131 research outputs found
van der Waals interactions of the benzene dimer: towards treatment of polycyclic aromatic hydrocarbon dimers
Although density functional theory (DFT) in principle includes even
long-range interactions, standard implementations employ local or semi-local
approximations of the interaction energy and fail at describing the van der
Waals interactions. We show how to modify a recent density functional that
includes van der Waals interactions in planar systems [Phys. Rev. Lett. 91,
126402 (2003)] to also give an approximate interaction description of planar
molecules. As a test case we use this modified functional to calculate the
binding distance and energy for benzene dimers, with the perspective of
treating also larger, flat molecules, such as the polycyclic aromatic
hydrocarbons (PAH).Comment: 7 pages, 2 figures (3 figure files) submitted to Materials Science
and Engineering
Mutations in splicing factor PRPF3, causing retinal degeneration, form detrimental aggregates in photoreceptor cells.
PRPF3 is an element of the splicing machinery ubiquitously expressed, yet mutations in this gene are associated with a tissue-specific phenotype: autosomal dominant retinitis pigmentosa (RP). Here, we studied the subcellular localization of endogenous- and mutant-transfected PRPF3. We found that (i) subcellular distribution of the endogenous wild-type protein co-localizes with small nuclear ribonucleoproteins, partially with a nucleolar marker and accumulates in speckles labeled by SC35; (ii) in human retinas, PRPF3 does not show a distinctive abundance in photoreceptors, the cells affected in RP and (iii) the RP causing mutant PRPF3, differently from the wild-type protein, forms abnormally big aggregates in transfected photoreceptor cells. Aggregation of T494M mutant PRPF3 inside the nucleus triggers apoptosis only in photoreceptor cells. On the basis of the observation that mutant PRPF3 accumulates in the nucleolus and that transcriptional, translational and proteasome inhibition can induce this phenomenon in non-photoreceptor cells, we hypothesize that mutation affects splicing factor recycling. Noteworthy, accumulation of the mutant protein in big aggregates also affects distribution of some other splicing factors. Our data suggest that the mutant protein has a cell-specific dominant effect in rod photoreceptors while appears not to be harmful to epithelial and fibroblast cells
Desorption of n-alkanes from graphene: a van der Waals density functional study
A recent study of temperature programmed desorption (TPD) measurements of
small n-alkanes (CNH2N+2) from C(0001) deposited on Pt(111) shows a linear
relationship of the desorption energy with increasing n-alkane chain length. We
here present a van der Waals density functional study of the desorption barrier
energy of the ten smallest n-alkanes (N = 1 to 10) from graphene. We find
linear scaling with N, including a nonzero intercept with the energy axis,
i.e., an offset at the extrapolation to N = 0. This calculated offset is
quantitatively similar to the results of the TPD measurements. From further
calculations of the polyethylene polymer we offer a suggestion for the origin
of the offset.Comment: 3 pictures, 1 tabl
Graphene transistors are insensitive to pH changes in solution
We observe very small gate-voltage shifts in the transfer characteristic of
as-prepared graphene field-effect transistors (GFETs) when the pH of the buffer
is changed. This observation is in strong contrast to Si-based ion-sensitive
FETs. The low gate-shift of a GFET can be further reduced if the graphene
surface is covered with a hydrophobic fluorobenzene layer. If a thin Al-oxide
layer is applied instead, the opposite happens. This suggests that clean
graphene does not sense the chemical potential of protons. A GFET can therefore
be used as a reference electrode in an aqueous electrolyte. Our finding sheds
light on the large variety of pH-induced gate shifts that have been published
for GFETs in the recent literature
Graphite and Hexagonal Boron-Nitride Possess the Same Interlayer Distance. Why?
Graphite and hexagonal boron nitride (h-BN) are two prominent members of the
family of layered materials possessing a hexagonal lattice. While graphite has
non-polar homo-nuclear C-C intra-layer bonds, h-BN presents highly polar B-N
bonds resulting in different optimal stacking modes of the two materials in
bulk form. Furthermore, the static polarizabilities of the constituent atoms
considerably differ from each other suggesting large differences in the
dispersive component of the interlayer bonding. Despite these major differences
both materials present practically identical interlayer distances. To
understand this finding, a comparative study of the nature of the interlayer
bonding in both materials is presented. A full lattice sum of the interactions
between the partially charged atomic centers in h-BN results in vanishingly
small monopolar electrostatic contributions to the interlayer binding energy.
Higher order electrostatic multipoles, exchange, and short-range correlation
contributions are found to be very similar in both materials and to almost
completely cancel out by the Pauli repulsions at physically relevant interlayer
distances resulting in a marginal effective contribution to the interlayer
binding. Further analysis of the dispersive energy term reveals that despite
the large differences in the individual atomic polarizabilities the
hetero-atomic B-N C6 coefficient is very similar to the homo-atomic C-C
coefficient in the hexagonal bulk form resulting in very similar dispersive
contribution to the interlayer binding. The overall binding energy curves of
both materials are thus very similar predicting practically the same interlayer
distance and very similar binding energies.Comment: 18 pages, 5 figures, 2 table
Mutations in SPATA13/ASEF2 cause primary angle closure glaucoma
Current estimates suggest 50% of glaucoma blindness worldwide is caused by primary angle-closure glaucoma (PACG) but the causative gene is not known. We used genetic linkage and whole genome sequencing to identify Spermatogenesis Associated Protein 13, SPATA13 (NM_001166271; NP_001159743, SPATA13 isoform I), also known as ASEF2 (Adenomatous polyposis coli-stimulated guanine nucleotide exchange factor 2), as the causal gene for PACG in a large seven-generation white British family showing variable expression and incomplete penetrance. The 9 bp deletion, c.1432_1440del; p.478_480del was present in all affected individuals with angle-closure disease. We show ubiquitous expression of this transcript in cell lines derived from human tissues and in iris, retina, retinal pigment and ciliary epithelia, cornea and lens. We also identified eight additional mutations in SPATA13 in a cohort of 189 unrelated PACS/PAC/PACG samples. This gene encodes a 1277 residue protein which localises to the nucleus with partial co-localisation with nuclear speckles. In cells undergoing mitosis SPATA13 isoform I becomes part of the kinetochore complex co-localising with two kinetochore markers, polo like kinase 1 (PLK-1) and centrosome-associated protein E (CENP-E). The 9 bp deletion reported in this study increases the RAC1-dependent guanine nucleotide exchange factors (GEF) activity. The increase in GEF activity was also observed in three other variants identified in this study. Taken together, our data suggest that SPATA13 is involved in the regulation of mitosis and the mutations dysregulate GEF activity affecting homeostasis in tissues where it is highly expressed, influencing PACG pathogenesis
A novel locus (CORD12) for autosomal dominant cone-rod dystrophy on chromosome 2q24.2-2q33.1
<p>Abstract</p> <p>Background</p> <p>Rod-cone dystrophy, also known as retinitis pigmentosa (RP), and cone-rod dystrophy (CRD) are degenerative retinal dystrophies leading to blindness. To identify new genes responsible for these diseases, we have studied one large non consanguineous French family with autosomal dominant (ad) CRD.</p> <p>Methods</p> <p>Family members underwent detailed ophthalmological examination. Linkage analysis using microsatellite markers and a whole-genome SNP analysis with the use of Affymetrix 250 K SNP chips were performed. Five candidate genes within the candidate region were screened for mutations by direct sequencing.</p> <p>Results</p> <p>We first excluded the involvement of known adRP and adCRD genes in the family by genotyping and linkage analysis. Then, we undertook a whole-genome scan on 22 individuals in the family. The analysis revealed a 41.3-Mb locus on position 2q24.2-2q33.1. This locus was confirmed by linkage analysis with specific markers of this region. The maximum LOD score was 2.86 at θ = 0 for this locus. Five candidate genes, <it>CERKL</it>, <it>BBS5, KLHL23, NEUROD1</it>, and <it>SF3B1 </it>within this locus, were not mutated.</p> <p>Conclusion</p> <p>A novel locus for adCRD, named <it>CORD12</it>, has been mapped to chromosome 2q24.2-2q33.1 in a non consanguineous French family.</p
Temporal and Tissue Specific Regulation of RP-Associated Splicing Factor Genes PRPF3, PRPF31 and PRPC8—Implications in the Pathogenesis of RP
Genetic mutations in several ubiquitously expressed RNA splicing genes such as PRPF3, PRP31 and PRPC8, have been found to cause retina-specific diseases in humans. To understand this intriguing phenomenon, most studies have been focused on testing two major hypotheses. One hypothesis assumes that these mutations interrupt retina-specific interactions that are important for RNA splicing, implying that there are specific components in the retina interacting with these splicing factors. The second hypothesis suggests that these mutations have only a mild effect on the protein function and thus affect only the metabolically highly active cells such as retinal photoreceptors.We examined the second hypothesis using the PRPF3 gene as an example. We analyzed the spatial and temporal expression of the PRPF3 gene in mice and found that it is highly expressed in retinal cells relative to other tissues and its expression is developmentally regulated. In addition, we also found that PRP31 and PRPC8 as well as snRNAs are highly expressed in retinal cells.Our data suggest that the retina requires a relatively high level of RNA splicing activity for optimal tissue-specific physiological function. Because the RP18 mutation has neither a debilitating nor acute effect on protein function, we suggest that retinal degeneration is the accumulative effect of decades of suboptimal RNA splicing due to the mildly impaired protein
ATP-Dependent Unwinding of U4/U6 snRNAs by the Brr2 Helicase Requires the C Terminus of Prp8
The spliceosome is a highly dynamic machine requiring multiple RNA-dependent ATPases of the DExD/H-box family. A fundamental unanswered question is how their activities are regulated. Brr2 function is necessary for unwinding the U4/U6 duplex, a step essential for catalytic activation of the spliceosome. Here we show that Brr2-dependent dissociation of U4/U6 snRNAs in vitro is activated by a fragment from the C terminus of the U5 snRNP protein Prp8. In contrast to its helicase-stimulating activity, this fragment inhibits Brr2 U4/U6-dependent ATPase activity. Notably, U4/U6 unwinding activity is not stimulated by fragments carrying alleles of prp8 that in humans confers an autosomal dominant form of retinitis pigmentosa. Because Brr2 activity must be restricted to prevent premature catalytic activation, our results have important implications for fidelity maintenance in the spliceosome
Zebrafish: a vertebrate tool for studying basal body biogenesis, structure, and function.
Understanding the role of basal bodies (BBs) during development and disease has been largely overshadowed by research into the function of the cilium. Although these two organelles are closely associated, they have specific roles to complete for successful cellular development. Appropriate development and function of the BB are fundamental for cilia function. Indeed, there are a growing number of human genetic diseases affecting ciliary development, known collectively as the ciliopathies. Accumulating evidence suggests that BBs establish cell polarity, direct ciliogenesis, and provide docking sites for proteins required within the ciliary axoneme. Major contributions to our knowledge of BB structure and function have been provided by studies in flagellated or ciliated unicellular eukaryotic organisms, specifically Tetrahymena and Chlamydomonas. Reproducing these and other findings in vertebrates has required animal in vivo models. Zebrafish have fast become one of the primary organisms of choice for modeling vertebrate functional genetics. Rapid ex-utero development, proficient egg laying, ease of genetic manipulation, and affordability make zebrafish an attractive vertebrate research tool. Furthermore, zebrafish share over 80 % of disease causing genes with humans. In this article, we discuss the merits of using zebrafish to study BB functional genetics, review current knowledge of zebrafish BB ultrastructure and mechanisms of function, and consider the outlook for future zebrafish-based BB studies
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