9,849 research outputs found
Nucleation at the DNA supercoiling transition
Twisting DNA under a constant applied force reveals a thermally activated
transition into a state with a supercoiled structure known as a plectoneme.
Using transition state theory, we predict the rate of this plectoneme
nucleation to be of order 10^4 Hz. We reconcile this with experiments that have
measured hopping rates of order 10 Hz by noting that the viscosity of the bead
used to manipulate the DNA limits the measured rate. We find that the intrinsic
bending caused by disorder in the base-pair sequence is important for
understanding the free energy barrier that governs the transition. Both
analytic and numerical methods are used in the calculations. We provide
extensive details on the numerical methods for simulating the elastic rod model
with and without disorder.Comment: 18 pages, 15 figure
Encoding folding paths of RNA switches
RNA co-transcriptional folding has long been suspected to play an active role
in helping proper native folding of ribozymes and structured regulatory motifs
in mRNA untranslated regions. Yet, the underlying mechanisms and coding
requirements for efficient co-transcriptional folding remain unclear.
Traditional approaches have intrinsic limitations to dissect RNA folding paths,
as they rely on sequence mutations or circular permutations that typically
perturb both RNA folding paths and equilibrium structures. Here, we show that
exploiting sequence symmetries instead of mutations can circumvent this problem
by essentially decoupling folding paths from equilibrium structures of designed
RNA sequences. Using bistable RNA switches with symmetrical helices conserved
under sequence reversal, we demonstrate experimentally that native and
transiently formed helices can guide efficient co-transcriptional folding into
either long-lived structure of these RNA switches. Their folding path is
controlled by the order of helix nucleations and subsequent exchanges during
transcription, and may also be redirected by transient antisense interactions.
Hence, transient intra- and intermolecular base pair interactions can
effectively regulate the folding of nascent RNA molecules into different native
structures, provided limited coding requirements, as discussed from an
information theory perspective. This constitutive coupling between RNA
synthesis and RNA folding regulation may have enabled the early emergence of
autonomous RNA-based regulation networks.Comment: 9 pages, 6 figure
Characterizing pre-transplant and post-transplant kidney rejection risk by B cell immune repertoire sequencing.
Studying immune repertoire in the context of organ transplant provides important information on how adaptive immunity may contribute and modulate graft rejection. Here we characterize the peripheral blood immune repertoire of individuals before and after kidney transplant using B cell receptor sequencing in a longitudinal clinical study. Individuals who develop rejection after transplantation have a more diverse immune repertoire before transplant, suggesting a predisposition for post-transplant rejection risk. Additionally, over 2 years of follow-up, patients who develop rejection demonstrate a specific set of expanded clones that persist after the rejection. While there is an overall reduction of peripheral B cell diversity, likely due to increased general immunosuppression exposure in this cohort, the detection of specific IGHV gene usage across all rejecting patients supports that a common pool of immunogenic antigens may drive post-transplant rejection. Our findings may have clinical implications for the prediction and clinical management of kidney transplant rejection
On the entropy of protein families
Proteins are essential components of living systems, capable of performing a
huge variety of tasks at the molecular level, such as recognition, signalling,
copy, transport, ... The protein sequences realizing a given function may
largely vary across organisms, giving rise to a protein family. Here, we
estimate the entropy of those families based on different approaches, including
Hidden Markov Models used for protein databases and inferred statistical models
reproducing the low-order (1-and 2-point) statistics of multi-sequence
alignments. We also compute the entropic cost, that is, the loss in entropy
resulting from a constraint acting on the protein, such as the fixation of one
particular amino-acid on a specific site, and relate this notion to the escape
probability of the HIV virus. The case of lattice proteins, for which the
entropy can be computed exactly, allows us to provide another illustration of
the concept of cost, due to the competition of different folds. The relevance
of the entropy in relation to directed evolution experiments is stressed.Comment: to appear in Journal of Statistical Physic
Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products
We developed a low-cost, high-throughput microbiome profiling method that
uses combinatorial sequence tags attached to PCR primers that amplify the rRNA
V6 region. Amplified PCR products are sequenced using an Illumina paired-end
protocol to generate millions of overlapping reads. Combinatorial sequence
tagging can be used to examine hundreds of samples with far fewer primers than
is required when sequence tags are incorporated at only a single end. The
number of reads generated permitted saturating or near-saturating analysis of
samples of the vaginal microbiome. The large number of reads al- lowed an
in-depth analysis of errors, and we found that PCR-induced errors composed the
vast majority of non-organism derived species variants, an ob- servation that
has significant implications for sequence clustering of similar high-throughput
data. We show that the short reads are sufficient to assign organisms to the
genus or species level in most cases. We suggest that this method will be
useful for the deep sequencing of any short nucleotide region that is
taxonomically informative; these include the V3, V5 regions of the bac- terial
16S rRNA genes and the eukaryotic V9 region that is gaining popularity for
sampling protist diversity.Comment: 28 pages, 13 figure
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