709 research outputs found
Systematic Analysis of Intracellular Trafficking Motifs Located within the Cytoplasmic Domain of Simian Immunodeficiency Virus Glycoprotein gp41
Previous studies have shown that truncation of the cytoplasmic-domain sequences of the simian immunodeficiency virus (SIV) envelope glycoprotein (Env) just prior to a potential intracellular-trafficking signal of the sequence YIHF can strongly increase Env protein expression on the cell surface, Env incorporation into virions and, at least in some contexts, virion infectivity. Here, all 12 potential intracellular-trafficking motifs (YXXΦ or LL/LI/IL) in the gp41 cytoplasmic domain (gp41CD) of SIVmac239 were analyzed by systematic mutagenesis. One single and 7 sequential combination mutants in this cytoplasmic domain were characterized. Cell-surface levels of Env were not significantly affected by any of the mutations. Most combination mutations resulted in moderate 3- to 8-fold increases in Env incorporation into virions. However, mutation of all 12 potential sites actually decreased Env incorporation into virions. Variant forms with 11 or 12 mutated sites exhibited 3-fold lower levels of inherent infectivity, while none of the other single or combination mutations that were studied significantly affected the inherent infectivity of SIVmac239. These minor effects of mutations in trafficking motifs form a stark contrast to the strong increases in cell-surface expression and Env incorporation which have previously been reported for large truncations of gp41CD. Surprisingly, mutation of potential trafficking motifs in gp41CD of SIVmac316, which differs by only one residue from gp41CD of SIVmac239, effectively recapitulated the increases in Env incorporation into virions observed with gp41CD truncations. Our results indicate that increases in Env surface expression and virion incorporation associated with truncation of SIVmac239 gp41CD are not fully explained by loss of consensus trafficking motifs
Breakdown and time-lag of dielectric materials : Breakdown of liquid carbon tetrachloride
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/32586/1/0000715.pd
Spitzer, Near-Infrared, and Submillimeter Imaging of the Relatively Sparse Young Cluster, Lynds 988e
We present {\it Spitzer} images of the relatively sparse, low luminosity
young cluster L988e, as well as complementary near-infrared (NIR) and
submillimeter images of the region. The cluster is asymmetric, with the western
region of the cluster embedded within the molecular cloud, and the slightly
less dense eastern region to the east of, and on the edge of, the molecular
cloud. With these data, as well as with extant H data of stars
primarily found in the eastern region of the cluster, and a molecular CO
gas emission map of the entire region, we investigate the distribution of
forming young stars with respect to the cloud material, concentrating
particularly on the differences and similarities between the exposed and
embedded regions of the cluster. We also compare star formation in this region
to that in denser, more luminous and more massive clusters already investigated
in our comprehensive multi-wavelength study of young clusters within 1 kpc of
the Sun.Comment: 21 pages, 6 tables, 13 figures. Full resolution figures at:
http://astro.pas.rochester.edu/~tom/Preprints/L988e.pd
Branching on multi-aggregated variables
open5siopenGamrath, Gerald; Melchiori, Anna; Berthold, Timo; Gleixner, Ambros M.; Salvagnin, DomenicoGamrath, Gerald; Melchiori, Anna; Berthold, Timo; Gleixner, Ambros M.; Salvagnin, Domenic
Safety and efficacy of direct- acting oral anticoagulants versus warfarin in kidney transplant recipients: a retrospective single- center cohort study
Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155941/1/tri13599.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155941/2/tri13599_am.pd
Fixed-Parameter Algorithms in Analysis of Heuristics for Extracting Networks in Linear Programs
We consider the problem of extracting a maximum-size reflected network in a
linear program. This problem has been studied before and a state-of-the-art SGA
heuristic with two variations have been proposed.
In this paper we apply a new approach to evaluate the quality of SGA\@. In
particular, we solve majority of the instances in the testbed to optimality
using a new fixed-parameter algorithm, i.e., an algorithm whose runtime is
polynomial in the input size but exponential in terms of an additional
parameter associated with the given problem.
This analysis allows us to conclude that the the existing SGA heuristic, in
fact, produces solutions of a very high quality and often reaches the optimal
objective values. However, SGA contain two components which leave some space
for improvement: building of a spanning tree and searching for an independent
set in a graph. In the hope of obtaining even better heuristic, we tried to
replace both of these components with some equivalent algorithms.
We tried to use a fixed-parameter algorithm instead of a greedy one for
searching of an independent set. But even the exact solution of this subproblem
improved the whole heuristic insignificantly. Hence, the crucial part of SGA is
building of a spanning tree. We tried three different algorithms, and it
appears that the Depth-First search is clearly superior to the other ones in
building of the spanning tree for SGA.
Thereby, by application of fixed-parameter algorithms, we managed to check
that the existing SGA heuristic is of a high quality and selected the component
which required an improvement. This allowed us to intensify the research in a
proper direction which yielded a superior variation of SGA
Machine-learning prediction of tumor antigen immunogenicity in the selection of therapeutic epitopes
Current tumor neoantigen calling algorithms primarily rely on epitope/major histocompatibility complex (MHC) binding affinity predictions to rank and select for potential epitope targets. These algorithms do not predict for epitope immunogenicity using approaches modeled from tumor-specific antigen data. Here, we describe peptide-intrinsic biochemical features associated with neoantigen and minor histocompatibility mismatch antigen immunogenicity and present a gradient boosting algorithm for predicting tumor antigen immunogenicity. This algorithm was validated in two murine tumor models and demonstrated the capacity to select for therapeutically active antigens. Immune correlates of neoantigen immunogenicity were studied in a pan-cancer data set from The Cancer Genome Atlas and demonstrated an association between expression of immunogenic neoantigens and immunity in colon and lung adenocarcinomas. Lastly, we present evidence for expression of an out-of-frame neoantigen that was capable of driving antitumor cytotoxic T-cell responses. With the growing clinical importance of tumor vaccine therapies, our approach may allow for better selection of therapeutically relevant tumor-specific antigens, including nonclas-sic out-of-frame antigens capable of driving antitumor immunity
Enteric Neurospheres Are Not Specific to Neural Crest Cultures: Implications for Neural Stem Cell Therapies
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited
DHODH modulates transcriptional elongation in the neural crest and melanoma
Melanoma is a tumour of transformed melanocytes, which are originally derived from the embryonic neural crest. It is unknown to what extent the programs that regulate neural crest development interact with mutations in the BRAF oncogene, which is the most commonly mutated gene in human melanoma1. We have used zebrafish embryos to identify the initiating transcriptional events that occur on activation of human BRAF(V600E) (which encodes an amino acid substitution mutant of BRAF) in the neural crest lineage. Zebrafish embryos that are transgenic for mitfa:BRAF(V600E) and lack p53 (also known as tp53) have a gene signature that is enriched for markers of multipotent neural crest cells, and neural crest progenitors from these embryos fail to terminally differentiate. To determine whether these early transcriptional events are important for melanoma pathogenesis, we performed a chemical genetic screen to identify small-molecule suppressors of the neural crest lineage, which were then tested for their effects on melanoma. One class of compound, inhibitors of dihydroorotate dehydrogenase (DHODH), for example leflunomide, led to an almost complete abrogation of neural crest development in zebrafish and to a reduction in the self-renewal of mammalian neural crest stem cells. Leflunomide exerts these effects by inhibiting the transcriptional elongation of genes that are required for neural crest development and melanoma growth. When used alone or in combination with a specific inhibitor of the BRAF(V600E) oncogene, DHODH inhibition led to a marked decrease in melanoma growth both in vitro and in mouse xenograft studies. Taken together, these studies highlight developmental pathways in neural crest cells that have a direct bearing on melanoma formation
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