341 research outputs found
Ring graphs and complete intersection toric ideals
We study the family of graphs whose number of primitive cycles equals its
cycle rank. It is shown that this family is precisely the family of ring
graphs. Then we study the complete intersection property of toric ideals of
bipartite graphs and oriented graphs. An interesting application is that
complete intersection toric ideals of bipartite graphs correspond to ring
graphs and that these ideals are minimally generated by Groebner bases. We
prove that any graph can be oriented such that its toric ideal is a complete
intersection with a universal Groebner basis determined by the cycles. It turns
out that bipartite ring graphs are exactly the bipartite graphs that have
complete intersection toric ideals for any orientation.Comment: Discrete Math., to appea
Symbolic powers of monomial ideals and Cohen-Macaulay vertex-weighted digraphs
In this paper we study irreducible representations and symbolic Rees algebras
of monomial ideals. Then we examine edge ideals associated to vertex-weighted
oriented graphs. These are digraphs having no oriented cycles of length two
with weights on the vertices. For a monomial ideal with no embedded primes we
classify the normality of its symbolic Rees algebra in terms of its primary
components. If the primary components of a monomial ideal are normal, we
present a simple procedure to compute its symbolic Rees algebra using Hilbert
bases, and give necessary and sufficient conditions for the equality between
its ordinary and symbolic powers. We give an effective characterization of the
Cohen--Macaulay vertex-weighted oriented forests. For edge ideals of transitive
weighted oriented graphs we show that Alexander duality holds. It is shown that
edge ideals of weighted acyclic tournaments are Cohen--Macaulay and satisfy
Alexander dualityComment: Special volume dedicated to Professor Antonio Campillo, Springer, to
appea
CRISPR-Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity.
Hexanucleotide-repeat expansions in the C9ORF72 gene are the most common cause of amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD). The nucleotide-repeat expansions are translated into dipeptide-repeat (DPR) proteins, which are aggregation prone and may contribute to neurodegeneration. We used the CRISPR-Cas9 system to perform genome-wide gene-knockout screens for suppressors and enhancers of C9ORF72 DPR toxicity in human cells. We validated hits by performing secondary CRISPR-Cas9 screens in primary mouse neurons. We uncovered potent modifiers of DPR toxicity whose gene products function in nucleocytoplasmic transport, the endoplasmic reticulum (ER), proteasome, RNA-processing pathways, and chromatin modification. One modifier, TMX2, modulated the ER-stress signature elicited by C9ORF72 DPRs in neurons and improved survival of human induced motor neurons from patients with C9ORF72 ALS. Together, our results demonstrate the promise of CRISPR-Cas9 screens in defining mechanisms of neurodegenerative diseases
Intrathecal immunoglobulin A and G antibodies to synapsin in a patient with limbic encephalitis
To report on the identification of intrathecally synthesized immunoglobulin A (IgA) and immunoglobulin G (IgG) antibodies to synapsin, a synaptic vesicle-associated protein, in a patient with limbic encephalitis
<i>C-elegans</i> model identifies genetic modifiers of alpha-synuclein inclusion formation during aging
Inclusions in the brain containing alpha-synuclein are the pathological hallmark of Parkinson's disease, but how these inclusions are formed and how this links to disease is poorly understood. We have developed a <i>C-elegans</i> model that makes it possible to monitor, in living animals, the formation of alpha-synuclein inclusions. In worms of old age, inclusions contain aggregated alpha-synuclein, resembling a critical pathological feature. We used genome-wide RNA interference to identify processes involved in inclusion formation, and identified 80 genes that, when knocked down, resulted in a premature increase in the number of inclusions. Quality control and vesicle-trafficking genes expressed in the ER/Golgi complex and vesicular compartments were overrepresented, indicating a specific role for these processes in alpha-synuclein inclusion formation. Suppressors include aging-associated genes, such as sir-2.1/SIRT1 and lagr-1/LASS2. Altogether, our data suggest a link between alpha-synuclein inclusion formation and cellular aging, likely through an endomembrane-related mechanism. The processes and genes identified here present a framework for further study of the disease mechanism and provide candidate susceptibility genes and drug targets for Parkinson's disease and other alpha-synuclein related disorders
The yeast P5 type ATPase, Spf1, regulates manganese transport into the endoplasmic reticulum
The endoplasmic reticulum (ER) is a large, multifunctional and essential organelle. Despite intense research, the function of more than a third of ER proteins remains unknown even in the well-studied model organism Saccharomyces cerevisiae. One such protein is Spf1, which is a highly conserved, ER localized, putative P-type ATPase. Deletion of SPF1 causes a wide variety of phenotypes including severe ER stress suggesting that this protein is essential for the normal function of the ER. The closest homologue of Spf1 is the vacuolar P-type ATPase Ypk9 that influences Mn2+ homeostasis. However in vitro reconstitution assays with Spf1 have not yielded insight into its transport specificity. Here we took an in vivo approach to detect the direct and indirect effects of deleting SPF1. We found a specific reduction in the luminal concentration of Mn2+ in ∆spf1 cells and an increase following it’s overexpression. In agreement with the observed loss of luminal Mn2+ we could observe concurrent reduction in many Mn2+-related process in the ER lumen. Conversely, cytosolic Mn2+-dependent processes were increased. Together, these data support a role for Spf1p in Mn2+ transport in the cell. We also demonstrate that the human sequence homologue, ATP13A1, is a functionally conserved orthologue. Since ATP13A1 is highly expressed in developing neuronal tissues and in the brain, this should help in the study of Mn2+-dependent neurological disorders
Cisplatin and Oxaliplatin Toxicity: Importance of Cochlear Kinetics as a Determinant for Ototoxicity
Background
Cisplatin is a commonly used platinum anti-cancer drug. Regrettably cisplatin
has dose-limiting ototoxic side effects, e.g. the drug can induce an irreversible
hearing loss. The ototoxic mechanisms of cisplatin have not been
elucidated in the human ear and no clinically useful oto-protectors are yet
available. Cisplatin is a necessary part of many treatment regimes. Its beneficial
therapeutic effects might be reduced if cisplatin was excluded from the
treatment in order to protect the hearing function. In this work the ototoxic
effects of cisplatin are studied with the aim to better understand the mechanisms
behind the irreversible hearing loss induced by this drug. Oxaliplatin is
a second generation platinum-derivative anti-cancer drug, free from ototoxic
side effects in clinical practice. The effects of oxaliplatin on the inner ear have
been studied in this work and the results are compared with cisplatin treatment.
The two drugs differ regarding both anti-cancer effects and side effects,
which could be attributed to differences in pharmacokinetic factors, cellular
uptake and apoptotic mechanisms. The thioredoxin redox system with the
enzyme thioredoxin reductase (TrxR) was studied in cochleae due to a suggested
DNA-independent apoptotic mechanism of the hair cells. The cochlear
pharmacokinetics of cisplatin was assessed and the transport protein organic
cation transporter 2 (OCT2) was studied in relation to the ototoxic effect of
cisplatin.
Material and methods
Cultured human colon carcinoma cells and cell cultures of rat organ of Corti
were used for apoptosis studies in vitro following exposure to cisplatin and
oxaliplatin. Cisplatin and oxaliplatin were administered i.v. to guinea pigs,
followed by in vivo sampling of blood, cerebrospinal fluid (CSF) and scala
tympani (ST) perilymph. Liquid chromatography with post-column derivatization
was used to determine the concentration of parent drug in the samples.
Electrophysiological hearing thresholds and the loss of hair cells were assessed
to evaluate their ototoxic effects. Phenformin, a potential blocker of
OCT2 was administered and the ototoxic side effect of cisplatin was evaluated.
For immunohistochemical studies, cochlea from rat, guinea pig and pig
were used, where TrxR and OCT2 were evaluated in the cochlea. TrxR-assays
were used to measure the TrxR activity in cochlear tissue, both in vivo and in
vitro.
Results
The results from the in vitro studies showed that addition of either cisplatin
or oxaliplatin to the culture medium in organ of Corti cell cultures caused a
similar amount of outer hair cell loss and inhibition of TrxR activity. Cisplatin
exposure to cultured human colon carcinoma cells also reduced the activity
of TrxR. The results from the in vivo studies showed that a considerable concentration
of cisplatin was present in ST perilymph as compared with weak
concentrations of oxaliplatin after high dose oxaliplatin i.v. Ten minutes after
cisplatin administration, its concentration in ST perilymph was 4-fold higher
in the basal turn of the cochlea as compared to the apex. Cisplatin could be
analysed in ST perilymph for up to 120 min. Phenformin i.v. did not reduce
the ototoxic side-effect of cisplatin. Positive immunoreactivity to TrxR was
evident in both hair cells and spiral ganglion cells. Futhermore, OCT2 was
expressed in the supporting cells of organ of Corti and in the spiral ganglion
cells.
Conclusion
The transport of cisplatin to the vulnerable cells of hearing seems to be of major
importance for the ototoxic effects. An early high concentration of cisplatin
in the base of the cochlea and delayed elimination of cisplatin from ST perilymph
may be related to the cisplatin-induced loss of outer hair cells in the
basal turn of the cochlea. Cisplatin and oxaliplatin both cause similar ototoxic
effects when the organ of Corti is directly exposed in vitro. The thioredoxin
redox system with the TrxR enzyme may well play a critical role in cisplatininduced
ototoxicity. The presence of OCT2 in the supporting cells indicates
that this transport protein is primarily not involved in the uptake of cisplatin
from the systemic circulation but rather from the deeper compartments of
the cochlea. The knowledge elicited in this work will hopefully suggest objectives
for further studies in order to develop oto-protective treatments to
preserve the hearing of cisplatin treated patients
Rapid selection of cyclic peptides that reduce alpha-synuclein toxicity in yeast and animal models
Phage display has demonstrated the utility of cyclic peptides as general protein ligands but cannot access proteins inside eukaryotic cells. Expanding a new chemical genetics tool, we describe the first expressed library of head-to-tail cyclic peptides in yeast (Saccharomyces cerevisiae). We applied the library to selections in a yeast model of alpha-synuclein toxicity that recapitulates much of the cellular pathology of Parkinson's disease. From a pool of 5 million transformants, we isolated two related cyclic peptide constructs that specifically reduced the toxicity of human alpha-synuclein. These expressed cyclic peptide constructs also prevented dopaminergic neuron loss in an established Caenorhabditis elegans Parkinson's model. This work highlights the speed and efficiency of using libraries of expressed cyclic peptides for forward chemical genetics in cellular models of human disease
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