CRISPR-CAS9 D10A nickase target-specific fluorescent labeling of double strand DNA for whole genome mapping and structural variation analysis

We have developed a new, sequence-specific DNA labeling strategy that will dramatically improve DNA mapping in complex and structurally variant genomic regions, as well as facilitate high-throughput automated whole-genome mapping. The method uses the Cas9 D10A protein, which contains a nuclease disabling mutation in one of the two nuclease domains of Cas9, to create a guide RNA-directed DNA nick in the context of an in vitro-assembled CRISPR-CAS9-DNA complex. Fluorescent nucleotides are then incorporated adjacent to the nicking site with a DNA polymerase to label the guide RNA-determined target sequences. This labeling strategy is very powerful in targeting repetitive sequences as well as in barcoding genomic regions and structural variants not amenable to current labeling methods that rely on uneven distributions of restriction site motifs in the DNA. Importantly, it renders the labeled double-stranded DNA available in long intact stretches for high-throughput analysis in nanochannel arrays as well as for lower throughput targeted analysis of labeled DNA regions using alternative methods for stretching and imaging the labeled long DNA molecules. Thus, this method will dramatically improve both automated high-throughput genome-wide mapping as well as targeted analyses of complex regions containing repetitive and structurally variant DNA.     

A Study of Normal Heart Sounds,Heart Size,Arterial Pressure and Electrocardiograms From Infancy to Early Adulthood in One Male and One Female

This study forms part of a project to define the range of normal for heart sounds and murmurs. Using the method of writing quantitative symbol phonocardiograms, data were collected on one female and one male subject from earliest infancy to adulthood (aged 27 and 25). Serial measurements of heart size, arterial pressure and records of electrocardiograms and electrophonocardiograms were made. The heart sounds are shorter and somewhat less loud under the age of two years than later. Physiologic splitting of the first and second sounds, a physiologic systolic murmur, the appearance and disappearance of a third sound are shown in the illustrations which epitomize this study. These longitudinal studies of age period changes in the electrocardiogram reveal what has been learned from the horizontal studies. The shape of the cardiac silhouette as recorded between the ages of 5 and 8 years seems to predict the adult shape. The adult type of arterial pressure became established in the early teens.     

An alkali-soluble polysaccharide from the cell walls of Coprinus lagopus

An alkali-soluble polysaccharide was isolated from the purified mycelial walls of Coprinus lagopus. The hydrolysis products, optical rotation, and infrared spectrum indicate a -glucan. Hydrolysis of the glucan after permethylation gave only 2,3,4,6-tetra-, 2,4,6-tri-, and 2,4-di-O-methyl-d-glucose. These methylated sugars and their relative quantities reveal that the glucan is a polysaccharide containing -1,3-linked glucose units with about 14% of the sugars having 1,6-linked branch points. Partial hydrolysis of the product derived from Smith degradation of the glucan released laminaribiose and gentiobiose suggesting that the branches are generally longer than a single glucose unit.Adapted from a portion of a dissertation submitted in partial fullfillment of the requirements for the Ph.D. degree in botany at the University of Connecticut under the direction of Dr. Ralph P. Collins     

Co-Expression of Anti-Rotavirus Proteins (Llama VHH Antibody Fragments) in Lactobacillus: Development and Functionality of Vectors Containing Two Expression Cassettes in Tandem

Rotavirus is an important pediatric pathogen, causing severe diarrhea and being associated with a high mortality rate causing approximately 500 000 deaths annually worldwide. Even though some vaccines are currently available, their efficacy is lower in the developing world, as compared to developed countries. Therefore, alternative or complementary treatment options are needed in the developing countries where the disease burden is the largest. The effect of Lactobacillus in promoting health and its use as a vehicle for delivery of protein and antibody fragments was previously shown. In this study, we have developed co-expression vectors enabling Lactobacillus paracasei BL23 to produce two VHH fragments against rotavirus (referred to as anti-rotavirus proteins 1 and 3, ARP1 and ARP3) as secreted and/or surface displayed products. ARP1 and ARP3 fragments were successfully co-expressed as shown by Western blot and flow cytometry. In addition, engineered Lactobacillus produced VHH antibody fragments were shown to bind to a broad range of rotavirus serotypes (including the human rotavirus strains 69M, Va70, F45, DS1, Wa and ST3 and simian rotavirus strains including RRV and SA11), by flow cytometry and ELISA. Hereby, we have demonstrated for the first time that when RRV was captured by one VHH displayed on the surface of co-expressor Lactobacillus, targeting other epitope was possible with another VHH secreted from the same bacterium. Therefore, Lactobacillus producing two VHH antibody fragments may potentially serve as treatment against rotavirus with a reduced risk of development of escape mutants. This co-expression and delivery platform can also be used for delivery of VHH fragments against a variety of mucosal pathogens or production of other therapeutic molecules.     

Electrostatic model of S4 motion in voltage-gated ion channels

The S4 transmembrane domain of the family of voltage-gated ion channels is generally thought to be the voltage sensor, whose translocation by an applied electric field produces the gating current. Experiments on hSkMI Na(+) channels and both Shaker and EAG K(+) channels indicate which S4 residues cross the membrane-solution interface during activation gating. Using this structural information, we derive the steady-state properties of gating-charge transfer for wild-type and mutant Shaker K(+) channels. Assuming that the energetics of gating is dominated by electrostatic forces between S4 charges and countercharges on neighboring transmembrane domains, we calculate the total energy as a function of transmembrane displacement and twist of the S4 domain. The resulting electrostatic energy surface exhibits a series of deep energy minima, corresponding to the transition states of the gating process. The steady-state gating-charge distribution is then given by a Boltzmann distribution among the transition states. The resulting gating-charge distributions are compared to experimental results on wild-type and charge-neutralized mutants of the Shaker K(+) channel.     

B cell selection defects underlie the development of diabetogenic APCs in nonobese diabetic mice

One mechanism whereby B cells contribute to type 1 diabetes in nonobese diabetic (NOD) mice is as a subset of APCs that preferentially presents MHC class II-bound pancreatic beta cell Ags to autoreactive CD4 T cells. This results from their ability to use cell surface Ig to specifically capture beta cell Ags. Hence, we postulated a diabetogenic role for defects in the tolerance mechanisms normally blocking the maturation and/or activation of B cells expressing autoreactive Ig receptors. We compared B cell tolerance mechanisms in NOD mice with nonautoimmune strains by using the IgHEL and Ig3-83 transgenic systems, in which the majority of B cells recognize one defined Ag. NOD- and nonautoimmune-prone mice did not differ in ability to delete or receptor edit B cells recognizing membrane-bound self Ags. However, in contrast to the nonautoimmune-prone background, B cells recognizing soluble self Ags in NOD mice did not undergo partial deletion and were also not efficiently anergized. The defective induction of B cell tolerance to soluble autoantigens is most likely responsible for the generation of diabetogenic APC in NOD mice.     

Third meeting of the International Society for Phylogenetic Nomenclature: a report

The Third Meeting of the International Society for Phylogenetic Nomenclature (ISPN) convened at Dalhousie University in Halifax, Canada, from 20 to 22 July 2008. In addition to contributed talks, the conference included a progress report on the PhyloCode 'Companion Volume', a discussion of how to complete this book in a timely fashion, a demonstration of the online registration data base (RegNum), plenary talks, and Council and business meetings. Topics discussed at the meeting include problems created by rank-based nomenclature in various eukaryotic taxa, dealing with hybrids in rank-based and phylogenetic nomenclature, phyloinformatics, the choice of names to use when the taxonomic content associated with available names varies, teaching phylogenetic nomenclature, and the application of phylogenetic nomenclature to specific taxa.     

A 50% reduction of excitability but not of intercellular coupling affects conduction velocity restitution and activation delay in the mouse heart

Introduction

Computer simulations suggest that intercellular coupling is more robust than membrane excitability with regard to changes in and safety of conduction. Clinical studies indicate that SCN5A (excitability) and/or Connexin43 (Cx43, intercellular coupling) expression in heart disease is reduced by approximately 50%. In this retrospective study we assessed the effect of reduced membrane excitability or intercellular coupling on conduction in mouse models of reduced excitability or intercellular coupling.

Methods and Results

Epicardial activation mapping of LV and RV was performed on Langendorff-perfused mouse hearts having the following: 1) Reduced excitability: Scn5a haploinsufficient mice; and 2) reduced intercellular coupling: Cx43^CreER(T)/fl mice, uninduced (50% Cx43) or induced (10% Cx43) with Tamoxifen. Wild type (WT) littermates were used as control. Conduction velocity (CV) restitution and activation delay were determined longitudinal and transversal to fiber direction during S₁S₁ pacing and S₁S₂ premature stimulation until the effective refractory period. In both animal models, CV restitution and activation delay in LV were not changed compared to WT. In contrast, CV restitution decreased and activation delay increased in RV during conduction longitudinal but not transverse to fiber direction in Scn5a heterozygous animals compared to WT. In contrast, a 50% reduction of intercellular coupling did not affect either CV restitution or activation delay. A decrease of 90% Cx43, however, resulted in decreased CV restitution and increased activation delay in RV, but not LV.

Conclusion

Reducing excitability but not intercellular coupling by 50% affects CV restitution and activation delay in RV, indicating a higher safety factor for intercellular coupling than excitability in RV.