Human embryonic stem cells carrying mutations for severe genetic disorders

Human embryonic stem cells (HESCs) carrying specific mutations potentially provide a valuable tool for studying genetic disorders in humans. One preferable approach for obtaining these cell lines is by deriving them from affected preimplantation genetically diagnosed embryos. These unique cells are especially important for modeling human genetic disorders for which there are no adequate research models. They can be further used to gain new insights into developmentally regulated events that occur during human embryo development and that are responsible for the manifestation of genetically inherited disorders. They also have great value for the exploration of new therapeutic protocols, including gene-therapy-based treatments and disease-oriented drug screening and discovery. Here, we report the establishment of 15 different mutant human embryonic stem cell lines derived from genetically affected embryos, all donated by couples undergoing preimplantation genetic diagnosis in our in vitro fertilization unit. For further information regarding access to HESC lines from our repository, for research purposes, please email dalitb@tasmc.health.gov.il.     

Identification of a novel alternatively spliced variant endothelin converting enzyme-1 lacking a transmembrane domain

Endothelin-converting enzyme (ECE)-1 cleaves big endothelins, as well as bradykinin and beta-amyloid peptide. Several isoforms of ECE-1 (ECE-1a, 1b, 1c, and 1d) have been identified to date, they differ only in their amino terminus and share the catalytic domain located in the C-terminal end. In addition to full-length ECE-1 forms, we identified novel, alternatively spliced messenger RNAs (mRNAs) of ECE-1b, 1c, and 1d. These splice variants (SVs) lack exon 3', which codes for the transmembrane (TM) region and is present in full-length forms. SV mRNAs were highly expressed in endothelial cells (EC) derived from macrovascular and microvascular beds. Analyses of ECE-1d and its SV forms in stably transfected human embryonic kidney (HEK)-293 cells revealed that both proteins were recognized by antibodies to C-terminal ECE-1, but an antibody to the N-terminal only bound ECE-1d. The novel protein, designated ECE-1sv, has an apparent molecular weight of 75 kDa. ECE-1sv lacks the TM sequence (or signal peptide) and, therefore, is expected to remain cytosolic. Presence of ECE-1sv in different cellular compartments than the full-length forms of the ECE-1 may suggest a distinct physiologic role for these proteins.     

The generality of the island rule reexamined

Aim  M.V. Lomolino and colleagues have recently reviewed the island rule in mammals and other vertebrates, claiming it is a general pattern. They have portrayed our recent analysis as weakly supporting the island rule, seeing weakness in our use of what they considered to be inadequate size indices (skulls and teeth, rather than mass or body length) and in our use of large islands. They argue that size evolution on islands points to a bauplan-specific fundamental size. We aim to test the generality of the rule and the adequacy of some of the data used to support it.
Location  Insular environments world-wide.
Methods  We collate and analyse data on skull sizes of carnivores and body masses of mammals in general to see whether there is a graded trend from dwarfism in large species to gigantism in smaller ones.
Results  The island rule is not supported with either the carnivore or the mammal data sets. Island area does not influence size change.
Main conclusions  Our results suggest that data recently advanced in support of the island rule are inadequate and that the island rule is not a general pattern for all mammals.     

Parabolic movement primitives and cortical states: merging optimality with geometric invariance

Previous studies have suggested that several types of rules govern the generation of complex arm movements. One class of rules consists of optimizing an objective function (e.g., maximizing motion smoothness). Another class consists of geometric and kinematic constraints, for instance the coupling between speed and curvature during drawing movements as expressed by the two-thirds power law. It has also been suggested that complex movements are composed of simpler elements or primitives. However, the ability to unify the different rules has remained an open problem. We address this issue by identifying movement paths whose generation according to the two-thirds power law yields maximally smooth trajectories. Using equi-affine differential geometry we derive a mathematical condition which these paths must obey. Among all possible solutions only parabolic paths minimize hand jerk, obey the two-thirds power law and are invariant under equi-affine transformations (which preserve the fit to the two-thirds power law). Affine transformations can be used to generate any parabolic stroke from an arbitrary parabolic template, and a few parabolic strokes may be concatenated to compactly form a complex path. To test the possibility that parabolic elements are used to generate planar movements, we analyze monkeys’ scribbling trajectories. Practiced scribbles are well approximated by long parabolic strokes. Of the motor cortical neurons recorded during scribbling more were related to equi-affine than to Euclidean speed. Unsupervised segmentation of simulta- neously recorded multiple neuron activity yields states related to distinct parabolic elements. We thus suggest that the cortical representation of movements is state-dependent and that parabolic elements are building blocks used by the motor system to generate complex movements.     

Phytoplankton in the physical environment: beyond nutrients, at the end, there is some light

This article summarizes the outcomes of the 15th Workshop of the International Association for Phytoplankton Taxonomy and Ecology. Four major issues dealing with the role of physical factors in phytoplankton ecology were addressed in the articles of this special volume: global change and its likely impacts on phytoplankton, the role of physical factors in the autecology of particular species, impacts on the inocula for the following years, and the role of light in shaping phytoplankton dynamics. Case studies from different types of aquatic environments (rivers, deep and shallow lakes, floodplain lakes, wetlands, oxbows, and even the deep ocean) and from diverse geographical locations (not only from the Mediterranean and temperate regions, but also from subtropical and tropical ones) have shown that physical forcing exerts a variety of selective pressures with impacts ranging from molding shape and size of organisms to modifying, through cascade effects, the structure of whole ecosystems.     

Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics

Mass spectrometry (MS)-based proteomics is increasingly applied in a quantitative format, often based on labeling of samples with stable isotopes that are introduced chemically or metabolically. In the stable isotope labeling by amino acids in cell culture (SILAC) method, two cell populations are cultured in the presence of heavy or light amino acids (typically lysine and/or arginine), one of them is subjected to a perturbation, and then both are combined and processed together. In this study, we describe a different approach--the use of SILAC as an internal or 'spike-in' standard--wherein SILAC is only used to produce heavy labeled reference proteins or proteomes. These are added to the proteomes under investigation after cell lysis and before protein digestion. The actual experiment is therefore completely decoupled from the labeling procedure. Spike-in SILAC is very economical, robust and in principle applicable to all cell- or tissue-based proteomic analyses. Applications range from absolute quantification of single proteins to the quantification of whole proteomes. Spike-in SILAC is especially advantageous when analyzing the proteomes of whole tissues or organisms. The protocol describes the quantitative analysis of a tissue sample relative to super-SILAC spike-in, a mixture of five SILAC-labeled cell lines that accurately represents the tissue. It includes the selection and preparation of the spike-in SILAC standard, the sample preparation procedure, and analysis and evaluation of the results.     

Gloeotrichia pisum in Lake Kinneret: A successful epiphytic cyanobacterium

With climate change and re-oligotrophication of lakes due to restoration efforts, the relative importance of benthic cyanobacteria is increasing, but they are much less studied than their planktonic counterparts. Following a major water level rise event that inundated massive reed stands in Lake Kinneret, Israel, we discovered the appearance of a vast abundance of Gloeotrichia pisum (cyanobacteria). This provided an opportunity to investigate the biology and ecology of a benthic epiphytic colonial cyanobacterium, proliferating under altered environmental conditions, with possible toxin production potential and as a model for an invasive epiphyte. The species was identified by its typical morphology, and by sequencing its 16S rRNA gene and the intragenic space. We report on the abundance and spatial distribution of the detected colonies, their morphological characteristics, and pigment composition. High phycoerythrin content provides a brownish color and supports growth at low light levels. Genomic community composition analysis revealed that G. pisum colonies host a diverse microbial community of microalgae, cyanobacteria, bacteria, and archaea with a conserved and characteristic taxonomic composition. The Synechococcales order showed high relative abundance in the colony, as well as other prokaryotes producing secondary metabolites, such as the rhodopsin producer Pseudorhodobacter. The microbial consortium in the colonies performed nitrogen fixation. The diazotroph's phylogenetic relations were demonstrated. Tests for the presence of cyanotoxins (microcystin and cylindrospermopsin) proved negative. This study is the first documentation of this genus in Israel, providing insights into the invasive nature of G. pisum and the ecological implications of its appearance in a lake ecosystem.     

Phase-resetting curve determines how BK currents affect neuronal firing

BK channels are large conductance potassium channels gated by calcium and voltage. Paradoxically, blocking these channels has been shown experimentally to increase or decrease the firing rate of neurons, depending on the neural subtype and brain region. The mechanism for how this current can alter the firing rates of different neurons remains poorly understood. Using phase-resetting curve (PRC) theory, we determine when BK channels increase or decrease the firing rates in neural models. The addition of BK currents always decreases the firing rate when the PRC has only a positive region. When the PRC has a negative region (type II), BK currents can increase the firing rate. The influence of BK channels on firing rate in the presence of other conductances, such as I _m and I _h , as well as with different amplitudes of depolarizing input, were also investigated. These results provide a formal explanation for the apparently contradictory effects of BK channel antagonists on firing rates.     

A Simple Solvation Model Along with A Multibody Dynamics Strategy (MBO(N)D) Produces Stable DNA Simulations that are Faster than Traditional Atomistic Methods

Abstract

We are developing solvation strategies that complement the speed advantage of MBO(N)D (a multibody simulation approach developed by Moldyn) for simulating biomolecular systems. In this report we propose to approximate the effect of bulk waters on DNA by using only a thin layer of waters proximate to the surface of DNA (which we will call the ‘thin shell approach’ or TSA). We will show that the TSA combined with substructuring (the grouping of atoms into rigid or flexible bodies) of the Dickerson dodecamer produces good comparisons with standard atomistic methods (over a nanosecond trajectory) as judged by a variety of DNA specific geometric (e.g., CURVES output) and dynamics (power spectra) properties. The MBO(N)D method, however, was faster than atomistic by a factor of six using the same solvation strategy and factor of 70 when compared to fully solvated atomistic system. The key to the speed of MBO(N)D is in its ability to use large time steps during dynamics. By keeping only a shell of molecules of water proximate to the dodecamer, we limit artifacts due to surface tension at the water-vacuum interface. These proximate waters are fairly immobile as compared to those in bulk and therefore do not severely limit the time step in the simulation. The strengths and limitations of this solvation approach, and future directions, will also be discussed.