition has downstream effects on the 3D nuclear organization of the genome. This was assessed by measuring the 3D telomeric architecture of normal and tumor cells in vitro and ex vivo. Our data demonstrate for the first time a rapid and preferential disruption of the 3D nuclear organization of telomeres in tumor cell lines and in primary cells ex vivo derived from treatment‐naïve newly diagnosed multiple myeloma patients. Normal primary cells in culture as well as healthy lymphocyte control cells from the same patients were minimally affected. Using both lymphoid and non‐lymphoid tumor cell lines, we found that the downstream effects on the 3D nuclear telomere structure are independent of tumor type. We conclude that the 3D nuclear organization of telomeres is a sensitive indicator of cellular response when treated with XPO1 inhibitors. J. Cell. Physiol. 231: 2711–2719, 2016. © 2016 The Authors. Journal of Cellular Physiology published by Wiley Periodicals, Inc.