803 research outputs found
Statoviruses, a novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals
Periodic One-Dimensional Hopping Model with one Mobile Directional Impurity
Analytic solution is given in the steady state limit for the system of Master
equations describing a random walk on one-dimensional periodic lattices with
arbitrary hopping rates containing one mobile, directional impurity (defect
bond). Due to the defect, translational invariance is broken, even if all other
rates are identical. The structure of Master equations lead naturally to the
introduction of a new entity, associated with the walker-impurity pair which we
call the quasi-walker. The velocities and diffusion constants for both the
random walker and impurity are given, being simply related to that of the
quasi-particle through physically meaningful equations. Applications in driven
diffusive systems are shown, and connections with the Duke-Rubinstein reptation
models for gel electrophoresis are discussed.Comment: 31 LaTex pages, 5 Postscript figures included, to appear in Journal
of Statistical Physic
Algebraic Aspects of Abelian Sandpile Models
The abelian sandpile models feature a finite abelian group G generated by the
operators corresponding to particle addition at various sites. We study the
canonical decomposition of G as a product of cyclic groups G = Z_{d_1} X
Z_{d_2} X Z_{d_3}...X Z_{d_g}, where g is the least number of generators of G,
and d_i is a multiple of d_{i+1}. The structure of G is determined in terms of
toppling matrix. We construct scalar functions, linear in height variables of
the pile, that are invariant toppling at any site. These invariants provide
convenient coordinates to label the recurrent configurations of the sandpile.
For an L X L square lattice, we show that g = L. In this case, we observe that
the system has nontrivial symmetries coming from the action of the cyclotomic
Galois group of the (2L+2)th roots of unity which operates on the set of
eigenvalues of the toppling matrix. These eigenvalues are algebraic integers,
whose product is the order |G|. With the help of this Galois group, we obtain
an explicit factorizaration of |G|. We also use it to define other simpler,
though under-complete, sets of toppling invariants.Comment: 39 pages, TIFR/TH/94-3
Domain wall QCD with physical quark masses
We present results for several light hadronic quantities (, ,
, , , , ) obtained from simulations of 2+1
flavor domain wall lattice QCD with large physical volumes and nearly-physical
pion masses at two lattice spacings. We perform a short, O(3)%, extrapolation
in pion mass to the physical values by combining our new data in a simultaneous
chiral/continuum `global fit' with a number of other ensembles with heavier
pion masses. We use the physical values of , and to
determine the two quark masses and the scale - all other quantities are outputs
from our simulations. We obtain results with sub-percent statistical errors and
negligible chiral and finite-volume systematics for these light hadronic
quantities, including: = 130.2(9) MeV; = 155.5(8) MeV; the
average up/down quark mass and strange quark mass in the scheme
at 3 GeV, 2.997(49) and 81.64(1.17) MeV respectively; and the neutral kaon
mixing parameter, , in the RGI scheme, 0.750(15) and the
scheme at 3 GeV, 0.530(11).Comment: 131 pages, 30 figures. Updated to match published versio
Effect of chemical modifications on modulation of gene expression by duplex antigene RNAs that are complementary to non-coding transcripts at gene promoters
Antigene RNAs (agRNAs) are small RNA duplexes that target non-coding transcripts rather than mRNA and specifically suppress or activate gene expression in a sequence-dependent manner. For many applications in vivo, it is likely that agRNAs will require chemical modification. We have synthesized agRNAs that contain different classes of chemical modification and have tested their ability to modulate expression of the human progesterone receptor gene. We find that both silencing and activating agRNAs can retain activity after modification. Both guide and passenger strands can be modified and functional agRNAs can contain 2′F-RNA, 2′OMe-RNA, and locked nucleic acid substitutions, or combinations of multiple modifications. The mechanism of agRNA activity appears to be maintained after chemical modification: both native and modified agRNAs modulate recruitment of RNA polymerase II, have the same effect on promoter-derived antisense transcripts, and must be double-stranded. These data demonstrate that agRNA activity is compatible with a wide range of chemical modifications and may facilitate in vivo applications
Involvement of argonaute proteins in gene silencing and activation by RNAs complementary to a non-coding transcript at the progesterone receptor promoter
Double-stranded RNAs that are complementary to non-coding transcripts at gene promoters can activate or inhibit gene expression in mammalian cells. Understanding the mechanism for modulating gene expression by promoter-targeted antigene RNAs (agRNAs) will require identification of the proteins involved in recognition. Previous reports have implicated argonaute (AGO) proteins, but identifications have differed with involvement of AGO1, AGO2, or both AGO1 and AGO2 being reported by different studies. The roles of AGO3 and AGO4 have not been investigated. Here, we examine the role of AGO 1–4 in gene silencing and activation of the progesterone receptor (PR) gene. Expression of AGO2 is necessary for efficient gene silencing or activation and AGO2 is recruited to the non-coding transcript that overlaps the promoter during both gene silencing and activation. Expression of AGO1, AGO3 and AGO4 are not necessary for gene silencing or activation nor are AGO1, AGO3, or AGO4 recruited to the target non-coding transcript during gene activation. These data indicate that AGO2 is the primary AGO variant involved in modulating expression of PR by agRNAs
Mn-based methacrylated gellan gum hydrogels for MRI-guided cell delivery and imaging
This work aims to engineer a new stable injectable Mn-based methacrylated gellan gum (Mn/GG-MA) hydrogel for real-time monitored cell delivery into the central nervous system. To enable the hydrogel visualization under Magnetic Resonance Imaging (MRI), GG-MA solutions were supplemented with paramagnetic Mn2+ ions before its ionic crosslink with artificial cerebrospinal fluid (aCSF). The resulting formulations were stable, detectable by T1-weighted MRI scans and also injectable. Cell-laden hydrogels were prepared using the Mn/GG-MA formulations, extruded into aCSF for crosslink, and after 7 days of culture, the encapsulated human adipose-derived stem cells remained viable, as assessed by Live/Dead assay. In vivo tests, using double mutant MBPshi/shi/rag2 immunocompromised mice, showed that the injection of Mn/GG-MA solutions resulted in a continuous and traceable hydrogel, visible on MRI scans. Summing up, the developed formulations are suitable for both non-invasive cell delivery techniques and image-guided neurointerventions, paving the way for new therapeutic procedures.Sílvia Vieira acknowledges the FCT Ph.D. scholarship (SFRH/BD/102710/2014). J. Miguel
Oliveira and J. Silva-Correia acknowledge the FCT grants under the Investigator FCT program
(IF/01285/2015 and IF/00115/2015, respectively). The authors also acknowledge the funds provided under the project NanoTech4ALS, funded under the EU FP7 M-ERA.NET program, and ESF
(POWR.03.02.00-00-I028/17-00)
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